Mercurial > repos > greg > cfsan_snp_pipeline_call_sites
comparison cfsan_snp_pipeline_call_sites.xml @ 3:5bfc9e1ce9e9 draft default tip
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author | greg |
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date | Thu, 23 Nov 2023 19:33:24 +0000 |
parents | 991fbae39ee6 |
children |
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2:991fbae39ee6 | 3:5bfc9e1ce9e9 |
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5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 cp '$reference' 'reference.fasta' && | 8 cp '$reference' 'reference.fasta' && |
9 samtools faidx 'reference.fasta' && | 9 samtools faidx 'reference.fasta' && |
10 picard MarkDuplicates INPUT='$input' OUTPUT=/dev/stdout METRICS_FILE='$metrics' | samtools mpileup -f ./reference.fasta - -o '$pileup' && | 10 samtools view -b -F 4 '$input' -o ./unsorted.bam && |
11 samtools sort -o ./sorted.bam -O BAM ./unsorted.bam && | |
12 picard MarkDuplicates INPUT=./sorted.bam OUTPUT=/dev/stdout METRICS_FILE='$metrics' | samtools mpileup -f ./reference.fasta - -o '$pileup' && | |
11 varscan mpileup2snp '$pileup' --min_var-freq 0.90 --output-vcf 1 > '$calls' | 13 varscan mpileup2snp '$pileup' --min_var-freq 0.90 --output-vcf 1 > '$calls' |
12 ]]></command> | 14 ]]></command> |
13 <inputs> | 15 <inputs> |
14 <param name="input" label="Read alignment to reference" type="data" format="bam"/> | 16 <param name="input" label="Read alignment to reference" type="data" format="sam"/> |
15 <param name="reference" label="FASTA Reference from your history" type="data" format="fasta"/> | 17 <param name="reference" label="FASTA Reference from your history" type="data" format="fasta"/> |
16 </inputs> | 18 </inputs> |
17 <outputs> | 19 <outputs> |
18 <data name="calls" label="Call Sites (unfiltered SNPs)" format="vcf"/> | 20 <data name="calls" label="Call Sites (unfiltered SNPs)" format="vcf"/> |
19 <data name="pileup" label="Call Sites (pileup)" format="pileup"/> | 21 <data name="pileup" label="Call Sites (pileup)" format="pileup"/> |
20 <data name="metrics" label="Call sites (Picard metrics)" format="txt"/> | 22 <data name="metrics" label="Call sites (Picard metrics)" format="txt"/> |
21 </outputs> | 23 </outputs> |
22 <tests> | 24 <tests> |
23 <test> | 25 <test> |
24 <param name="reference" value="lambda_virus.fasta"/> | 26 <param name="reference" value="lambda_virus.fasta"/> |
25 <param name="input" value="reads.bam"/> | 27 <param name="input" value="reads.sam"/> |
26 <output name="calls" ftype="vcf"> | 28 <output name="calls" ftype="vcf"> |
27 <assert_contents> | 29 <assert_contents> |
28 <has_size value="9976" delta="100"/> | 30 <has_size value="9976" delta="100"/> |
29 </assert_contents> | 31 </assert_contents> |
30 </output> | 32 </output> |