# HG changeset patch # User iuc # Date 1524200785 14400 # Node ID e0f4a651c6b90776f97c29696b2bcc4d65727e6b # Parent 467486f1c5680515d7af7adb11faf9d55c87c316 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 diff -r 467486f1c568 -r e0f4a651c6b9 generate_test_data.sh --- a/generate_test_data.sh Sun Jan 14 09:55:46 2018 -0500 +++ b/generate_test_data.sh Fri Apr 20 01:06:25 2018 -0400 @@ -1,25 +1,23 @@ #!/usr/bin/env bash # 1st test -mkdir multiqc_WDir +mkdir -p 'multiqc_WDir/cutadapt' +cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt/cutadapt.txt' +sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt/cutadapt.txt' -mkdir 'multiqc_WDir/cutadapt_0' -cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt_0/cutadapt.txt' -sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt.txt' +mkdir -p 'multiqc_WDir/fastqc/data_0/file_0' +cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc/data_0/file_0/fastqc_data.txt' +mkdir -p 'multiqc_WDir/fastqc/data_0/file_1' +cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc/data_0/file_1/fastqc_data.txt' -mkdir -p 'multiqc_WDir/fastqc_1/data_0/file_0' -cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc_1/data_0/file_0/fastqc_data.txt' -mkdir 'multiqc_WDir/fastqc_1/data_0/file_1' -cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc_1/data_0/file_1/fastqc_data.txt' +mkdir -p 'multiqc_WDir/flexbar' +cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar/flexbar.txt' -mkdir 'multiqc_WDir/flexbar_2' -cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar_2/flexbar.txt' +mkdir -p 'multiqc_WDir/sortmerna' +cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna/sortmerna.txt' -mkdir 'multiqc_WDir/sortmerna_3' -cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna_3/sortmerna.txt' - -mkdir 'multiqc_WDir/trimmomatic_4' -cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic_4/trimmomatic.txt' +mkdir -p 'multiqc_WDir/trimmomatic' +cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic/trimmomatic.txt' multiqc multiqc_WDir @@ -36,33 +34,37 @@ rm -rf 'multiqc_data/' # 2nd test -mkdir multiqc_WDir +mkdir -p 'multiqc_WDir/bismark' +cp 'test-data/bismark.txt' 'multiqc_WDir/bismark/bismark_SE_report.txt' -mkdir 'multiqc_WDir/bismark_0' -cp 'test-data/bismark.txt' 'multiqc_WDir/bismark_0/bismark_SE_report.txt' +mkdir -p 'multiqc_WDir/bowtie2' +cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2/bowtie2_1.txt' +cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2/bowtie2_2.txt' -mkdir 'multiqc_WDir/bowtie2_1' -cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2_1/bowtie2_1.txt' -cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2_1/bowtie2_2.txt' +mkdir -p 'multiqc_WDir/hisat2' +cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2/hisat2_1.txt' +cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2/hisat2_2.txt' -mkdir 'multiqc_WDir/hisat2_3' -cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2_3/hisat2_1.txt' -cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2_3/hisat2_2.txt' +mkdir -p 'multiqc_WDir/hicexplorer' +cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/' +cp 'test-data/hicexplorer2.log' 'multiqc_WDir/hicexplorer/' -mkdir 'multiqc_WDir/kallisto_4' -cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto_4/kallisto_1.txt' -cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto_4/kallisto_2.txt' - -mkdir -p 'multiqc_WDir/salmon_5/fld_0/file_0' -cp 'test-data/salmon.txt' 'multiqc_WDir/salmon_5/fld_0/file_0/flenDist.txt' +mkdir -p 'multiqc_WDir/kallisto' +cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto/kallisto_1.txt' +cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto/kallisto_2.txt' -mkdir -p 'multiqc_WDir/star_6/log_0' -cp 'test-data/star_log.txt' 'multiqc_WDir/star_6/log_0/star_log_Log.final.out' -mkdir 'multiqc_WDir/star_6/genecounts_1' -cp 'test-data/star_counts.txt' 'multiqc_WDir/star_6/genecounts_1/star_counts_ReadsPerGene.out.tab' +#mkdir -p 'multiqc_WDir/salmon/fld_0/file_0' +#cp 'test-data/salmon_flenDist.txt' 'multiqc_WDir/salmon/fld_0/file_0/flenDist.txt' +#mkdir -p 'multiqc_WDir/salmon/fld_1/file_0' +#cp 'test-data/salmon_meta_info.json' 'multiqc_WDir/salmon/fld_1/file_0/meta_info.json' -mkdir 'multiqc_WDir/tophat_7' -cp 'test-data/tophat.txt' 'multiqc_WDir/tophat_7/tophat_align_summary.txt' +mkdir -p 'multiqc_WDir/star/log_0' +cp 'test-data/star_log.txt' 'multiqc_WDir/star/log_0/star_log_Log.final.out' +mkdir -p 'multiqc_WDir/star/genecounts_1' +cp 'test-data/star_counts.txt' 'multiqc_WDir/star/genecounts_1/star_counts_ReadsPerGene.out.tab' + +mkdir -p 'multiqc_WDir/tophat' +cp 'test-data/tophat.txt' 'multiqc_WDir/tophat/tophat_align_summary.txt' multiqc multiqc_WDir @@ -79,63 +81,69 @@ rm -rf 'multiqc_data/' # 3rd test -mkdir multiqc_WDir - -mkdir 'multiqc_WDir/bamtools_0' -cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools_0/bamtools.txt' +mkdir -p 'multiqc_WDir/bamtools' +cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools/bamtools.txt' -mkdir 'multiqc_WDir/bcftools_1' -cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools_1/bcftools.txt' +mkdir -p 'multiqc_WDir/bcftools' +cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools/bcftools.txt' -mkdir 'multiqc_WDir/busco_2' -cp 'test-data/busco.txt' 'multiqc_WDir/busco_2/short_summary_busco.txt' - -mkdir 'multiqc_WDir/featureCounts_3' -cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts_3/featureCounts.summary' +mkdir -p 'multiqc_WDir/busco' +cp 'test-data/busco.txt' 'multiqc_WDir/busco/short_summary_busco.txt' -mkdir 'multiqc_WDir/gatk_4' -cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk_4/gatk_BaseRecalibrator.txt' -cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk_4/gatk_varianteval.txt' - -mkdir 'multiqc_WDir/htseq_5' -cp 'test-data/htseq.txt' 'multiqc_WDir/htseq_5/htseq.txt' +mkdir -p 'multiqc_WDir/deeptools' +cp 'test-data/deeptools_bamPEFragmentSize.txt' 'multiqc_WDir/deeptools/' +cp 'test-data/deeptools_estimateReadFiltering.txt' 'multiqc_WDir/deeptools/' +cp 'test-data/deeptools_plotCoverageOutRawCounts.txt' 'multiqc_WDir/deeptools/' +cp 'test-data/deeptools_plotCoverageStdout.txt' 'multiqc_WDir/deeptools/' +cp 'test-data/deeptools_plotEnrichment.txt' 'multiqc_WDir/deeptools/' +cp 'test-data/deeptools_plotFingerprintOutRawCounts.txt' 'multiqc_WDir/deeptools/' -mkdir 'multiqc_WDir/picard_6' -cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard_6/picard_collectGcBias.txt' -cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectInsertSizeMetrics.txt' -cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard_6/picard_MarkDuplicates.txt' -cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard_6/picard_CollectBaseDistributionByCycle.txt' -cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectRnaSeqMetrics.txt' -cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectAlignmentSummaryMetrics.txt' +mkdir -p 'multiqc_WDir/featureCounts' +cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts/featureCounts.summary' + +mkdir -p 'multiqc_WDir/gatk' +cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk/gatk_BaseRecalibrator.txt' +cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk/gatk_varianteval.txt' + +mkdir -p 'multiqc_WDir/htseq' +cp 'test-data/htseq.txt' 'multiqc_WDir/htseq/htseq.txt' -mkdir 'multiqc_WDir/prokka_7' -cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka_7/prokka_1.txt' -cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka_7/prokka_2.txt' +mkdir -p 'multiqc_WDir/picard' +cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard/picard_collectGcBias.txt' +cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard/picard_CollectInsertSizeMetrics.txt' +cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard/picard_MarkDuplicates.txt' +cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard/picard_CollectBaseDistributionByCycle.txt' +cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard/picard_CollectRnaSeqMetrics.txt' +cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard/picard_CollectAlignmentSummaryMetrics.txt' -mkdir -p 'multiqc_WDir/quast_8/file_0' -cp 'test-data/quast.tsv' 'multiqc_WDir/quast_8/file_0/report.tsv' +mkdir -p 'multiqc_WDir/prokka' +cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka/prokka_1.txt' +cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka/prokka_2.txt' -#mkdir 'multiqc_WDir/rsem_9' -#cp 'test-data/rsem.txt' 'multiqc_WDir/rsem_9/rsem.cnt' +mkdir -p 'multiqc_WDir/quast/file_0' +cp 'test-data/quast.tsv' 'multiqc_WDir/quast/file_0/report.tsv' -mkdir -p 'multiqc_WDir/rseqc_10/read_gc_0' -cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc_10/read_gc_0/rseq.GC.xls' +#mkdir -p 'multiqc_WDir/rsem' +#cp 'test-data/rsem.txt' 'multiqc_WDir/rsem/rsem.cnt' -mkdir 'multiqc_WDir/samblaster_11' -cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster_11/samblaster.txt' +mkdir -p 'multiqc_WDir/rseqc/read_gc_0' +cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc/read_gc_0/rseq.GC.xls' + +mkdir -p 'multiqc_WDir/samblaster' +cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster/samblaster.txt' -mkdir -p 'multiqc_WDir/samtools_12/stats_0' -cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools_12/stats_0/samtools_stats.txt' -mkdir 'multiqc_WDir/samtools_12/flagstat_1' -cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/flagstat_1/samtools_flagstat.txt' -mkdir 'multiqc_WDir/samtools_12/idxstats_2' -cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/idxstats_2/samtools_idxstats_idxstat' +mkdir -p 'multiqc_WDir/samtools/stats_0' +cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools/stats_0/samtools_stats.txt' +mkdir -p 'multiqc_WDir/samtools/flagstat_1' +cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools/flagstat_1/samtools_flagstat.txt' +mkdir -p 'multiqc_WDir/samtools/idxstats_2' +cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools/idxstats_2/samtools_idxstats_idxstat' -#mkdir 'multiqc_WDir/snpeff_13' -#cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff_13/snpeff.txt' +mkdir -p 'multiqc_WDir/snpeff' +cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff/snpeff.txt' -mkdir -p 'multiqc_WDir/vcftools_14/tstv_by_qual_0' -cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools_14/tstv_by_qual_0/vcftools.TsTv.qual' +mkdir -p 'multiqc_WDir/vcftools/tstv_by_qual_0' +cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools/tstv_by_qual_0/vcftools.TsTv.qual' multiqc multiqc_WDir @@ -155,19 +163,16 @@ mv 'multiqc_data/multiqc_prokka.txt' 'test-data/prokka_stats.tabular' mv 'multiqc_data/multiqc_quast.txt' 'test-data/quast_stats.tabular' #mv 'multiqc_data/multiqc_rsem.txt' 'test-data/rsem_stats.tabular' -mv 'multiqc_data/multiqc_rseqc.txt' 'test-data/rseqc_stats.tabular' mv 'multiqc_data/multiqc_samblaster.txt' 'test-data/samblaster_stats.tabular' mv 'multiqc_data/multiqc_samtools_flagstat.txt' 'test-data/samtools_flagstat_stats.tabular' mv 'multiqc_data/multiqc_samtools_stats.txt' 'test-data/samtools_stats_stats.tabular' -#mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular' +mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular' rm -rf 'multiqc_WDir' rm -rf 'multiqc_data/' # 4th test -mkdir multiqc_WDir - -mkdir 'multiqc_WDir/custom_content_0' +mkdir -p 'multiqc_WDir/custom_content_0' cp 'test-data/cc_ko15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_0.tsv' cp 'test-data/cc_wt15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_1.tsv' diff -r 467486f1c568 -r e0f4a651c6b9 multiqc.xml --- a/multiqc.xml Sun Jan 14 09:55:46 2018 -0500 +++ b/multiqc.xml Fri Apr 20 01:06:25 2018 -0400 @@ -1,26 +1,49 @@ - + aggregate results from bioinformatics analyses into a single report - 1.3 + 1.5 + + + + + + + + @@ -30,6 +53,9 @@ multiqc --version &2 ; exit 1; } && mkdir multiqc_WDir && @@ -37,7 +63,7 @@ #set $configfile="F" #for $i, $repeat in enumerate( $results ) - #set software_dir = 'multiqc_WDir/' + str($repeat.software_cond.software) + '_' + str($i) + #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i)) mkdir $software_dir && #if str($repeat.software_cond.software) == "bamtools" @@ -48,26 +74,36 @@ @LN_FILES@ #elif str($repeat.software_cond.software) == "bismark" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set file_prefix = $software_dir + '/' + str($repeat2.type) + '_' + str($j) + @CREATE_REPEAT_DIR_1@ #if str($repeat2.type) == "align" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}_SE_report.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "dedup" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}_deduplication_report.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "meth_extract" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}_splitting_report.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "m_bias" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}_M-bias.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "bam2nuc" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}.nucleotide_stats.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt') + ln -s '$file' '$file_path' && #end for #end if #end for @@ -77,40 +113,68 @@ #elif str($repeat.software_cond.software) == "busco" ## Searches for files "short_summary_[samplename].txt" #for $file in $repeat.software_cond.input - ln -s '$file' '$software_dir/short_summary_${file.element_identifier}' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier)) + ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "cutadapt" #set $pattern = "This is cutadapt" #for $file in $repeat.software_cond.input - #set file_path = $software_dir + '/' + str($file.element_identifier) + '.txt' + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + '.txt') ln -s '$file' '$file_path' && ## replace header for old cutadapt release sed -i.old 's/You are running/This is/' '$file_path' && grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && #end for + #elif str($repeat.software_cond.software) == "deeptools" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #if str($repeat2.type) == "bamPEFragmentSize" + #set $pattern = "Frag." + @LN_2_FILES@ + #elif str($repeat2.type) == "estimateReadFiltering" + #set $pattern = "Internally-determined Duplicate" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotCoverageStdout" + #set $pattern = "sample" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotCoverageOutRawCounts" + #set $pattern = "#plotCoverage --outRawCounts" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotEnrichment" + #set $pattern = "featureReadCount" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotFingerprintOutRawCounts" + #set $pattern = "#plotFingerprint --outRawCounts" + @LN_2_FILES@ + #end if + #end for #elif str($repeat.software_cond.software) == "fastqc" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type) + '_' + str($j) - mkdir '$repeat_dir' && + @CREATE_REPEAT_DIR_1@ #if str($repeat2.type) == "data" #for $k, $file in enumerate($repeat2.input) - #set file_dir = $repeat_dir + '/file_' + str($k) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir, 'fastqc_data.txt') mkdir '$file_dir' && - ln -s '$file' '$file_dir/fastqc_data.txt' && + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "theoretical_gc" #for $file in $repeat2.input - ln -s '$file' '$repeat_dir/${file.element_identifier}_fastqc_theoretical_gc' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc') + ln -s '$file' '$file_path' && #end for #end if #end for #elif str($repeat.software_cond.software) == "featureCounts" #for $file in $repeat.software_cond.input - #set file_prefix = $software_dir + '/' + str($file.element_identifier) + @ESCAPE_IDENTIFIER@ + #set file_prefix = os.path.join($software_dir, str($identifier)) if grep -qw Status '$file'; then ln -s '$file' '${file_prefix}.summary'; else - echo -e 'Status\t$file.element_identifier' > '${file_prefix}.summary'; + echo -e 'Status\t${identifier}' > '${file_prefix}.summary'; cat '$file' >> '${file_prefix}.summary'; fi && #end for @@ -129,7 +193,9 @@ #end for #elif str($repeat.software_cond.software) == "hicup" #for $file in $repeat.software_cond.input - ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier)) + ln -s '${file}' '$file_path' && #end for #elif str($repeat.software_cond.software) == "hisat2" #set $pattern = "HISAT2 summary stats:" @@ -185,35 +251,40 @@ @LN_FILES@ #elif str($repeat.software_cond.software) == "quast" #for $k, $file in enumerate($repeat.software_cond.input) - #set file_dir = $software_dir + '/file_' + str($k) + #set file_dir = os.path.join($software_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir, 'report.tsv') mkdir '$file_dir' && - ln -s '$file' '$file_dir/report.tsv' && + ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "rsem" #for $file in $repeat.software_cond.input - ln -s '$file' '$software_dir/${file.element_identifier}.cnt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + '.cnt') + ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "rseqc" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir '$repeat_dir' && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "bam_stat" #set $pattern = "Proper-paired reads map to different chrom:" @LN_3_FILES@ #elif str($repeat2.type.type) == "gene_body_coverage" #for $k, $file in enumerate($repeat2.type.input) - ln -s '$file' '$repeat_dir/file_${k}.geneBodyCoverage.txt' && + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "inner_distance" #for $k, $file in enumerate($repeat2.type.input) - ln -s '${file}' '$repeat_dir/file_${k}.inner_distance_freq.txt' && + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt') + ln -s '${file}' '$file_path' && #end for #elif str($repeat2.type.type) == "junction_annotation" #set $pattern = "Partial Novel Splicing Junctions:" @LN_3_FILES@ #elif str($repeat2.type.type) == "read_gc" #for $k, $file in enumerate($repeat2.type.input) - ln -s '$file' '$repeat_dir/file_${k}.GC.xls' && + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "junction_annotation" #set $pattern = "Group Total_bases Tag_count Tags/Kb" @@ -223,31 +294,34 @@ @LN_3_FILES@ #elif str($repeat2.type.type) == "read_duplication_pos" #for $k, $file in enumerate($repeat2.type.input) - ln -s '$file' '$repeat_dir/file_${k}.pos.DupRate.xls' && + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "infer_experiment" #set $pattern = "Fraction of reads explained by" #for $k, $file in enumerate($repeat2.type.input) + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '_infer_experiment.txt') grep -q "$pattern" $file || die "'$pattern' not found in the file" && - ln -s '$file' '$repeat_dir/$file_${k}_infer_experiment.txt' && + ln -s '$file' '$file_path' && #end for #end if #end for #elif str($repeat.software_cond.software) == "salmon" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir '$repeat_dir' && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "meta" #for $k, $file in enumerate($repeat2.type.input) - #set file_dir = $repeat_dir + '/file_' + str($k) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir, 'meta_info.json') mkdir '$file_dir' && - ln -s '$file' '$file_dir/meta_info.json' && + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "fld" #for $k, $file in enumerate($repeat2.type.input) - #set file_dir = $repeat_dir + '/file_' + str($k) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir,'flenDist.txt') mkdir '$file_dir' && - ln -s '$file' '$file_dir/flenDist.txt' && + ln -s '$file' '$file_path' && #end for #end if #end for @@ -256,8 +330,7 @@ @LN_FILES@ #elif str($repeat.software_cond.software) == "samtools" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir '$repeat_dir' && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "stats" #set $pattern = "This file was produced by samtools stats" @LN_3_FILES@ @@ -266,7 +339,9 @@ @LN_3_FILES@ #elif str($repeat2.type.type) == "idxstats" #for $file in $repeat2.type.input - ln -s '$file' '$repeat_dir/${file.element_identifier}_idxstat' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "rmdup" #set $pattern = "[bam_rmdup" @@ -281,60 +356,81 @@ @LN_FILES@ #else if str($repeat.software_cond.software) == "star": #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir $repeat_dir && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "log" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}_Log.final.out' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "genecounts" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}_ReadsPerGene.out.tab' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab') + ln -s '$file' '$file_path' && #end for #end if #end for #elif str($repeat.software_cond.software) == "tophat" #for $file in $repeat.software_cond.input - ln -s '$file' '$software_dir/${file.element_identifier}align_summary.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "trimmomatic" #set $pattern = "Trimmomatic" @LN_FILES@ #elif str($repeat.software_cond.software) == "vcftools" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set file_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir $file_dir && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "relatedness2" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}.relatedness2' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "tstv_by_count" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.count' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "tstv_by_qual" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.qual' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "tstv_summary" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.summary' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary') + ln -s '$file' '$file_path' && #end for #end if #end for #else if str($repeat.software_cond.software) == "custom_content": #set $configfile = "T" #for $j, $file in enumerate( $repeat.software_cond.input ) - ln -s '$file' '${software_dir}/file_${i}_${j}' && + #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j)) + ln -s '$file' '$file_path' && more $file && #end for #end if #end for multiqc multiqc_WDir +--filename "report" + +#if str($title) + --title "$title" +#end if +#if str($comment) + --comment "$comment" +#end if #if $configfile == "T" - -c '$multiqc_config' + --config '$multiqc_config' #end if ]]> @@ -371,6 +467,7 @@ + @@ -380,19 +477,23 @@ + + + - + + @@ -407,19 +508,22 @@ - + + - - + + + + @@ -450,13 +554,29 @@ + + + + + + + + + + + + + + - + + value is not None and value.extension != "html" + @@ -584,6 +704,9 @@ + + + @@ -647,15 +770,18 @@ + + + - - + + saveLog - + @@ -693,9 +819,13 @@ + + + + @@ -785,9 +915,9 @@ - + - + @@ -815,6 +945,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -921,6 +1080,12 @@ + + + + + + @@ -936,6 +1101,7 @@ + @@ -948,17 +1114,17 @@ - + - + - + - + @@ -975,6 +1141,7 @@ + @@ -1005,7 +1172,7 @@ ---- -The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio `_ and Rennes GenOuest Bio-informatics Core Facility). +The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio `_ and Rennes GenOuest Bio-informatics Core Facility). It is now maintained by the `Intergalactic Utilities Commission `_. ]]> 10.1093/bioinformatics/btw354 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/aligner_soft_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligner_soft_report.html Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,5608 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
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        If you use plots from MultiQC in a publication or presentation, please cite:

        +
        + MultiQC: Summarize analysis results for multiple tools and samples in a single report
        + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        + Bioinformatics (2016)
        + doi: 10.1093/bioinformatics/btw354
        + PMID: 27312411 +
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        About MultiQC

        +

        This report was generated using MultiQC, version 1.5

        +

        You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

        +

        For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

        +

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

        +

        MultiQC is published in Bioinformatics:

        +
        + MultiQC: Summarize analysis results for multiple tools and samples in a single report
        + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        + Bioinformatics (2016)
        + doi: 10.1093/bioinformatics/btw354
        + PMID: 27312411 +
        +
        + +
        + +
        + + +
        + + + +

        + + + + +

        + + + +

        + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

        + + + + + + + + + + +
        +

        Report generated on 2018-04-06, 16:47 based on data in: + /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_WDir + +

        + + + +
        + + + + + + + + +
        +

        General Statistics

        + + + + + + + + + + Showing 15/15 rows and 14/15 columns. + +
        +
        + +
        Sample Name% AlignedM Pairs% Used pairs% MappedMin RE distMax RE distFrag LengthM Aligned% AlignedM Aligned% Aligned% AlignedM Aligned% Trimmed
        HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1
        5.9%
        HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1
        83.7%
        167.9bp
        48.5
        HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2
        31.0%
        HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1
        7.7%
        HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1
        84.5%
        169.4bp
        59.3
        HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2
        32.2%
        bismark_SE_report
        69.7%
        bowtie2_1
        98.3%
        bowtie2_2
        98.3%
        hicexplorer_hicexplorer1_small_test
        0.1
        37.3%
        91.2%
        303 bp
        800 bp
        hicexplorer_hicexplorer2_small_test_rf
        0.1
        35.9%
        91.2%
        152 bp
        1500 bp
        hisat2_1
        96.2%
        hisat2_2
        96.2%
        star_log
        89.0%
        0.0
        tophat_align
        99.5%
        0.3
        + + +
        + + + + + + +
        +

        Bismark

        +

        Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

        + + + + +
        + +

        + Alignment Rates + +

        + + + + +
        + + +
        +
        loading..
        +
        + +
        +
        + + + + +
        + +

        + Strand Alignment + +

        + + + + +
        + + +
        +
        loading..
        +
        + + +
        + + +
        +
        + + + +
        +

        HiCExplorer

        +

        HiCExplorer addresses the common tasks of Hi-C analysis from processing to visualization.

        + + + + +
        + +

        + Mapping statistics + + + +

        + +

        This shows how the sequenced read pairs were mapped and those filtered due to mapping problems.

        + + +
        +
          +
        • Pairs mappable, unique and high quality
            +
          • The count of reads that were considered as valid reads and were not one of the following:
          • +
          +
        • +
        • One mate unmapped
            +
          • Filtered out read because one mate was not mapped.
          • +
          +
        • +
        • One mate not unique
            +
          • Filtered out read because one mate was not unique.
          • +
          +
        • +
        • One mate low quality
            +
          • Filtered out because one mate was having a low quality.
          • +
          +
        • +
        +
        + +
        + + +
        +
        loading..
        +
        + +
        +
        + + + + +
        + +

        + Read filtering + + + +

        + +

        This figure contains the number of reads that were finally used to build the Hi-C matrix along with the reads that where filtered out.

        + + +
        +
          +
        • Dangling ends
            +
          • These are reads that start with the restriction site and constitute reads that were digested but no ligated.
          • +
          +
        • +
        • Same fragment
            +
          • These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between.
          • +
          • These read pairs are not valid Hi-C pairs.
          • +
          +
        • +
        • Self circle
            +
          • Self circles are defined as pairs within 25kb with 'outward' read orientation
          • +
          +
        • +
        • Self ligation
            +
          • These are read pairs with a restriction site in between that are within 800 bp.
          • +
          +
        • +
        +
        + +
        + + +
        +
        loading..
        +
        + +
        +
        + + + + +
        + +

        + Contact distance + + + +

        + +

        This figure contains information about the distance and location of the valid pairs used.

        + + +
        +
          +
        • Long range
            +
          • Pairs with a distance greater than 20 kilobases
          • +
          +
        • +
        • Short range
            +
          • Pairs with a distance less than 20 kilobases
          • +
          +
        • +
        • Inter chromosomal
            +
          • Interchromosomal pairs.
          • +
          +
        • +
        +
        + +
        + + +
        +
        loading..
        +
        + +
        +
        + + + + +
        + +

        + Read orientation + + + +

        + +

        This figure contains information about the orientation of the read pairs.

        + + +
        +
          +
        • Inward pairs
            +
          • First mate is a forward read, second is reverse.
          • +
          • ---------------> <----------------
          • +
          +
        • +
        • Outward pairs
            +
          • First mate is a reverse read, second is forward.
          • +
          • ---------------> <----------------
          • +
          +
        • +
        • Left pairs
            +
          • Both are reverse reads.
          • +
          • <--------------- <----------------
          • +
          +
        • +
        • Right pairs
            +
          • Both are forward reads.
          • +
          • ---------------> ---------------->
          • +
          +
        • +
        +
        + +
        + + +
        +
        loading..
        +
        + + +
        + + +
        +
        + + + +
        +

        Kallisto

        +

        Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.

        + + + + +
        + + + + +
        + + +
        +
        loading..
        +
        + + +
        + + +
        +
        + + + +
        +

        STAR

        +

        STAR is an ultrafast universal RNA-seq aligner.

        + + + + +
        + +

        + Alignment Scores + +

        + + + + +
        + + +
        +
        loading..
        +
        + +
        +
        + + + + +
        + +

        + Gene Counts + +

        + +

        Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

        + + +
        + + +
           
        + + + +
        + +
        +
        loading..
        +
        + + +
        + + +
        +
        + + + +
        +

        HISAT2

        +

        HISAT2 is a fast and sensitive alignment program for mapping NGS reads (both DNA and RNA) against a reference genome or population of reference genomes.

        + + + + +
        + + + + +
        + + +
        +
        loading..
        +
        + + +
        + + +
        +
        + + + +
        +

        Tophat

        +

        Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes.

        + + + + +
        + + + + +
        + + +
        +
        loading..
        +
        + + +
        + + +
        +
        + + + +
        +

        Bowtie 2

        +

        Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

        + + + + + + +
        + +

        This plot shows the number of reads aligning to the reference in different ways.

        + + +
        +

        There are 3 possible types of alignment: + SE Mapped uniquely: Read has only one occurence in the reference genome. + SE Multimapped: Read has multiple occurence. +* SE No aligned: Read has no occurence.

        +
        + +
        + + +
        +
        loading..
        +
        + + +
        + + +
        +
        + + + +
        +

        Cutadapt

        +

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        + + + + +
        + +

        This plot shows the number of reads with certain lengths of adapter trimmed. + Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak + may be related to adapter length. See the + cutadapt documentation + for more information on how these numbers are generated.

        + + +
        + + +
        + +
        loading..
        +
        + + +
        + + +
        + + + + +
        + + + + + + + + + + + + + + + + diff -r 467486f1c568 -r e0f4a651c6b9 test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/aligner_soft_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,16 +1,16 @@ -Sample Cutadapt_percent_trimmed-1 Kallisto_percent_aligned-1-1 Kallisto_pseudoaligned_reads-1 Kallisto_fragment_length-1 Bismark_aligned_reads-1 Bismark_percent_aligned-2 Bowtie 2_overall_alignment_rate-1-1 HiCExplorer_Pairs_considered-1 HiCExplorer_Min_rest_site_distance-1 HiCExplorer_Mapped-1 HiCExplorer_Max_rest_site_distance-1 HiCExplorer_Pairs_used-1 HISAT2_overall_alignment_rate-2 STAR_uniquely_mapped_percent-1 STAR_uniquely_mapped-1 Tophat_overall_aligned_percent-1 Tophat_aligned_not_multimapped_discordant-1 +Sample Cutadapt_mqc-generalstats-percent_trimmed Kallisto_mqc-generalstats-pseudoaligned_reads Kallisto_mqc-generalstats-fragment_length Kallisto_mqc-generalstats-percent_aligned Bismark_mqc-generalstats-aligned_reads Bismark_mqc-generalstats-percent_aligned Bowtie 2_mqc-generalstats-overall_alignment_rate HiCExplorer_mqc-generalstats-Mapped HiCExplorer_mqc-generalstats-Pairs_used HiCExplorer_mqc-generalstats-Min_rest_site_distance HiCExplorer_mqc-generalstats-Pairs_considered HiCExplorer_mqc-generalstats-Max_rest_site_distance HISAT2_mqc-generalstats-overall_alignment_rate STAR_mqc-generalstats-uniquely_mapped_percent STAR_mqc-generalstats-uniquely_mapped Tophat_mqc-generalstats-overall_aligned_percent Tophat_mqc-generalstats-aligned_not_multimapped_discordant HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 83.65114569077758 48531088.0 167.866 +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 48531088.0 167.866 83.65114569077758 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 84.50278473550448 59280920.0 169.418 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 59280920.0 169.418 84.50278473550448 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 -align_0 220558.0 69.71079996207212 +bismark_SE_report 220558.0 69.71079996207212 bowtie2_1 98.33 bowtie2_2 98.31 -hicexplorer_3_small_test 99983.0 303.0 0.08778492343698428 800.0 0.3732734564876029 -hicexplorer_3_small_test_rf 99983.0 152.0 0.08778492343698428 1500.0 0.35940109818669175 +hicexplorer_hicexplorer1_small_test 0.08778492343698428 0.3732734564876029 303.0 99983.0 800.0 +hicexplorer_hicexplorer2_small_test_rf 0.08778492343698428 0.35940109818669175 152.0 99983.0 1500.0 hisat2_1 96.15 hisat2_2 96.15 star_log 89.0 89.0 -tophat 99.5 307733.0 +tophat_align 99.5 307733.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/bamtools_stats.tabular --- a/test-data/bamtools_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/bamtools_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample mapped_reads mapped_reads_pct forward_strand_pct read_2 read_1 duplicates both_mapped reverse_strand_pct duplicates_pct reverse_strand forward_strand failed_qc_pct both_mapped_pct failed_qc singletons total_reads singletons_pct paired_end paired_end_pct -bamtools 316585701.0 93.125 53.4381 169978965.0 169978965.0 0.0 314020716.0 46.5619 0.0 158290963.0 181666967.0 0.0 92.3705 0.0 2564985.0 339957930.0 0.754501 339957930.0 100.0 +Sample total_reads forward_strand mapped_reads both_mapped_pct read_1 mapped_reads_pct failed_qc_pct forward_strand_pct reverse_strand paired_end paired_end_pct duplicates_pct singletons read_2 both_mapped failed_qc reverse_strand_pct singletons_pct duplicates +bamtools 339957930.0 181666967.0 316585701.0 92.3705 169978965.0 93.125 0.0 53.4381 158290963.0 339957930.0 100.0 0.0 2564985.0 169978965.0 314020716.0 0.0 46.5619 0.754501 0.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/bcftools_stats.tabular --- a/test-data/bcftools_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/bcftools_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample number_of_records ts_1st_ALT substitution_type_G>C tv substitution_type_A>G substitution_type_A>C number_of_multiallelic_SNP_sites number_of_multiallelic_sites substitution_type_A>T number_of_SNPs number_of_MNPs substitution_type_T>G tstv_1st_ALT tstv number_of_no-ALTs substitution_type_C>G substitution_type_C>T ts number_of_samples substitution_type_T>C substitution_type_G>T substitution_type_T>A substitution_type_C>A number_of_indels tv_1st_ALT number_of_others substitution_type_G>A -Test1 5522770.0 2968539.0 197866.0 1505704.0 721395.0 190164.0 0.0 0.0 166827.0 4474244.0 72330.0 189578.0 1.97 1.97 0.0 197211.0 762114.0 2968539.0 1.0 721436.0 201005.0 166222.0 196831.0 902934.0 1505704.0 73262.0 763594.0 +Sample number_of_samples tstv substitution_type_C>T substitution_type_A>C substitution_type_T>C number_of_multiallelic_sites tv_1st_ALT substitution_type_A>T substitution_type_A>G substitution_type_T>A ts number_of_multiallelic_SNP_sites substitution_type_C>A substitution_type_G>A substitution_type_G>C number_of_MNPs tstv_1st_ALT number_of_records number_of_others tv number_of_SNPs number_of_indels number_of_no-ALTs substitution_type_T>G substitution_type_C>G substitution_type_G>T ts_1st_ALT +Test1 1.0 1.97 762114.0 190164.0 721436.0 0.0 1505704.0 166827.0 721395.0 166222.0 2968539.0 0.0 196831.0 763594.0 197866.0 72330.0 1.97 5522770.0 73262.0 1505704.0 4474244.0 902934.0 0.0 189578.0 197211.0 201005.0 2968539.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/bismark_stats.tabular --- a/test-data/bismark_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/bismark_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ Sample aligned_reads ambig_reads discarded_reads meth_chg meth_chh meth_cpg no_alignments percent_aligned percent_chg_meth percent_chh_meth percent_cpg_meth strand_ctob strand_ctot strand_ob strand_ot total_c total_reads unmeth_chg unmeth_chh unmeth_cpg -align_0 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.71079996207212 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0 +bismark_SE_report 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.71079996207212 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/bowtie2_stats.tabular --- a/test-data/bowtie2_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/bowtie2_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,3 +1,3 @@ -Sample overall_alignment_rate unpaired_total unpaired_aligned_one unpaired_aligned_none unpaired_aligned_multi total_reads -bowtie2_1 98.33 21040602 13299463 351563 7389576 21040602 -bowtie2_2 98.31 16199126 10087714 274008 5837404 16199126 +Sample unpaired_total unpaired_aligned_multi overall_alignment_rate unpaired_aligned_none total_reads unpaired_aligned_one +bowtie2_1 21040602 7389576 98.33 351563 21040602 13299463 +bowtie2_2 16199126 5837404 98.31 274008 16199126 10087714 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/busco_stats.tabular --- a/test-data/busco_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/busco_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample fragmented complete missing complete_single_copy total lineage_dataset complete_duplicated -short 5.0 257.0 28.0 255.0 290.0 fungi_odb9 2.0 +Sample fragmented complete_single_copy total complete missing lineage_dataset complete_duplicated +busco 5.0 255.0 290.0 257.0 28.0 fungi_odb9 2.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/cutadapt_stats.tabular --- a/test-data/cutadapt_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/cutadapt_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample too_short percent_trimmed too_long bp_trimmed bp_processed r_trimmed r_processed -dataset_33 0 10.776820436239396 0 3443775 31955390 68795 316390 +Sample r_trimmed percent_trimmed too_long too_short r_processed bp_processed bp_trimmed +dataset_33 68795 10.776820436239396 0 0 316390 31955390 3443775 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_bamPEFragmentSize.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_bamPEFragmentSize.txt Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,6 @@ + Frag. Sampled Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu. Frag. Len. Max Frag. Len. Std. Frag. Med. Abs. Dev. Frag. Len. 10% Frag. Len. 20% Frag. Len. 30% Frag. Len. 40% Frag. Len. 60% Frag. Len. 70% Frag. Len. 80% Frag. Len. 90% Frag. Len. 99% Reads Sampled Read Len. Min. Read Len. 1st. Qu. Read Len. Mean Read Len. Median Read Len. 3rd Qu. Read Len. Max Read Len. Std. Read Med. Abs. Dev. Read Len. 10% Read Len. 20% Read Len. 30% Read Len. 40% Read Len. 60% Read Len. 70% Read Len. 80% Read Len. 90% Read Len. 99% +bwameth_se.pbat.bam 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51142 40.0 101.0 98.0356654022 101.0 101.0 101.0 10.864939372 0.0 99.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 +bismark_se.pbat.bam 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34118 21.0 101.0 99.5840905094 101.0 101.0 101.0 7.089489864 0.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 101.0 +/data/boehm/group/lawir/A757/bams_bismark/dnmt1MUT_mat2aMUT_1_RGi.bam 15504 174.0 185.0 184.99245356 185.0 185.0 186.0 0.175975291035 0.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 15504 148.0 148.0 148.0 148.0 148.0 148.0 0.0 0.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 +/data/boehm/group/lawir/A757/bams_bismark/dnmt1MUT_mat2aMUT_2_RGi.bam 17327 176.0 185.0 184.989957869 185.0 185.0 186.0 0.19282636998 0.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 17327 148.0 148.0 148.0 148.0 148.0 148.0 0.0 0.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 +/data/boehm/group/lawir/A757/bams_bismark/dnmt1MUT_mat2aMUT_3_RGi.bam 15266 104.0 185.0 184.98545788 185.0 185.0 186.0 0.676996184607 0.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 185.0 15266 102.0 148.0 147.996986768 148.0 148.0 148.0 0.372289663166 0.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 148.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_estimateReadFiltering.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_estimateReadFiltering.txt Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,3 @@ +Sample Total Reads Mapped Reads Alignments in blacklisted regions Estimated mapped reads filtered Below MAPQ Missing Flags Excluded Flags Internally-determined Duplicates Marked Duplicates Singletons Wrong strand +bwameth_se.pbat.bam 71373361 46192726 0 14151494.8 5163035.6 0.0 0.0 20264594.9 0.0 0.0 4596084.6 +bismark_se.pbat.bam 30924955 30924955 0 13624010.0 10983580.2 0.0 0.0 13414682.1 0.0 0.0 1542611.8 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_plotCoverageOutRawCounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_plotCoverageOutRawCounts.txt Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,20000 @@ +#plotCoverage --outRawCounts +#'chr' 'start' 'end' 'bwameth_se.pbat.bam' 'bismark_se.pbat.bam' +KI270589.1 43386 43387 4.0 0.0 +13 16229463 16229464 1.0 0.0 +13 16257354 16257355 1.0 0.0 +13 16306938 16306939 1.0 0.0 +13 16430898 16430899 1.0 0.0 +13 16554858 16554859 1.0 0.0 +13 16604442 16604443 2.0 0.0 +13 16787283 16787284 1.0 0.0 +13 16812075 16812076 1.0 0.0 +13 16821372 16821373 1.0 0.0 +13 16880253 16880254 1.0 0.0 +13 16892649 16892650 1.0 0.0 +13 16929837 16929838 1.0 0.0 +13 17156064 17156065 1.0 0.0 +13 17187054 17187055 1.0 0.0 +13 17301717 17301718 1.0 0.0 +13 17326509 17326510 1.0 0.0 +13 17422578 17422579 1.0 0.0 +13 17434974 17434975 1.0 0.0 +13 17450469 17450470 1.0 0.0 +13 17549637 17549638 1.0 0.0 +13 17599221 17599222 1.0 0.0 +13 17633310 17633311 1.0 0.0 +13 17645706 17645707 1.0 0.0 +13 17673597 17673598 1.0 0.0 +13 17754171 17754172 1.0 0.0 +13 17909121 17909122 1.0 0.0 +13 18191130 18191131 18.0 7.0 +13 18194229 18194230 95.0 24.0 +13 18197328 18197329 1.0 1.0 +13 18200427 18200428 1.0 0.0 +13 18206625 18206626 3.0 1.0 +13 18212823 18212824 1.0 0.0 +13 18231417 18231418 1.0 0.0 +13 18234516 18234517 1.0 0.0 +13 18256209 18256210 2.0 0.0 +13 18265506 18265507 1.0 2.0 +13 18268605 18268606 1.0 0.0 +13 18274803 18274804 14.0 7.0 +13 18277902 18277903 9.0 6.0 +13 18281001 18281002 1.0 0.0 +13 18290298 18290299 23.0 0.0 +13 18296496 18296497 11.0 0.0 +13 18299595 18299596 12.0 6.0 +13 18302694 18302695 22.0 8.0 +13 18311991 18311992 4.0 0.0 +13 18324387 18324388 33.0 13.0 +13 18336783 18336784 1.0 0.0 +13 18408060 18408061 5.0 2.0 +13 18420456 18420457 3.0 0.0 +13 18423555 18423556 5.0 0.0 +13 18435951 18435952 1.0 0.0 +13 18476238 18476239 1.0 1.0 +13 18485535 18485536 1.0 0.0 +13 18525822 18525823 1.0 0.0 +13 18547515 18547516 1.0 0.0 +13 18609495 18609496 3.0 1.0 +13 18612594 18612595 4.0 4.0 +13 18621891 18621892 1.0 0.0 +13 18659079 18659080 1.0 0.0 +13 18665277 18665278 2.0 1.0 +13 18674574 18674575 3.0 0.0 +13 18680772 18680773 3.0 1.0 +13 18727257 18727258 17.0 10.0 +13 18736554 18736555 1.0 0.0 +13 18745851 18745852 1.0 0.0 +13 18748950 18748951 1.0 1.0 +13 18773742 18773743 1.0 0.0 +13 18779940 18779941 1.0 0.0 +13 18795435 18795436 1.0 0.0 +13 18798534 18798535 2.0 2.0 +13 18807831 18807832 3.0 1.0 +13 18810930 18810931 1.0 0.0 +13 18814029 18814030 2.0 0.0 +13 18848118 18848119 1.0 0.0 +13 18869811 18869812 1.0 1.0 +13 18888405 18888406 4.0 0.0 +13 18894603 18894604 12.0 8.0 +13 18900801 18900802 2.0 1.0 +13 18903900 18903901 1.0 0.0 +13 18916296 18916297 2.0 0.0 +13 18944187 18944188 39.0 19.0 +13 18953484 18953485 21.0 14.0 +13 18962781 18962782 19.0 8.0 +13 18972078 18972079 1.0 0.0 +13 19003068 19003069 2.0 0.0 +13 19009266 19009267 8.0 4.0 +13 19012365 19012366 1.0 1.0 +13 19061949 19061950 3.0 2.0 +13 19068147 19068148 7.0 0.0 +13 19089840 19089841 2.0 2.0 +13 19117731 19117732 8.0 6.0 +13 19120830 19120831 1.0 1.0 +13 19123929 19123930 1.0 1.0 +13 19151820 19151821 1.0 1.0 +13 19154919 19154920 10.0 6.0 +13 19170414 19170415 13.0 8.0 +13 19173513 19173514 14.0 8.0 +13 19179711 19179712 61.0 47.0 +13 19182810 19182811 5.0 1.0 +13 19185909 19185910 8.0 5.0 +13 19198305 19198306 7.0 0.0 +13 19226196 19226197 1.0 0.0 +13 19229295 19229296 2.0 0.0 +13 19241691 19241692 2.0 2.0 +13 19263384 19263385 110.0 75.0 +13 19275780 19275781 4.0 0.0 +13 19278879 19278880 1.0 0.0 +13 19306770 19306771 2.0 0.0 +13 19322265 19322266 1.0 0.0 +13 19340859 19340860 7.0 6.0 +13 19343958 19343959 1.0 1.0 +13 19347057 19347058 137.0 108.0 +13 19356354 19356355 1.0 1.0 +13 19381146 19381147 10.0 7.0 +13 19402839 19402840 1.0 1.0 +13 19405938 19405939 1.0 1.0 +13 19412136 19412137 2.0 0.0 +13 19415235 19415236 1.0 0.0 +13 19458621 19458622 10.0 1.0 +13 19489611 19489612 2.0 0.0 +13 19557789 19557790 10.0 9.0 +13 19560888 19560889 6.0 4.0 +13 19563987 19563988 26.0 4.0 +13 19570185 19570186 1.0 0.0 +13 19582581 19582582 3.0 0.0 +13 19585680 19585681 2.0 1.0 +13 19601175 19601176 4.0 1.0 +13 19622868 19622869 1.0 0.0 +13 19632165 19632166 1.0 1.0 +13 19635264 19635265 2.0 1.0 +13 19638363 19638364 1.0 1.0 +13 19647660 19647661 2.0 1.0 +13 19669353 19669354 50.0 34.0 +13 19672452 19672453 1.0 1.0 +13 19678650 19678651 1.0 0.0 +13 19694145 19694146 8.0 0.0 +13 19715838 19715839 1.0 0.0 +13 19749927 19749928 1.0 0.0 +13 19756125 19756126 1.0 0.0 +13 19762323 19762324 1.0 1.0 +13 19768521 19768522 1.0 0.0 +13 19771620 19771621 25.0 0.0 +13 19774719 19774720 3.0 0.0 +13 19784016 19784017 4.0 4.0 +13 19790214 19790215 1.0 1.0 +13 19808808 19808809 1.0 0.0 +13 19818105 19818106 95.0 65.0 +13 19830501 19830502 1.0 1.0 +13 19845996 19845997 18.0 13.0 +13 19864590 19864591 209.0 153.0 +13 19867689 19867690 1.0 0.0 +13 19889382 19889383 2.0 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39317013 39317014 61.0 46.0 +15 39320112 39320113 1.0 1.0 +15 39332508 39332509 23.0 14.0 +15 39372795 39372796 1.0 0.0 +15 39434775 39434776 18.0 11.0 +15 39447171 39447172 1.0 1.0 +15 39450270 39450271 1.0 0.0 +15 39475062 39475063 4.0 0.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_plotCoverageStdout.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_plotCoverageStdout.txt Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,3 @@ +sample mean std min 25% 50% 75% max +bwameth_se.pbat.bam 4.48 23.43 0 0.0 0.0 0.0 2589 +bismark_se.pbat.bam 3.00 16.46 0 0.0 0.0 0.0 959 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_plotEnrichment.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_plotEnrichment.txt Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,17 @@ +file featureType percent featureReadCount totalReadCount +bwameth_se.pbat.bam gene 75.58 34911152 46192726 +bwameth_se.pbat.bam Selenocysteine 0.00 820 46192726 +bwameth_se.pbat.bam UTR 13.66 6308386 46192726 +bwameth_se.pbat.bam exon 31.37 14488419 46192726 +bwameth_se.pbat.bam stop_codon 0.76 352502 46192726 +bwameth_se.pbat.bam CDS 13.84 6395119 46192726 +bwameth_se.pbat.bam start_codon 1.49 687421 46192726 +bwameth_se.pbat.bam transcript 75.58 34910782 46192726 +bismark_se.pbat.bam gene 77.05 23828612 30924955 +bismark_se.pbat.bam Selenocysteine 0.00 667 30924955 +bismark_se.pbat.bam UTR 14.53 4492824 30924955 +bismark_se.pbat.bam exon 33.06 10224247 30924955 +bismark_se.pbat.bam stop_codon 0.86 266447 30924955 +bismark_se.pbat.bam CDS 14.94 4618943 30924955 +bismark_se.pbat.bam start_codon 1.65 509377 30924955 +bismark_se.pbat.bam transcript 77.05 23828340 30924955 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/deeptools_plotFingerprintOutRawCounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deeptools_plotFingerprintOutRawCounts.txt Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,20000 @@ +#plotFingerprint --outRawCounts +'bwameth_se.pbat.bam' 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3161 +12235 8818 +78 0 +4250 1530 +23635 14456 +73 0 +41 0 +46 17 +5050 3905 +396 0 +26 0 +18827 13339 +222 0 +394 293 +807 309 +176 169 +83 0 +3049 2418 +4075 3439 +3775 3213 +183 146 +120 7 +8777 7019 +8765 6908 +7399 5206 +172 101 +2844 2020 +13124 9592 +10971 8276 +101 101 +8801 7586 +25844 20222 +101 101 +13 0 +6753 4760 +218 218 +221 0 +34401 26595 +297 262 +736 497 +3668 2829 +101 101 +11432 9067 +102 0 +1515 0 +82 82 +278 278 +13 0 +71 0 +63 0 +59 0 +5423 3800 +865 0 +98 98 +740 657 +50 0 +4034 2976 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/fastqc_stats.tabular --- a/test-data/fastqc_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/fastqc_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,3 +1,3 @@ -Sample per_base_sequence_quality total_deduplicated_percentage sequence_duplication_levels basic_statistics Filename sequence_length_distribution avg_sequence_length per_sequence_quality_scores per_base_sequence_content adapter_content Total Sequences per_sequence_gc_content File type Encoding per_tile_sequence_quality per_base_n_content kmer_content Sequences flagged as poor quality Sequence length overrepresented_sequences %GC -poulet5_1 warn 63.69408840068983 warn pass poulet5_1 pass 101.0 warn fail pass 267849.0 pass Conventional base calls Sanger / Illumina 1.9 pass pass warn 0.0 101.0 pass 48.0 -poulet5_2 warn 63.826611251945884 warn pass poulet5_2 pass 101.0 warn fail pass 267849.0 pass Conventional base calls Sanger / Illumina 1.9 pass pass warn 0.0 101.0 pass 48.0 +Sample Filename File type Total Sequences sequence_duplication_levels overrepresented_sequences per_base_sequence_content per_base_sequence_quality per_base_n_content sequence_length_distribution %GC Encoding total_deduplicated_percentage per_sequence_quality_scores per_tile_sequence_quality Sequence length avg_sequence_length per_sequence_gc_content basic_statistics adapter_content Sequences flagged as poor quality kmer_content +poulet5_1 poulet5_1 Conventional base calls 267849.0 warn pass fail warn pass pass 48.0 Sanger / Illumina 1.9 63.69408840068983 warn pass 101.0 101.0 pass pass pass 0.0 warn +poulet5_2 poulet5_2 Conventional base calls 267849.0 warn pass fail warn pass pass 48.0 Sanger / Illumina 1.9 63.826611251945884 warn pass 101.0 101.0 pass pass pass 0.0 warn diff -r 467486f1c568 -r e0f4a651c6b9 test-data/featureCounts_stats.tabular --- a/test-data/featureCounts_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/featureCounts_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,7 +1,7 @@ -Sample Unassigned_Nonjunction percent_assigned Total Unassigned_FragmentLength Unassigned_MultiMapping Unassigned_NoFeatures Unassigned_Secondary Unassigned_MappingQuality Unassigned_Duplicate Unassigned_Ambiguity Unassigned_Unmapped Assigned Unassigned_Chimera -70: TopHat on data 1, data 4, and data 3: accepted_hits 0 70.82267755353567 454370 0 19123 111117 0 0 0 2333 0 321797 0 -75: TopHat on data 1, data 6, and data 5: accepted_hits 0 69.58585803304067 639515 0 25293 165786 0 0 0 3424 0 445012 0 -80: TopHat on data 1, data 8, and data 7: accepted_hits 0 71.76957768385707 550346 0 22580 129664 0 0 0 3121 0 394981 0 -85: TopHat on data 1, data 10, and data 9: accepted_hits 0 72.02454351337069 607411 0 19907 146327 0 0 0 3692 0 437485 0 -90: TopHat on data 1, data 12, and data 11: accepted_hits 0 71.33130826437625 544179 0 21164 132063 0 0 0 2782 0 388170 0 -95: TopHat on data 1, data 14, and data 13: accepted_hits 0 70.72517103678439 641821 0 23533 160805 0 0 0 3554 0 453929 0 +Sample Unassigned_MappingQuality Unassigned_Nonjunction Unassigned_Unmapped Unassigned_Chimera percent_assigned Unassigned_NoFeatures Unassigned_Secondary Assigned Unassigned_FragmentLength Unassigned_Duplicate Unassigned_MultiMapping Unassigned_Ambiguity Total +70: TopHat on data 1, data 4, and data 3: accepted_hits 0 0 0 0 70.82267755353567 111117 0 321797 0 0 19123 2333 454370 +75: TopHat on data 1, data 6, and data 5: accepted_hits 0 0 0 0 69.58585803304067 165786 0 445012 0 0 25293 3424 639515 +80: TopHat on data 1, data 8, and data 7: accepted_hits 0 0 0 0 71.76957768385707 129664 0 394981 0 0 22580 3121 550346 +85: TopHat on data 1, data 10, and data 9: accepted_hits 0 0 0 0 72.02454351337069 146327 0 437485 0 0 19907 3692 607411 +90: TopHat on data 1, data 12, and data 11: accepted_hits 0 0 0 0 71.33130826437625 132063 0 388170 0 0 21164 2782 544179 +95: TopHat on data 1, data 14, and data 13: accepted_hits 0 0 0 0 70.72517103678439 160805 0 453929 0 0 23533 3554 641821 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/flexbar_stats.tabular --- a/test-data/flexbar_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/flexbar_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample processed_bases discarded_reads_overall finally_skipped_short_reads skipped_due_to_uncalled_bases removed_bases remaining_bases remaining_reads short_prior_to_adapter_removal removed_bases_pct processed_reads -result_right 422 3 3 0 191 231 10 0 45.26066350710901 13 +Sample remaining_reads removed_bases finally_skipped_short_reads skipped_due_to_uncalled_bases short_prior_to_adapter_removal processed_reads processed_bases removed_bases_pct discarded_reads_overall remaining_bases +result_right 10 191 3 0 0 13 422 45.26066350710901 3 231 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/gatk_varianteval_stats.tabular --- a/test-data/gatk_varianteval_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/gatk_varianteval_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample nocalls mnps novel_titv mixed deletions snps known_titv titv_reference complex symbolic insertions -varianteval_1_gatk_varianteval 1330372586 0 2.2 0 0 19199310 0.0 none 0 0 0 +Sample mnps symbolic complex nocalls deletions known_titv titv_reference novel_titv snps mixed insertions +gatk_varianteval 0 0 0 1330372586 0 0.0 none 2.2 19199310 0 0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/hisat2_stats.tabular --- a/test-data/hisat2_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/hisat2_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,3 +1,3 @@ -Sample overall_alignment_rate unpaired_aligned_multi unpaired_aligned_none unpaired_total unpaired_aligned_one -hisat2_1 96.15 9953 3849 99978 86176 -hisat2_2 96.15 9953 3849 99978 86176 +Sample unpaired_aligned_multi overall_alignment_rate unpaired_aligned_none unpaired_total unpaired_aligned_one +hisat2_1 9953 96.15 3849 99978 86176 +hisat2_2 9953 96.15 3849 99978 86176 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/htseq_stats.tabular --- a/test-data/htseq_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/htseq_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample alignment_not_unique percent_assigned total_count assigned not_aligned no_feature ambiguous too_low_aQual -htseq 0 0.0 1355 0 1336 19 0 0 +Sample alignment_not_unique assigned total_count not_aligned percent_assigned no_feature too_low_aQual ambiguous +htseq 0 0 1355 1336 0.0 19 0 0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/kallisto_stats.tabular --- a/test-data/kallisto_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/kallisto_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,3 +1,3 @@ -Sample fragment_length percent_aligned total_reads not_pseudoaligned_reads pseudoaligned_reads -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.6511456908 58016047.0 9484959.0 48531088.0 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.5027847355 70152623.0 10871703.0 59280920.0 +Sample pseudoaligned_reads not_pseudoaligned_reads total_reads percent_aligned fragment_length +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 48531088.0 9484959.0 58016047.0 83.65114569077758 167.866 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 59280920.0 10871703.0 70152623.0 84.50278473550448 169.418 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/picard_AlignmentSummaryMetrics_stats.tabular --- a/test-data/picard_AlignmentSummaryMetrics_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/picard_AlignmentSummaryMetrics_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample PF_HQ_ALIGNED_READS READS_ALIGNED_IN_PAIRS MEAN_READ_LENGTH BAD_CYCLES PF_INDEL_RATE PCT_READS_ALIGNED_IN_PAIRS TOTAL_READS PCT_CHIMERAS PF_HQ_ERROR_RATE PF_ALIGNED_BASES PCT_PF_READS LIBRARY PF_READS PCT_ADAPTER PCT_PF_READS_ALIGNED READ_GROUP SAMPLE PF_NOISE_READS STRAND_BALANCE PF_HQ_ALIGNED_Q20_BASES CATEGORY PF_HQ_MEDIAN_MISMATCHES PF_HQ_ALIGNED_BASES PF_MISMATCH_RATE PF_READS_ALIGNED -D11_H4K16ac_Rep1_R1_fastq_gz 11288718.0 0.0 74.733459 0.0 0.000848 0.0 16199126.0 0.0 0.006165 1189439864.0 1.0 16199126.0 1.4e-05 0.983085 112.0 0.494061 802235299.0 UNPAIRED 0.0 843872901.0 0.011597 15925118.0 +Sample CATEGORY PF_HQ_ALIGNED_Q20_BASES PF_HQ_ALIGNED_BASES READ_GROUP PF_HQ_ALIGNED_READS PF_MISMATCH_RATE LIBRARY PCT_READS_ALIGNED_IN_PAIRS MEAN_READ_LENGTH PF_HQ_MEDIAN_MISMATCHES SAMPLE PF_HQ_ERROR_RATE READS_ALIGNED_IN_PAIRS PF_READS TOTAL_READS PF_INDEL_RATE PCT_ADAPTER STRAND_BALANCE PCT_PF_READS PF_READS_ALIGNED PF_NOISE_READS BAD_CYCLES PCT_CHIMERAS PF_ALIGNED_BASES PCT_PF_READS_ALIGNED +D11_H4K16ac_Rep1_R1_fastq_gz UNPAIRED 802235299.0 843872901.0 11288718.0 0.011597 0.0 74.733459 0.0 0.006165 0.0 16199126.0 16199126.0 0.000848 1.4e-05 0.494061 1.0 15925118.0 112.0 0.0 0.0 1189439864.0 0.983085 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/picard_RnaSeqMetrics_stats.tabular --- a/test-data/picard_RnaSeqMetrics_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/picard_RnaSeqMetrics_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample PCT_CODING_BASES RIBOSOMAL_BASES PF_NOT_ALIGNED_BASES PCT_MRNA_BASES CORRECT_STRAND_READS MEDIAN_CV_COVERAGE PCT_RIBOSOMAL_BASES PCT_INTRONIC_BASES MEDIAN_3PRIME_BIAS PF_ALIGNED_BASES LIBRARY MEDIAN_5PRIME_BIAS PCT_USABLE_BASES PF_BASES READ_GROUP IGNORED_READS SAMPLE INTERGENIC_BASES INTRONIC_BASES MEDIAN_5PRIME_TO_3PRIME_BIAS PCT_INTERGENIC_BASES PCT_CORRECT_STRAND_READS INCORRECT_STRAND_READS CODING_BASES UTR_BASES PCT_UTR_BASES -picard_CollectRnaSeqMetrics_bam 0.0 158.0 79.6231 0.0 0.91593 0.0 0.235755 48712.0 0.430026 79.3657 48870.0 0.0 9926.0 0.0 1.402829 20.3769 0.0 0.0 0.0 38786.0 79.6231 +Sample READ_GROUP INCORRECT_STRAND_READS PF_NOT_ALIGNED_BASES PCT_CODING_BASES PCT_USABLE_BASES MEDIAN_5PRIME_TO_3PRIME_BIAS PCT_CORRECT_STRAND_READS RIBOSOMAL_BASES LIBRARY IGNORED_READS PCT_INTRONIC_BASES INTRONIC_BASES PCT_INTERGENIC_BASES PCT_RIBOSOMAL_BASES MEDIAN_3PRIME_BIAS SAMPLE MEDIAN_CV_COVERAGE UTR_BASES INTERGENIC_BASES CORRECT_STRAND_READS PCT_UTR_BASES CODING_BASES MEDIAN_5PRIME_BIAS PCT_MRNA_BASES PF_BASES PF_ALIGNED_BASES +picard_CollectRnaSeqMetrics_bam 0.0 158.0 0.0 79.36569999999999 1.402829 0.0 0.0 0.0 0.0 20.3769 0.235755 0.91593 38786.0 9926.0 0.0 79.62310000000001 0.0 0.430026 79.62310000000001 48870.0 48712.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/picard_baseContent_stats.tabular --- a/test-data/picard_baseContent_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/picard_baseContent_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample mean_pct_a mean_pct_g sum_pct_g mean_pct_t sum_pct_a mean_pct_c sum_pct_t sum_pct_c sum_pct_n cycle_count -D11_H4K16ac_Rep1_R1_fastq_gz 30.02120486666666 21.205210626666666 1590.390797 28.154420613333333 2251.5903649999996 20.61250701333334 2111.581546 1545.9380260000005 0.49925800000000015 75 +Sample mean_pct_t mean_pct_g sum_pct_c sum_pct_t mean_pct_c mean_pct_a sum_pct_n cycle_count sum_pct_g sum_pct_a +D11_H4K16ac_Rep1_R1_fastq_gz 28.154420613333333 21.205210626666666 1545.9380260000005 2111.581546 20.61250701333334 30.02120486666666 0.49925800000000015 75 1590.390797 2251.5903649999996 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/picard_dups_stats.tabular --- a/test-data/picard_dups_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/picard_dups_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample LIBRARY UNPAIRED_READS_EXAMINED ESTIMATED_LIBRARY_SIZE READ_PAIR_DUPLICATES UNPAIRED_READ_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION UNMAPPED_READS READ_PAIRS_EXAMINED -dataset_114 Unknown Library 2900.0 77973949.0 629.0 2257.0 0.0 0.005582 0.0 313405.0 +Sample READ_PAIR_DUPLICATES UNPAIRED_READS_EXAMINED LIBRARY READ_PAIRS_EXAMINED UNPAIRED_READ_DUPLICATES UNMAPPED_READS ESTIMATED_LIBRARY_SIZE PERCENT_DUPLICATION READ_PAIR_OPTICAL_DUPLICATES +dataset_114 629.0 2900.0 Unknown Library 313405.0 2257.0 0.0 77973949.0 0.005582 0.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/post_aligner_soft_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/post_aligner_soft_report.html Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,7363 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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              If you use plots from MultiQC in a publication or presentation, please cite:

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              + MultiQC: Summarize analysis results for multiple tools and samples in a single report
              + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
              + Bioinformatics (2016)
              + doi: 10.1093/bioinformatics/btw354
              + PMID: 27312411 +
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              About MultiQC

              +

              This report was generated using MultiQC, version 1.5

              +

              You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

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              For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

              +

              You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

              +

              MultiQC is published in Bioinformatics:

              +
              + MultiQC: Summarize analysis results for multiple tools and samples in a single report
              + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
              + Bioinformatics (2016)
              + doi: 10.1093/bioinformatics/btw354
              + PMID: 27312411 +
              +
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              + + + +

              + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

              + + + + + + + + + + +
              +

              Report generated on 2018-04-06, 18:29 based on data in: + /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_WDir + +

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              +

              General Statistics

              + + + + + + + + + + Showing 21/21 rows and 31/34 columns. + +
              +
              + +
              Sample NameM Reads MappedN50 (Kbp)Length (Mbp)Change rateTs/TvM VariantsTiTV ratio (known)TiTV ratio (novel)% AssignedM AssignedVarsSNPIndelTs/TvM Assigned% rRNA% mRNA% AlignedInsert Size% DupsOrganismContigsCDS% DupsError rateM Non-PrimaryM Reads Mapped% MappedM Total seqs% Duplicates% Mapped
              14892_1#15
              115.1Kbp
              18.4Mbp
              70: TopHat on data 1, data 4, and data 3: accepted_hits
              70.8%
              0.3
              75: TopHat on data 1, data 6, and data 5: accepted_hits
              69.6%
              0.4
              80: TopHat on data 1, data 8, and data 7: accepted_hits
              71.8%
              0.4
              85: TopHat on data 1, data 10, and data 9: accepted_hits
              72.0%
              0.4
              90: TopHat on data 1, data 12, and data 11: accepted_hits
              71.3%
              0.4
              95: TopHat on data 1, data 14, and data 13: accepted_hits
              70.7%
              0.5
              D11_H4K16ac_Rep1_R1_fastq_gz
              98%
              Sample1
              Helicobacter pylori
              30.0
              1548
              Sample2
              Escherichia coli
              52.0
              1548
              Test1
              5522770
              4474244
              902934
              1.97
              bamtools
              0.0%
              93.1%
              dataset_114
              0.6%
              dataset_197
              176 bp
              gatk_varianteval
              0.0
              2.2
              htseq
              0.0%
              0.0
              picard_CollectRnaSeqMetrics_bam
              %
              79.6%
              samtools_flagstat
              20.7
              samtools_stats
              0.42%
              0.0
              0.6
              100.0%
              0.6
              snpeff
              3190
              0.000
              0.97
              virtual-normal
              1.3%
              + + +
              + + + + + + +
              +

              QUAST

              +

              QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

              + + + + +
              + +

              + Assembly Statistics + +

              + + + + +
              + + + + + + + + + Showing 1/1 rows and 12/12 columns. + +
              +
              + +
              Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenesGenes (Partial)Genome Fraction
              14892_1#15
              115.1Kbp
              62.3Kbp
              0.0K
              100.0K
              435.5Kbp
              18.4Mbp
              107.0
              262.21
              33.75
              7280
              968
              95.5%
              + +
              + +
              +
              + + + + +
              + +

              + Number of Contigs + +

              + +

              This plot shows the number of contigs found for each assembly, broken + down by length.

              + + +
              + + +
              +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              RSeQC

              +

              RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

              + + + + +
              + +

              + Read GC Content + +

              + +

              read_GC calculates a histogram of read GC content.

              + + +
              + + +
              + +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              BUSCO

              +

              BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

              + + + + +
              + +

              + Lineage: fungi_odb9 + +

              + + + + +
              + + +
              +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              deepTools

              +

              deepTools is a suite of tools to process and analyze deep sequencing data.

              + + + + +
              + +

              + Filtering metrics + +

              + +

              Estimated percentages of alignments filtered independently for each setting in estimateReadFiltering

              + + +
              + + + + + + + + + Showing 2/2 rows and 10/10 columns. + +
              +
              + +
              Sample NameM entries% Aligned% Tot. Filtered% Blacklisted% Missing Flags% Forbidden Flags% deepTools Dupes% Duplication% Singletons% Strand Filtered
              bismark_se.pbat
              30.9
              100.0
              44.1
              0.0
              0.0
              0.0
              43.4
              0.0
              0.0
              5.0
              bwameth_se.pbat
              71.4
              64.7
              19.8
              0.0
              0.0
              0.0
              28.4
              0.0
              0.0
              6.4
              + +
              + +
              +
              + + + + +
              + +

              + Coverage metrics + +

              + + + + +
              + + + + + + + + + Showing 2/2 rows and 7/7 columns. + +
              +
              + +
              Sample NameMin1st QuartileMedianMean3rd QuartileMaxStd. Dev.
              bismark_se.pbat
              0.0
              0.0
              0.0
              3.0
              0.0
              959.0
              16.5
              bwameth_se.pbat
              0.0
              0.0
              0.0
              4.5
              0.0
              2589.0
              23.4
              + +
              + +
              +
              + + + + +
              + +

              + Coverage distribution + +

              + +

              The fraction of bases with a given number of read/fragment coverage

              + + +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Read lengths + +

              + + + + +
              + + + + + + + + + Showing 5/5 rows and 9/9 columns. + +
              +
              + +
              Sample Name# SampledMin1st QuartileMeanMedian3rd QuartileMaxStd. Dev.MAD
              bismark_se.pbat
              34118
              21
              101
              99.6
              101
              101
              101
              7.1
              0.0
              bwameth_se.pbat
              51142
              40
              101
              98.0
              101
              101
              101
              10.9
              0.0
              dnmt1MUT_mat2aMUT_1_RGi
              15504
              148
              148
              148.0
              148
              148
              148
              0.0
              0.0
              dnmt1MUT_mat2aMUT_2_RGi
              17327
              148
              148
              148.0
              148
              148
              148
              0.0
              0.0
              dnmt1MUT_mat2aMUT_3_RGi
              15266
              102
              148
              148.0
              148
              148
              148
              0.4
              0.0
              + +
              + +
              +
              + + + + +
              + +

              + Fragment lengths + +

              + + + + +
              + + + + + + + + + Showing 3/3 rows and 9/9 columns. + +
              +
              + +
              Sample Name# SampledMin1st QuartileMeanMedian3rd QuartileMaxStd. Dev.MAD
              dnmt1MUT_mat2aMUT_1_RGi
              15504
              174
              185
              185
              185
              185
              186
              0.2
              0.0
              dnmt1MUT_mat2aMUT_2_RGi
              17327
              176
              185
              185
              185
              185
              186
              0.2
              0.0
              dnmt1MUT_mat2aMUT_3_RGi
              15266
              104
              185
              185
              185
              185
              186
              0.7
              0.0
              + +
              + +
              +
              + + + + +
              + +

              + Read/fragment length distribution + +

              + + + + +
              + + +
              + +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Signal enrichment per feature + +

              + +

              Signal enrichment per feature according to plotEnrichment

              + + +
              + + +
              + +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Fingerprint + +

              + +

              Signal fingerprint according to plotFingerprint

              + + +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              SnpEff

              +

              SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).

              + + + + +
              + +

              + Variants by Genomic Region + + + +

              + +

              The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

              + + +
              +

              The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

              +
              + +
              + + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Variant Effects by Impact + + + +

              + +

              The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

              + + +
              +

              There are four levels of impacts predicted by SnpEff:

              • High: High impact (like stop codon)
              • Moderate: Middle impact (like same type of amino acid substitution)
              • Low: Low impact (ie silence mutation)
              • Modifier: No impact

              +
              + +
              + + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Variant Effects by Class + + + +

              + +

              The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

              + + +
              +

              This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

              • Silent: The amino acid does not change.
              • Missense: The amino acid is different.
              • Nonsense: The variant generates a stop codon.

              +
              + +

              Error - was not able to plot data.

              + +
              +
              + + + + +
              + +

              + Variant Qualities + + + +

              + +

              The line plot shows the quantity as function of the variant quality score.

              + + +
              +

              The quality score corresponds to the QUAL column of the VCF file. This score is set by the variant caller.

              +
              + +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              GATK

              +

              GATK is a toolkit offering a wide variety of tools with a primary focus on variant discovery and genotyping.

              + + + + +
              + +

              + Observed Quality Scores + + + +

              + +

              This plot shows the distribution of base quality scores in each sample before and after base quality score recalibration (BQSR). Applying BQSR should broaden the distribution of base quality scores.

              + + +
              +

              For more information see the Broad's description of BQSR.

              +
              + +
              + + +
              + +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Variant Counts + +

              + + + + +
              + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Compare Overlap + +

              + + + + +
              + + + + + Showing 0/0 rows and 0/0 columns. + +
              +
              + +
              Sample Name
              + +
              + + +
              + + +
              +
              + + + +
              +

              HTSeq Count

              +

              HTSeq Count is part of the HTSeq Python package - it takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature.

              + + + + +
              + + + + +
              + + +
              +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              Bcftools

              +

              Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.

              + + + + +
              + +

              + Variant Substitution Types + +

              + + + + +
              + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Indel Distribution + +

              + + + + +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Variant depths + +

              + +

              Read depth support distribution for called variants

              + + +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              featureCounts

              +

              Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

              + + + + +
              + + + + +
              + + +
              +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              Picard

              +

              Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

              + + + + +
              + +

              + Alignment Summary + +

              + +

              Plase note that Picard's read counts are divided by two for paired-end data.

              + + +
              + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Base Distribution + +

              + +

              Plot shows the distribution of bases by cycle.

              + + +
              + + + + + +
              + +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + GC Coverage Bias + +

              + +

              This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.

              + + +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Insert Size + +

              + +

              Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

              + + +
              + + +
              + +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Mark Duplicates + +

              + + + + +
              + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + RnaSeqMetrics Assignment + +

              + +

              Number of bases in primary alignments that align to regions in the reference genome.

              + + +
              + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Gene Coverage + +

              + + + + +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              Prokka

              +

              Prokka is a software tool for the rapid annotation of prokaryotic genomes.

              + + + + + + +
              + +

              This barplot shows the distribution of different types of features found in each contig.

              + + +
              +

              Prokka can detect different features:

              +
                +
              • CDS
              • +
              • rRNA
              • +
              • tmRNA
              • +
              • tRNA
              • +
              • miscRNA
              • +
              • signal peptides
              • +
              • CRISPR arrays
              • +
              +

              This barplot shows you the distribution of these different types of features found in each contig.

              +
              + +
              + + +
              +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              Samblaster

              +

              Samblaster is a tool to mark duplicates and extract discordant and split reads from sam files.

              + + + + +
              + + + + +
              + + +
              +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              Samtools

              +

              Samtools is a suite of programs for interacting with high-throughput sequencing data.

              + + + + +
              + +

              + Percent Mapped + + + +

              + +

              Alignment metrics from samtools stats; mapped vs. unmapped reads.

              + + +
              +

              For a set of samples that have come from the same multiplexed library, +similar numbers of reads for each sample are expected. Large differences in numbers might +indicate issues during the library preparation process. Whilst large differences in read +numbers may be controlled for in downstream processings (e.g. read count normalisation), +you may wish to consider whether the read depths achieved have fallen below recommended +levels depending on the applications.

              +

              Low alignment rates could indicate contamination of samples (e.g. adapter sequences), +low sequencing quality or other artefacts. These can be further investigated in the +sequence level QC (e.g. from FastQC).

              +
              + +
              + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Alignment metrics + +

              + +

              This module parses the output from samtools stats. All numbers in millions.

              + + +
              +
              loading..
              +
              + +
              +
              + + + + +
              + +

              + Samtools Flagstat + +

              + +

              This module parses the output from samtools flagstat. All numbers in millions.

              + + +
              +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              Bamtools

              +

              Bamtools provides both a programmer's API and an end-user's toolkit for handling BAM files.

              + + + + +
              + +

              + Bamtools Stats + +

              + + + + +
              +
              loading..
              +
              + + +
              + + +
              +
              + + + +
              +

              VCFTools

              +

              VCFTools is a program for working with and reporting on VCF files.

              + + + + +
              + +

              + TsTv by Qual + + + +

              + +

              Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.

              + + +
              +

              Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. +Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. +Quality here is the Phred-scaled quality score as given in the QUAL column of VCF. +Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) +Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-qual

              +
              + +
              loading..
              +
              + + +
              + + +
              + + + + +
              + + + + + + + + + + + + + + + + diff -r 467486f1c568 -r e0f4a651c6b9 test-data/post_aligner_soft_stats.tabular --- a/test-data/post_aligner_soft_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/post_aligner_soft_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,21 +1,22 @@ -Sample QUAST_N50-2-1 QUAST_Total_length-2-1 featureCounts_Assigned-1 featureCounts_percent_assigned-1-1 Picard_PCT_PF_READS_ALIGNED-1 Prokka_contigs-1 Prokka_bases-1 Prokka_CDS-1 Prokka_organism-1 Bcftools Stats_number_of_SNPs-1 Bcftools Stats_tstv-1 Bcftools Stats_number_of_records-1 Bcftools Stats_number_of_MNPs-1 Bcftools Stats_number_of_indels-1 Bamtools_duplicates_pct-1-1 Bamtools_mapped_reads_pct-1-1 Picard_PERCENT_DUPLICATION-1 Picard_summed_mean-1 Picard_summed_median-1 HTSeq Count_percent_assigned-2 HTSeq Count_assigned-1 Picard_PCT_RIBOSOMAL_BASES-1 Picard_PCT_MRNA_BASES-1 Samtools Flagstat_mapped_passed-1-1 Samtools Stats_reads_mapped_percent-1 Samtools Stats_raw_total_sequences-1-1 Samtools Stats_reads_mapped-1 Samtools Stats_error_rate-1 Samtools Stats_non_primary_alignments-1 GATK VariantEval_known_titv-1 GATK VariantEval_novel_titv-1 Samblaster_pct_dups-1 -14892_1#15 115136.0 18435361.0 -70: TopHat on data 1, data 4, and data 3: accepted_hits 321797 70.82267755353567 -75: TopHat on data 1, data 6, and data 5: accepted_hits 445012 69.58585803304067 -80: TopHat on data 1, data 8, and data 7: accepted_hits 394981 71.76957768385707 -85: TopHat on data 1, data 10, and data 9: accepted_hits 437485 72.02454351337069 -90: TopHat on data 1, data 12, and data 11: accepted_hits 388170 71.33130826437625 -95: TopHat on data 1, data 14, and data 13: accepted_hits 453929 70.72517103678439 -D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 -Sample1 30 1629978 1548 Helicobacter pylori -Sample2 52 162997532523 1548 Escherichia coli -Test1 4474244.0 1.97 5522770.0 72330.0 902934.0 -bamtools 0.0 93.125 -dataset_114 0.005582 -dataset_197 271.809759 176 -htseq 0.0 0 -picard_CollectRnaSeqMetrics_bam 79.62310000000001 -samtools_flagstat 20689039 -samtools_stats 100.0 641821.0 641821.0 0.004248509 12111.0 -varianteval_1_gatk_varianteval 0.0 2.2 -virtual-normal 1.28 +Sample QUAST_mqc-generalstats-N50 QUAST_mqc-generalstats-Total_length featureCounts_mqc-generalstats-percent_assigned featureCounts_mqc-generalstats-Assigned Picard_mqc-generalstats-PCT_PF_READS_ALIGNED Prokka_mqc-generalstats-contigs Prokka_mqc-generalstats-organism Prokka_mqc-generalstats-bases Prokka_mqc-generalstats-CDS Bcftools Stats_mqc-generalstats-tstv Bcftools Stats_mqc-generalstats-number_of_MNPs Bcftools Stats_mqc-generalstats-number_of_indels Bcftools Stats_mqc-generalstats-number_of_SNPs Bcftools Stats_mqc-generalstats-number_of_records Bamtools_mqc-generalstats-duplicates_pct Bamtools_mqc-generalstats-mapped_reads_pct Picard_mqc-generalstats-PERCENT_DUPLICATION Picard_mqc-generalstats-summed_median Picard_mqc-generalstats-summed_mean GATK VariantEval_mqc-generalstats-known_titv GATK VariantEval_mqc-generalstats-novel_titv HTSeq Count_mqc-generalstats-percent_assigned HTSeq Count_mqc-generalstats-assigned Picard_mqc-generalstats-PCT_MRNA_BASES Picard_mqc-generalstats-PCT_RIBOSOMAL_BASES Samtools Flagstat_mqc-generalstats-mapped_passed Samtools Stats_mqc-generalstats-raw_total_sequences Samtools Stats_mqc-generalstats-non_primary_alignments Samtools Stats_mqc-generalstats-reads_mapped Samtools Stats_mqc-generalstats-error_rate Samtools Stats_mqc-generalstats-reads_mapped_percent SnpEff_mqc-generalstats-Ts_Tv_ratio SnpEff_mqc-generalstats-Number_of_variants_before_filter SnpEff_mqc-generalstats-Change_rate Samblaster_mqc-generalstats-pct_dups +14892_1#15 115136.0 18435361.0 +70: TopHat on data 1, data 4, and data 3: accepted_hits 70.82267755353567 321797 +75: TopHat on data 1, data 6, and data 5: accepted_hits 69.58585803304067 445012 +80: TopHat on data 1, data 8, and data 7: accepted_hits 71.76957768385707 394981 +85: TopHat on data 1, data 10, and data 9: accepted_hits 72.02454351337069 437485 +90: TopHat on data 1, data 12, and data 11: accepted_hits 71.33130826437625 388170 +95: TopHat on data 1, data 14, and data 13: accepted_hits 70.72517103678439 453929 +D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 +Sample1 30 Helicobacter pylori 1629978 1548 +Sample2 52 Escherichia coli 162997532523 1548 +Test1 1.97 72330.0 902934.0 4474244.0 5522770.0 +bamtools 0.0 93.125 +dataset_114 0.005582 +dataset_197 176 271.809759 +gatk_varianteval 0.0 2.2 +htseq 0.0 0 +picard_CollectRnaSeqMetrics_bam 79.62310000000001 +samtools_flagstat 20689039 +samtools_stats 641821.0 12111.0 641821.0 0.004248509 100.0 +snpeff 0.0 972155.0 3190.0 +virtual-normal 1.28 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/pre_alignment_soft_log.txt --- a/test-data/pre_alignment_soft_log.txt Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/pre_alignment_soft_log.txt Fri Apr 20 01:06:25 2018 -0400 @@ -1,75 +1,85 @@ -[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/miniconda3/envs/multiqc2/lib/python2.7/site-packages/multiqc-1.2-py2.7.egg/multiqc_config.yaml -[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/.multiqc_config.yaml -[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2017-09-28 17:24:01,554] multiqc [DEBUG ] Command used: /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir -[2017-09-28 17:24:02,209] multiqc [DEBUG ] Latest MultiQC version is v1.2 -[2017-09-28 17:24:02,210] multiqc [INFO ] This is MultiQC v1.2 -[2017-09-28 17:24:02,210] multiqc [DEBUG ] Command : /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir -[2017-09-28 17:24:02,210] multiqc [DEBUG ] Working dir : /Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc -[2017-09-28 17:24:02,210] multiqc [INFO ] Template : default -[2017-09-28 17:24:02,210] multiqc [INFO ] Searching 'multiqc_WDir' -[2017-09-28 17:24:02,211] multiqc [DEBUG ] Analysing modules: afterqc, custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rseqc, busco, goleft_indexcov, disambiguate, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bismark, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, fastqc, clusterflow, bcl2fastq -[2017-09-28 17:24:02,249] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig -[2017-09-28 17:24:05,021] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,098] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found -[2017-09-28 17:24:05,144] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,235] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,259] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,306] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 -[2017-09-28 17:24:05,306] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,315] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2017-09-28 17:24:05,329] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,347] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('multiqc_WDir',) -[2017-09-28 17:24:05,394] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('multiqc_WDir',) -[2017-09-28 17:24:05,424] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,430] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,469] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('multiqc_WDir',) -[2017-09-28 17:24:05,475] multiqc.modules.disambiguate.disambiguate [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2017-09-28 17:24:05,499] multiqc.modules.homer.homer [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,513] multiqc.modules.macs2.macs2 [DEBUG ] Could not find any MACS2 data in ('multiqc_WDir',) -[2017-09-28 17:24:05,552] multiqc.modules.theta2.theta2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,571] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2017-09-28 17:24:05,637] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,693] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,757] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,787] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,868] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,874] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('multiqc_WDir',) -[2017-09-28 17:24:05,881] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2017-09-28 17:24:05,915] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,931] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:05,942] multiqc.modules.jellyfish.jellyfish [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2017-09-28 17:24:06,029] multiqc.modules.vcftools.vcftools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,064] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,083] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2017-09-28 17:24:06,107] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2017-09-28 17:24:06,145] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,187] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. -[2017-09-28 17:24:06,207] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,225] multiqc.modules.hisat2.hisat2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,238] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,245] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,250] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,263] multiqc.modules.leehom.leehom [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,273] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,299] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports -[2017-09-28 17:24:06,351] multiqc.modules.flexbar.flexbar [INFO ] Found 1 logs -[2017-09-28 17:24:06,378] multiqc.modules.trimmomatic.trimmomatic [INFO ] Found 1 logs -[2017-09-28 17:24:06,403] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2017-09-28 17:24:06,421] multiqc.modules.sortmerna.sortmerna [INFO ] Found 1 logs -[2017-09-28 17:24:06,441] multiqc.modules.biobloomtools.biobloomtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,448] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,605] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports -[2017-09-28 17:24:06,908] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2017-09-28 17:24:06,914] multiqc.modules.bcl2fastq.bcl2fastq [DEBUG ] Could not find any bcl2fastq data in ('multiqc_WDir',) -[2017-09-28 17:24:06,923] multiqc [INFO ] Compressing plot data -[2017-09-28 17:24:07,121] multiqc [INFO ] Report : multiqc_report.html -[2017-09-28 17:24:07,121] multiqc [INFO ] Data : multiqc_data -[2017-09-28 17:24:07,121] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_cutadapt.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' -[2017-09-28 17:24:07,121] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_fastqc.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' -[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_flexbar.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' -[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_general_stats.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' -[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_sortmerna.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' -[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_sources.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' -[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_trimmomatic.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' -[2017-09-28 17:24:07,952] multiqc [INFO ] MultiQC complete +[2018-04-05 12:06:46,534] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/miniconda3/envs/multiqc/lib/python3.5/site-packages/multiqc_config.yaml +[2018-04-05 12:06:46,534] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/.multiqc_config.yaml +[2018-04-05 12:06:46,534] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2018-04-05 12:06:46,534] multiqc [DEBUG ] Command used: /Users/bebatut/miniconda3/envs/multiqc/bin/multiqc multiqc_WDir +[2018-04-05 12:06:47,547] multiqc [DEBUG ] Latest MultiQC version is v1.5 +[2018-04-05 12:06:47,547] multiqc [INFO ] This is MultiQC v1.5 +[2018-04-05 12:06:47,548] multiqc [DEBUG ] Command : /Users/bebatut/miniconda3/envs/multiqc/bin/multiqc multiqc_WDir +[2018-04-05 12:06:47,548] multiqc [DEBUG ] Working dir : /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc +[2018-04-05 12:06:47,548] multiqc [INFO ] Template : default +[2018-04-05 12:06:47,548] multiqc [INFO ] Searching 'multiqc_WDir' +[2018-04-05 12:06:47,549] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, dedup, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bbmap, bismark, hicexplorer, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastqc, clusterflow, bcl2fastq, interop +[2018-04-05 12:06:47,554] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93 +[2018-04-05 12:06:48,019] multiqc [DEBUG ] No samples found: custom_content +[2018-04-05 12:06:48,025] multiqc [DEBUG ] No samples found: conpair +[2018-04-05 12:06:48,030] multiqc [DEBUG ] No samples found: peddy +[2018-04-05 12:06:48,035] multiqc [DEBUG ] No samples found: methylQA +[2018-04-05 12:06:48,040] multiqc [DEBUG ] No samples found: qualimap +[2018-04-05 12:06:48,045] multiqc [DEBUG ] No samples found: preseq +[2018-04-05 12:06:48,050] multiqc [DEBUG ] No samples found: quast +[2018-04-05 12:06:48,054] multiqc [DEBUG ] No samples found: qorts +[2018-04-05 12:06:48,059] multiqc [DEBUG ] No samples found: rna_seqc +[2018-04-05 12:06:48,063] multiqc [DEBUG ] No samples found: rsem +[2018-04-05 12:06:48,070] multiqc [DEBUG ] No samples found: rseqc +[2018-04-05 12:06:48,074] multiqc [DEBUG ] No samples found: busco +[2018-04-05 12:06:48,079] multiqc [DEBUG ] No samples found: goleft_indexcov +[2018-04-05 12:06:48,083] multiqc [DEBUG ] No samples found: disambiguate +[2018-04-05 12:06:48,088] multiqc [DEBUG ] No samples found: supernova +[2018-04-05 12:06:48,097] multiqc [DEBUG ] No samples found: deeptools +[2018-04-05 12:06:48,103] multiqc [DEBUG ] No samples found: sargasso +[2018-04-05 12:06:48,108] multiqc [DEBUG ] No samples found: verifybamid +[2018-04-05 12:06:48,113] multiqc [DEBUG ] No samples found: homer +[2018-04-05 12:06:48,118] multiqc [DEBUG ] No samples found: macs2 +[2018-04-05 12:06:48,124] multiqc [DEBUG ] No samples found: theta2 +[2018-04-05 12:06:48,130] multiqc [DEBUG ] No samples found: snpeff +[2018-04-05 12:06:48,136] multiqc [DEBUG ] No samples found: gatk +[2018-04-05 12:06:48,141] multiqc [DEBUG ] No samples found: htseq +[2018-04-05 12:06:48,145] multiqc [DEBUG ] No samples found: bcftools +[2018-04-05 12:06:48,151] multiqc [DEBUG ] No samples found: featureCounts +[2018-04-05 12:06:48,157] multiqc [DEBUG ] No samples found: dedup +[2018-04-05 12:06:48,166] multiqc [DEBUG ] No samples found: picard +[2018-04-05 12:06:48,170] multiqc [DEBUG ] No samples found: prokka +[2018-04-05 12:06:48,174] multiqc [DEBUG ] No samples found: samblaster +[2018-04-05 12:06:48,180] multiqc [DEBUG ] No samples found: samtools +[2018-04-05 12:06:48,184] multiqc [DEBUG ] No samples found: bamtools +[2018-04-05 12:06:48,189] multiqc [DEBUG ] No samples found: jellyfish +[2018-04-05 12:06:48,194] multiqc [DEBUG ] No samples found: vcftools +[2018-04-05 12:06:48,202] multiqc [DEBUG ] No samples found: bbmap +[2018-04-05 12:06:48,206] multiqc [DEBUG ] No samples found: bismark +[2018-04-05 12:06:48,211] multiqc [DEBUG ] No samples found: hicexplorer +[2018-04-05 12:06:48,215] multiqc [DEBUG ] No samples found: hicup +[2018-04-05 12:06:48,219] multiqc [DEBUG ] No samples found: salmon +[2018-04-05 12:06:48,225] multiqc [DEBUG ] No samples found: kallisto +[2018-04-05 12:06:48,231] multiqc [DEBUG ] No samples found: slamdunk +[2018-04-05 12:06:48,236] multiqc [DEBUG ] No samples found: star +[2018-04-05 12:06:48,242] multiqc [DEBUG ] No samples found: hisat2 +[2018-04-05 12:06:48,246] multiqc [DEBUG ] No samples found: tophat +[2018-04-05 12:06:48,250] multiqc [DEBUG ] No samples found: bowtie2 +[2018-04-05 12:06:48,255] multiqc [DEBUG ] No samples found: bowtie1 +[2018-04-05 12:06:48,259] multiqc [DEBUG ] No samples found: leehom +[2018-04-05 12:06:48,263] multiqc [DEBUG ] No samples found: adapterRemoval +[2018-04-05 12:06:48,268] multiqc [DEBUG ] No samples found: clipandmerge +[2018-04-05 12:06:48,276] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports +[2018-04-05 12:06:48,307] multiqc.modules.flexbar.flexbar [INFO ] Found 1 logs +[2018-04-05 12:06:48,318] multiqc.modules.trimmomatic.trimmomatic [INFO ] Found 1 logs +[2018-04-05 12:06:48,325] multiqc [DEBUG ] No samples found: skewer +[2018-04-05 12:06:48,334] multiqc.modules.sortmerna.sortmerna [INFO ] Found 1 logs +[2018-04-05 12:06:48,339] multiqc [DEBUG ] No samples found: biobloomtools +[2018-04-05 12:06:48,346] multiqc [DEBUG ] No samples found: fastq_screen +[2018-04-05 12:06:48,352] multiqc [DEBUG ] No samples found: afterqc +[2018-04-05 12:06:48,434] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports +[2018-04-05 12:06:48,495] multiqc [DEBUG ] No samples found: clusterflow +[2018-04-05 12:06:48,500] multiqc [DEBUG ] No samples found: bcl2fastq +[2018-04-05 12:06:48,505] multiqc [DEBUG ] No samples found: interop +[2018-04-05 12:06:48,514] multiqc [INFO ] Compressing plot data +[2018-04-05 12:06:48,596] multiqc [INFO ] Report : multiqc_report.html +[2018-04-05 12:06:48,597] multiqc [INFO ] Data : multiqc_data +[2018-04-05 12:06:48,597] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_cutadapt.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' +[2018-04-05 12:06:48,597] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_data.json' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' +[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_fastqc.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' +[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_flexbar.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' +[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_general_stats.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' +[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_sortmerna.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' +[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_sources.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' +[2018-04-05 12:06:48,599] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_trimmomatic.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' +[2018-04-05 12:06:48,809] multiqc [INFO ] MultiQC complete diff -r 467486f1c568 -r e0f4a651c6b9 test-data/pre_alignment_soft_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pre_alignment_soft_report.html Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,5990 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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                    Note that additional data was saved in multiqc_data when this report was generated.

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                    If you use plots from MultiQC in a publication or presentation, please cite:

                    +
                    + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                    + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                    + Bioinformatics (2016)
                    + doi: 10.1093/bioinformatics/btw354
                    + PMID: 27312411 +
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                    About MultiQC

                    +

                    This report was generated using MultiQC, version 1.5

                    +

                    You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

                    +

                    For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                    +

                    You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                    +

                    MultiQC is published in Bioinformatics:

                    +
                    + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                    + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                    + Bioinformatics (2016)
                    + doi: 10.1093/bioinformatics/btw354
                    + PMID: 27312411 +
                    +
                    + +
                    + +
                    + + +
                    + + + +

                    + + + + +

                    + + + +

                    + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                    + + + + + + + + + + +
                    +

                    Report generated on 2018-04-05, 12:06 based on data in: + /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_WDir + +

                    + + + +
                    + + + + + + + + +
                    +

                    General Statistics

                    + + + + + + + + + + Showing 6/6 rows and 7/9 columns. + +
                    +
                    + +
                    Sample Name% Trimmed% bp Trimmed% Dropped% rRNA% Dups% GCM Seqs
                    25839_merged
                    1.1%
                    C2
                    18.0%
                    dataset_33
                    10.8%
                    poulet5_1
                    36.3%
                    48%
                    0.3
                    poulet5_2
                    36.2%
                    48%
                    0.3
                    result_right
                    45.3%
                    + + +
                    + + + + + + +
                    +

                    Cutadapt

                    +

                    Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

                    + + + + +
                    + +

                    This plot shows the number of reads with certain lengths of adapter trimmed. + Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak + may be related to adapter length. See the + cutadapt documentation + for more information on how these numbers are generated.

                    + + +
                    + + +
                    + +
                    loading..
                    +
                    + + +
                    + + +
                    +
                    + + + +
                    +

                    Flexbar

                    +

                    Flexbar is a barcode and adapter removal tool.

                    + + + + +
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                    + + +
                    +
                    loading..
                    +
                    + + +
                    + + +
                    +
                    + + + +
                    +

                    Trimmomatic

                    +

                    Trimmomatic is a flexible read trimming tool for Illumina NGS data.

                    + + + + +
                    + + + + +
                    + + +
                    +
                    loading..
                    +
                    + + +
                    + + +
                    +
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                    +

                    SortMeRNA

                    +

                    SortMeRNA is a program for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data.

                    + + + + +
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                    + + +
                    +
                    loading..
                    +
                    + + +
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                    +
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                    +

                    FastQC

                    +

                    FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

                    + + + + +
                    + +

                    + Sequence Quality Histograms + +

                    + +

                    The mean quality value across each base position in the read. See the FastQC help.

                    + + +
                    loading..
                    +
                    + +
                    +
                    + + + + +
                    + +

                    + Per Sequence Quality Scores + +

                    + +

                    The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

                    + + +
                    loading..
                    +
                    + +
                    +
                    + + + + +
                    + +

                    + Per Base Sequence Content + +

                    + + + + +
                    +

                    The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

                    +
                    + + Click a sample row to see a line plot for that dataset. +
                    +
                    Rollover for sample name
                    + +
                    + Position: - +
                    %T: -
                    +
                    %C: -
                    +
                    %A: -
                    +
                    %G: -
                    +
                    +
                    +
                    + +
                    +
                    +
                    +
                    + +
                    +
                    + + + + +
                    + +

                    + Per Sequence GC Content + +

                    + +

                    The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. + See the FastQC help.

                    + + +
                    + + +
                    + +
                    loading..
                    +
                    + +
                    +
                    + + + + +
                    + +

                    + Per Base N Content + +

                    + +

                    The percentage of base calls at each position for which an N was called. See the FastQC help.

                    + + +
                    loading..
                    +
                    + +
                    +
                    + + + + +
                    + +

                    + Sequence Length Distribution + +

                    + +
                    All samples have sequences of a single length (101bp).
                    + + +
                    + +
                    +
                    + + + + +
                    + +

                    + Sequence Duplication Levels + +

                    + +

                    The relative level of duplication found for every sequence. See the FastQC help.

                    + + +
                    loading..
                    +
                    + +
                    +
                    + + + + +
                    + +

                    + Overrepresented sequences + +

                    + +

                    The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

                    + + +
                    2 samples had less than 1% of reads made up of overrepresented sequences
                    + +
                    +
                    + + + + +
                    + +

                    + Adapter Content + +

                    + +

                    The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

                    + + +
                    No samples found with any adapter contamination > 0.1%
                    + + +
                    + + +
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                    + + + + + + + + + + + + + + + + diff -r 467486f1c568 -r e0f4a651c6b9 test-data/pre_alignment_soft_stats.tabular --- a/test-data/pre_alignment_soft_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/pre_alignment_soft_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,7 +1,7 @@ -Sample SortMeRNA_rRNA_pct-1 Trimmomatic_dropped_pct-1 Cutadapt_percent_trimmed-1 FastQC_percent_gc-1 FastQC_total_sequences-1 FastQC_avg_sequence_length-1 FastQC_percent_duplicates-1 FastQC_percent_fails-1 Flexbar_removed_bases_pct-1 +Sample SortMeRNA_mqc-generalstats-rRNA_pct Trimmomatic_mqc-generalstats-dropped_pct Cutadapt_mqc-generalstats-percent_trimmed FastQC_mqc-generalstats-avg_sequence_length FastQC_mqc-generalstats-percent_fails FastQC_mqc-generalstats-percent_duplicates FastQC_mqc-generalstats-percent_gc FastQC_mqc-generalstats-total_sequences Flexbar_mqc-generalstats-removed_bases_pct 25839_merged 1.099299750020029 C2 17.98 dataset_33 10.776820436239396 -poulet5_1 48.0 267849.0 101.0 36.30591159931017 8.333333333333332 -poulet5_2 48.0 267849.0 101.0 36.173388748054116 8.333333333333332 +poulet5_1 101.0 8.333333333333332 36.30591159931017 48.0 267849.0 +poulet5_2 101.0 8.333333333333332 36.173388748054116 48.0 267849.0 result_right 45.26066350710901 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/prokka_stats.tabular --- a/test-data/prokka_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/prokka_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,3 +1,3 @@ -Sample tRNA CDS rRNA repeat_region bases organism contigs sig_peptide tmRNA misc_RNA -Sample1 36 1548 2 15 1629978 Helicobacter pylori 30 88 1 -Sample2 1548 2 162997532523 Escherichia coli 52 5152 +Sample repeat_region sig_peptide bases organism tmRNA contigs tRNA rRNA CDS misc_RNA +Sample1 15 88 1629978 Helicobacter pylori 1 30 36 2 1548 +Sample2 162997532523 Escherichia coli 52 2 1548 5152 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/quast_stats.tabular --- a/test-data/quast_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/quast_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample # mismatches per 100 kbp # misassembled contigs Largest contig # indels per 100 kbp LG75 # local misassemblies Total length (>= 25000 bp) Total length N50 NGA50 Reference GC (%) # contigs (>= 10000 bp) LA75 NG50 # genes_partial # unaligned contigs Total length (>= 50000 bp) LA50 # contigs (>= 25000 bp) NA75 GC (%) LG50 NA50 LGA75 # contigs (>= 0 bp) Largest alignment Total length (>= 0 bp) # genes # misassemblies NGA75 Total length (>= 10000 bp) # contigs (>= 5000 bp) L75 Total length (>= 1000 bp) # unaligned contigs_partial # contigs (>= 50000 bp) Total length (>= 5000 bp) N75 # contigs (>= 1000 bp) LGA50 Duplication ratio Genome fraction (%) NG75 Unaligned length # N's per 100 kbp Misassembled contigs length Reference length L50 # contigs -14892_1#15 262.21 82.0 435484.0 33.75 106.0 132.0 17353907.0 18435361.0 115136.0 99244.0 48.21 215.0 117.0 112874.0 968.0 8.0 15112131.0 56.0 181.0 54365.0 48.17 50.0 102129.0 124.0 545.0 356982.0 18465341.0 7280.0 107.0 51757.0 17893099.0 242.0 100.0 18373173.0 59.0 123.0 18079934.0 62262.0 376.0 59.0 1.016 95.482 56990.0 88446.0 929.55 4540800.0 18916112.0 48.0 467.0 +Sample LG50 # contigs # misassemblies # local misassemblies # misassembled contigs NA50 # genes # indels per 100 kbp Reference length # contigs (>= 10000 bp) Total length (>= 1000 bp) GC (%) Reference GC (%) Unaligned length Misassembled contigs length Genome fraction (%) Largest alignment L75 NG75 # contigs (>= 1000 bp) Largest contig N75 NGA50 NA75 LA50 LGA75 Total length LG75 Total length (>= 50000 bp) # contigs (>= 50000 bp) # mismatches per 100 kbp Total length (>= 25000 bp) Total length (>= 10000 bp) Total length (>= 5000 bp) Total length (>= 0 bp) # unaligned contigs_partial # contigs (>= 25000 bp) LA75 # contigs (>= 0 bp) N50 LGA50 # genes_partial NGA75 # contigs (>= 5000 bp) Duplication ratio NG50 # unaligned contigs # N's per 100 kbp L50 +14892_1#15 50.0 467.0 107.0 132.0 82.0 102129.0 7280.0 33.75 18916112.0 215.0 18373173.0 48.17 48.21 88446.0 4540800.0 95.482 356982.0 100.0 56990.0 376.0 435484.0 62262.0 99244.0 54365.0 56.0 124.0 18435361.0 106.0 15112131.0 123.0 262.21 17353907.0 17893099.0 18079934.0 18465341.0 59.0 181.0 117.0 545.0 115136.0 59.0 968.0 51757.0 242.0 1.016 112874.0 8.0 929.55 48.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/report_manual_custom_content.html --- a/test-data/report_manual_custom_content.html Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/report_manual_custom_content.html Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,4823 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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                          + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                          + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                          + Bioinformatics (2016)
                          + doi: 10.1093/bioinformatics/btw354
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                          + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                          + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                          + Bioinformatics (2016)
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                          BPC Sum of intensity (Y) of the most intense peaks at each retention time(X)

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                          + + + + + + + + + + + + + + + + diff -r 467486f1c568 -r e0f4a651c6b9 test-data/salmon.txt --- a/test-data/salmon.txt Sun Jan 14 09:55:46 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -8.54794e-14 8.88776e-14 9.23963e-14 9.60394e-14 9.98106e-14 1.03714e-13 1.07752e-13 1.11931e-13 1.16253e-13 1.20724e-13 1.25347e-13 1.30126e-13 1.35067e-13 1.40173e-13 1.4545e-13 1.50902e-13 1.56533e-13 1.6235e-13 1.68356e-13 1.74557e-13 1.80958e-13 1.87565e-13 1.94382e-13 2.01416e-13 2.08672e-13 2.16156e-13 2.23872e-13 2.31828e-13 2.4003e-13 2.48482e-13 2.57192e-13 2.66166e-13 2.7541e-13 2.8493e-13 2.94734e-13 3.04827e-13 3.15216e-13 3.25909e-13 3.36912e-13 3.48231e-13 3.59875e-13 3.7185e-13 3.84164e-13 3.96823e-13 4.09835e-13 4.23208e-13 4.36949e-13 4.51066e-13 4.65566e-13 4.80457e-13 4.95747e-13 5.11443e-13 5.27555e-13 5.44088e-13 5.61052e-13 5.78455e-13 5.96304e-13 6.14608e-13 6.33375e-13 6.52613e-13 6.7233e-13 6.92535e-13 7.13235e-13 7.34439e-13 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8.48451e-20 8.48451e-20 4.52923e-08 1.81169e-07 2.71754e-07 1.81169e-07 4.52923e-08 8.48451e-20 2.42376e-07 9.69503e-07 1.45426e-06 9.69503e-07 2.42376e-07 8.48451e-20 1.27948e-07 5.11793e-07 7.72222e-07 5.29923e-07 3.56237e-07 8.22506e-07 1.2111e-06 8.04377e-07 2.01094e-07 1.19543e-07 4.85833e-07 7.47897e-07 5.59316e-07 2.9093e-07 2.18785e-07 1.4075e-07 3.51876e-08 8.48451e-20 1.7085e-09 6.83399e-09 1.0251e-08 4.48392e-07 1.76794e-06 2.64935e-06 1.76623e-06 4.41558e-07 2.28063e-07 9.20891e-07 1.40294e-06 9.70858e-07 3.1919e-07 1.67271e-07 2.04131e-07 9.36586e-07 3.27659e-06 4.87062e-06 3.25897e-06 8.59342e-07 7.1358e-08 4.7572e-08 1.1893e-08 8.48451e-20 1.19543e-07 4.78174e-07 7.17261e-07 4.78174e-07 1.19543e-07 8.48451e-20 8.48451e-20 8.48451e-20 3.652e-07 1.4608e-06 2.1912e-06 1.4608e-06 3.652e-07 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 2.88646e-09 1.31089e-07 4.95492e-07 7.28806e-07 4.8106e-07 1.19543e-07 8.48451e-20 2.11966e-06 8.47864e-06 1.2718e-05 8.49079e-06 2.16829e-06 3.62843e-07 1.88217e-06 4.44733e-06 5.20328e-06 2.98569e-06 6.76004e-07 8.22241e-09 1.23336e-08 8.22241e-09 4.1112e-09 8.22241e-09 1.23336e-08 8.22241e-09 2.0556e-09 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 5.08647e-07 2.89843e-06 6.66338e-06 7.84217e-06 4.90082e-06 2.61356e-05 9.87451e-05 0.000147884 + diff -r 467486f1c568 -r e0f4a651c6b9 test-data/salmon_meta_info.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salmon_meta_info.json Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,15 @@ +{ + "salmon_version": "0.6.0", + "samp_type": "none", + "frag_dist_length": 2001, + "bias_correct": true, + "num_bias_bins": 4096, + "mapping_type": "mapping", + "num_targets": 209539, + "num_bootstraps": 0, + "num_processed": 439147, + "num_mapped": 367866, + "percent_mapped": 83.76830537382699, + "call": "quant", + "start_time": "Thu Mar 31 13:09:43 2016" +} \ No newline at end of file diff -r 467486f1c568 -r e0f4a651c6b9 test-data/samblaster_stats.tabular --- a/test-data/samblaster_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/samblaster_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample n_dups pct_dups n_tot n_nondups -virtual-normal 1 1.28 78 77 +Sample n_nondups n_tot n_dups pct_dups +virtual-normal 77 78 1 1.28 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/samtools_flagstat_stats.tabular --- a/test-data/samtools_flagstat_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/samtools_flagstat_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample mapped_passed duplicates_failed secondary_passed paired in sequencing_failed duplicates_passed read2_passed read1_failed read1_passed with mate mapped to a different chr_passed total_failed properly paired_passed_pct singletons_passed supplementary_passed singletons_passed_pct mapped_failed_pct mapped_passed_pct supplementary_failed with itself and mate mapped_failed mapped_failed total_passed properly paired_failed flagstat_total with mate mapped to a different chr (mapQ >= 5)_passed properly paired_failed_pct with mate mapped to a different chr (mapQ >= 5)_failed with itself and mate mapped_passed read2_failed with mate mapped to a different chr_failed properly paired_passed paired in sequencing_passed singletons_failed secondary_failed singletons_failed_pct -samtools_flagstat 20689039 0 0 0 5448463 0 0 0 0 0 nan 0 0 nan nan 98.33 0 0 0 21040602 0 21040602 0 nan 0 0 0 0 0 0 0 0 nan +Sample read2_passed mapped_failed_pct with mate mapped to a different chr (mapQ >= 5)_passed properly paired_passed read1_passed total_passed supplementary_failed duplicates_failed singletons_failed mapped_passed_pct secondary_passed properly paired_passed_pct properly paired_failed_pct singletons_passed with mate mapped to a different chr (mapQ >= 5)_failed supplementary_passed duplicates_passed flagstat_total mapped_passed with mate mapped to a different chr_failed secondary_failed properly paired_failed with itself and mate mapped_failed with mate mapped to a different chr_passed paired in sequencing_failed with itself and mate mapped_passed singletons_passed_pct total_failed paired in sequencing_passed read1_failed mapped_failed read2_failed singletons_failed_pct +samtools_flagstat 0 nan 0 0 0 21040602 0 0 0 98.33 0 nan nan 0 0 0 5448463 21040602 20689039 0 0 0 0 0 0 0 nan 0 0 0 0 0 nan diff -r 467486f1c568 -r e0f4a651c6b9 test-data/samtools_stats_stats.tabular --- a/test-data/samtools_stats_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/samtools_stats_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample insert_size_average reads_mapped_and_paired reads_QC_failed_percent outward_oriented_pairs 1st_fragments bases_duplicated reads_MQ0 bases_mapped maximum_length bases_trimmed reads_duplicated inward_oriented_pairs sequences error_rate insert_size_standard_deviation non-primary_alignments reads_unmapped_percent mismatches reads_mapped_and_paired_percent reads_mapped_percent raw_total_sequences reads_mapped pairs_on_different_chromosomes reads_MQ0_percent pairs_with_other_orientation reads_paired_percent total_length reads_unmapped average_length reads_duplicated_percent bases_mapped_(cigar) average_quality reads_properly_paired reads_properly_paired_percent reads_QC_failed last_fragments filtered_sequences reads_paired is_sorted -samtools_stats 719.7 638746.0 0.0 1294.0 320981.0 0.0 70.0 64823921.0 101.0 0.0 0.0 317512.0 641821.0 0.004248509 1223.0 12111.0 0.0 275405.0 99.52089445499603 100.0 641821.0 641821.0 0.0 0.010906467691147531 30.0 100.0 64823921.0 0.0 101.0 0.0 64823921.0 26.0 635626.0 99.03477760933345 0.0 320840.0 0.0 641821.0 1.0 +Sample is_sorted insert_size_standard_deviation reads_paired_percent reads_QC_failed bases_mapped 1st_fragments reads_mapped_and_paired_percent error_rate mismatches reads_properly_paired bases_mapped_(cigar) reads_MQ0 reads_duplicated reads_duplicated_percent inward_oriented_pairs sequences non-primary_alignments reads_MQ0_percent reads_mapped_percent reads_mapped_and_paired average_length last_fragments average_quality outward_oriented_pairs total_length bases_duplicated raw_total_sequences bases_trimmed pairs_on_different_chromosomes reads_properly_paired_percent reads_mapped reads_unmapped_percent maximum_length reads_paired reads_QC_failed_percent insert_size_average reads_unmapped filtered_sequences pairs_with_other_orientation +samtools_stats 1.0 1223.0 100.0 0.0 64823921.0 320981.0 99.52089445499603 0.004248509 275405.0 635626.0 64823921.0 70.0 0.0 0.0 317512.0 641821.0 12111.0 0.010906467691147531 100.0 638746.0 101.0 320840.0 26.0 1294.0 64823921.0 0.0 641821.0 0.0 0.0 99.03477760933345 641821.0 0.0 101.0 641821.0 0.0 719.7 0.0 0.0 30.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/snpeff_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snpeff_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -0,0 +1,2 @@ +Sample MODERATE splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant_percent splice_region_variant+non_coding_exon_variant frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant frameshift_variant+start_lost+splice_region_variant_percent NONE intragenic_variant_percent splice_region_variant+non_coding_exon_variant_percent UTR_3_PRIME splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant Ts_Tv_ratio splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent inframe_insertion+splice_region_variant_percent UTR_3_PRIME_percent inframe_deletion+splice_region_variant 5_prime_UTR_truncation+exon_loss_variant disruptive_inframe_deletion_percent INTRON LOW Het start_lost+disruptive_inframe_insertion frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant_percent inframe_deletion splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent non_coding_exon_variant frameshift_variant+stop_gained splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent DOWNSTREAM_percent disruptive_inframe_deletion+splice_region_variant MOTIF frameshift_variant+start_lost+splice_region_variant splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant frameshift_variant+stop_gained_percent EXON splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant upstream_gene_variant intron_variant_percent splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent inframe_deletion_percent HIGH_percent 3_prime_UTR_variant splice_donor_variant+intron_variant frameshift_variant+start_lost_percent disruptive_inframe_insertion non_coding_exon_variant_percent Change_rate 5_prime_UTR_truncation+exon_loss_variant_percent MODERATE_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent UTR_5_PRIME TRANSCRIPT frameshift_variant downstream_gene_variant MODIFIER_percent splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent LOW_percent frameshift_variant+splice_region_variant Missense_Silent_ratio Missing disruptive_inframe_deletion+splice_region_variant_percent splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent frameshift_variant+stop_lost frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant sequence_feature_percent intron_variant frameshift_variant+splice_region_variant_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant splice_donor_variant+5_prime_UTR_variant+intron_variant Number_of_known_variants
                          (i.e. non-empty ID)_percent start_lost+disruptive_inframe_insertion_percent splice_acceptor_variant+splice_donor_variant+intron_variant Transitions DOWNSTREAM SPLICE_SITE_DONOR_percent frameshift_variant+stop_lost_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent EXON_percent frameshift_variant_percent Number_of_variants_before_filter disruptive_inframe_insertion_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent splice_acceptor_variant+intron_variant stop_gained+inframe_insertion upstream_gene_variant_percent SPLICE_SITE_ACCEPTOR TF_binding_site_variant_percent SPLICE_SITE_REGION Genome_effective_length frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant_percent splice_acceptor_variant+5_prime_UTR_variant+intron_variant INTERGENIC_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant 5_prime_UTR_variant UPSTREAM_percent splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_region_variant+intron_variant 5_prime_UTR_variant_percent Type splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant Hom splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+splice_region_variant_percent UTR_5_PRIME_percent sequence_feature intergenic_region_percent transcript_percent HIGH frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant UPSTREAM splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent inframe_deletion+splice_region_variant_percent transcript splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent Genome_total_length Number_of_effects NONE_percent frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant SPLICE_SITE_ACCEPTOR_percent splice_acceptor_variant+intron_variant_percent splice_donor_variant+intron_variant_percent splice_donor_variant+5_prime_UTR_variant+intron_variant_percent splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent splice_acceptor_variant+splice_donor_variant+intron_variant_percent splice_donor_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent Transversions Genome disruptive_inframe_deletion MODIFIER splice_acceptor_variant+splice_region_variant+intron_variant_percent frameshift_variant+start_lost SPLICE_SITE_REGION_percent splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant INTRON_percent splice_acceptor_variant+5_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant TF_binding_site_variant MOTIF_percent frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant_percent inframe_insertion splice_region_variant+intron_variant stop_gained+inframe_insertion_percent inframe_insertion+splice_region_variant Number_of_known_variants
                          (i.e. non-empty ID) splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant 3_prime_UTR_variant_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent downstream_gene_variant_percent INTERGENIC splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+splice_region_variant splice_donor_variant+splice_region_variant+intron_variant_percent splice_region_variant splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+intron_variant_percent splice_region_variant_percent SPLICE_SITE_DONOR inframe_insertion_percent intergenic_region TRANSCRIPT_percent intragenic_variant +snpeff 3322.0 1.8e-05 462.0 0.000109 1.0 1.0 1.8e-05 2174772.0 0.004855 0.0084 15811.0 1.8e-05 2.0 0.0 9.1e-05 3.6e-05 0.287478 10.0 2.0 0.007418 2126738.0 2178258.0 524875.0 1.0 1.8e-05 159.0 0.000127 15320.0 21.0 3.6e-05 6.178119 2.0 986.0 1.0 3.0 0.000382 17369.0 1.0 354347.0 38.668709 1.8e-05 0.002891 0.024855 15811.0 41.0 0.000145 277.0 0.278551 3190.0 3.6e-05 0.060401 1.8e-05 3352.0 1.0 800.0 339790.0 60.30929 1.8e-05 39.605454 77.0 ? 0.0 3.6e-05 1.8e-05 3.0 2.0 39.535817 2126738.0 0.0014 13.0 2.0 78.616167 1.8e-05 61.0 0.0 339790.0 0.001473 5.5e-05 3.6e-05 9.1e-05 0.315806 0.014546 972155.0 0.005036 5.5e-05 224.0 3.0 6.442797 360.0 0.017928 5040.0 3101536026.0 3.6e-05 2.0 8.386471 5.0 3350.0 6.442797 12.0 1.0 32.0 0.06091 Count 1.0 392480.0 1.0 1.8e-05 0.060947 2174428.0 8.386471 0.0014 1367.0 3.0 354347.0 0.000236 0.000182 77.0 9.1e-05 32036512383.0 5499894.0 39.542071 6.0 0.006546 0.004073 0.000745 3.6e-05 0.000218 0.001109 15.0 1.8e-05 0.0 GRCh37.75 408.0 3316947.0 0.000582 8.0 0.091638 5.0 38.668709 3.6e-05 7.0 986.0 0.017928 5.5e-05 266.0 4390.0 5.5e-05 2.0 764271.0 5.0 0.287478 1.0 5.5e-05 6.178119 461247.0 2.0 1.0 0.000273 187.0 3.0 1.0 0.07982 0.0034 81.0 0.004836 461247.0 1.8e-05 267.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/sortmerna_stats.tabular --- a/test-data/sortmerna_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/sortmerna_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample non_rRNA silva-euk-18s-id95_count silva-euk-18s-id95_pct rRNA_pct silva-arc-16s-id95_count silva-euk-28s-id98_pct rfam-5.8s-database-id98_pct rRNA silva-bac-16s-id90_count rfam-5s-database-id98_count silva-bac-23s-id98_count silva-bac-23s-id98_pct rfam-5.8s-database-id98_count silva-arc-16s-id95_pct non_rRNA_pct rfam-5s-database-id98_pct silva-arc-23s-id98_count silva-arc-23s-id98_pct total silva-bac-16s-id90_pct silva-euk-28s-id98_count -25839_merged 4394708 11108.89 0.25 1.099299750020029 0.0 0.01 0.0 48848 26216.9804 0.0 10664.534399999999 0.24 0.0 0.0 98.90070024997996 0.0 0.0 0.0 4443556 0.59 444.35560000000004 +Sample silva-euk-28s-id98_count silva-arc-16s-id95_count silva-euk-18s-id95_pct silva-bac-23s-id98_pct silva-arc-23s-id98_pct rfam-5s-database-id98_count rRNA_pct silva-bac-16s-id90_count rfam-5.8s-database-id98_count silva-euk-18s-id95_count rRNA silva-euk-28s-id98_pct silva-arc-16s-id95_pct total rfam-5s-database-id98_pct non_rRNA_pct rfam-5.8s-database-id98_pct silva-bac-23s-id98_count silva-arc-23s-id98_count silva-bac-16s-id90_pct non_rRNA +25839_merged 444.35560000000004 0.0 0.25 0.24 0.0 0.0 1.099299750020029 26216.9804 0.0 11108.89 48848 0.01 0.0 4443556 0.0 98.90070024997996 0.0 10664.534399999999 0.0 0.59 4394708 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/star_stats.tabular --- a/test-data/star_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/star_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample unmapped_tooshort multimapped mismatch_rate num_splices total_reads num_GCAG_splices unmapped_mismatches_percent avg_mapped_read_length num_GTAG_splices deletion_length avg_input_read_length multimapped_percent deletion_rate uniquely_mapped unmapped_tooshort_percent unmapped_mismatches unmapped_other_percent insertion_length multimapped_toomany_percent num_noncanonical_splices unmapped_other multimapped_toomany insertion_rate num_annotated_splices uniquely_mapped_percent num_ATAC_splices -star_log 10 1.0 1.73 47.0 100.0 0.0 0.0 74.8 47.0 0.0 75.0 1.0 0.0 89.0 10.0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0.0 89.0 0.0 +Sample multimapped_percent insertion_rate multimapped_toomany_percent num_annotated_splices num_GTAG_splices uniquely_mapped unmapped_tooshort_percent deletion_length mismatch_rate insertion_length num_noncanonical_splices num_ATAC_splices deletion_rate multimapped_toomany total_reads num_GCAG_splices num_splices unmapped_mismatches_percent unmapped_other_percent unmapped_mismatches unmapped_tooshort multimapped unmapped_other avg_mapped_read_length uniquely_mapped_percent avg_input_read_length +star_log 1.0 0.0 0.0 0.0 47.0 89.0 10.0 0.0 1.73 0.0 0.0 0.0 0.0 0.0 100.0 0.0 47.0 0.0 0.0 0 10 1.0 0 74.8 89.0 75.0 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/tophat_stats.tabular --- a/test-data/tophat_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/tophat_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample unaligned_total aligned_total aligned_not_multimapped_discordant overall_aligned_percent aligned_multimap aligned_discordant total_reads concordant_aligned_percent -tophat_align 2985.0 313405.0 307733.0 99.5 5638.0 34.0 316390.0 99.0 +Sample aligned_not_multimapped_discordant concordant_aligned_percent unaligned_total aligned_total aligned_multimap total_reads aligned_discordant overall_aligned_percent +tophat_align 307733.0 99.0 2985.0 313405.0 5638.0 316390.0 34.0 99.5 diff -r 467486f1c568 -r e0f4a651c6b9 test-data/trimmomatic_stats.tabular --- a/test-data/trimmomatic_stats.tabular Sun Jan 14 09:55:46 2018 -0500 +++ b/test-data/trimmomatic_stats.tabular Fri Apr 20 01:06:25 2018 -0400 @@ -1,2 +1,2 @@ -Sample input_reads surviving_pct dropped surviving dropped_pct -C2 39733090.0 82.02 7142532.0 32590558.0 17.98 +Sample input_reads surviving dropped surviving_pct dropped_pct +C2 39733090.0 32590558.0 7142532.0 82.02 17.98