--- a/multiqc.xml	Sat Nov 21 12:54:24 2020 +0000
+++ b/multiqc.xml	Tue Mar 02 08:02:36 2021 +0000
@@ -53,6 +53,16 @@
     @CHECK_LN_FILE@
 #end for
         ]]></token>
+        <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text="">
+            <element name="@NAME@">
+                <assert_contents>
+                    <has_n_columns n="@COLUMNS@"/>
+                    <has_n_lines n="@LINES@"/>
+                    <has_text text="@TEXT@"/>
+                    <yield/>
+                </assert_contents>
+            </element>
+        </xml>
     </macros>
     <requirements>
        <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement>
@@ -339,7 +349,7 @@
                 @LN_3_FILES@
             #elif str($repeat2.type.type) == "read_duplication_pos"
                 #for $k, $file in enumerate($repeat2.type.input)
-                    #set file_path = os.path.join($repeat_dir, 'file_' + str($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"
@@ -931,14 +941,16 @@
                 </assert_contents>
             </output>
             <output_collection name="stats" type="list" count="10">
-                <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
-                <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/>
-                <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
-                <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
+                <expand macro="element_assert" name="cutadapt" columns="8" lines="2" text="dataset_33"/>
+                <expand macro="element_assert" name="fastp" columns="2" lines="3" text="R1_fq"/>
+                <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_1"/>
+                <expand macro="element_assert" name="flexbar" columns="11" lines="2" text="result_right"/>
+                <expand macro="element_assert" name="general_stats" columns="20" lines="11" text="bwa-mem-fastq1_fq"/>
+                <expand macro="element_assert" name="slamdunk_readrates_plus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>
+                <expand macro="element_assert" name="slamdunk_readrates_minus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>
+                <expand macro="element_assert" name="sortmerna" columns="22" lines="2" text="25839_merged"/>
+                <expand macro="element_assert" name="sources" columns="4" lines="7" text="Module"/>
+                <expand macro="element_assert" name="trimmomatic" columns="6" lines="2" text="C2"/>
             </output_collection>
             <output_collection name="plots" type="list" count="29"/>
         </test>
@@ -1019,16 +1031,18 @@
                     <has_text text="hicexplorer1_log_1" />
                 </assert_contents>
             </output>
-            <output_collection name="stats" type="list" count="8">
-                <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>
-                <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
-                <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/>
-                <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
-                <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="macs" file="macs_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
+            <output_collection name="stats" type="list" count="11">
+                <expand macro="element_assert" name="bismark_alignment" columns="21" lines="2" text="bismark_txt_SE_report"/>
+                <expand macro="element_assert" name="bowtie2" columns="7" lines="3" text="bowtie2_1_txt"/>
+                <expand macro="element_assert" name="cutadapt" columns="8" lines="5" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2"/>
+                <expand macro="element_assert" name="general_stats" columns="21" lines="19" text="treat2"/>
+                <expand macro="element_assert" name="hicexplorer" columns="41" lines="4" text="hicexplorer_3_hicexplorer2_log_small_test_rf"/>
+                <expand macro="element_assert" name="hisat2" columns="6" lines="3" text="hisat2_2_txt"/>
+                <expand macro="element_assert" name="kallisto" columns="6" lines="3" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1"/>
+                <expand macro="element_assert" name="macs" columns="11" lines="3" text="treat2"/>
+                <expand macro="element_assert" name="sources" columns="4" lines="18" text="Cutadapt"/>
+                <expand macro="element_assert" name="star" columns="27" lines="2" text="star_log_txt"/>
+                <expand macro="element_assert" name="tophat.txt" columns="9" lines="2" text="tophat_txtalign"/>
             </output_collection>
         </test>
         <test expect_num_outputs="2">
@@ -1231,32 +1245,32 @@
                     <has_text text="snpeff" />
                 </assert_contents>
             </output>
-            <output_collection name="stats" type="list" count="19">
-                <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/>
-                <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/>
-                <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/>
-                <element name="general_stats" file="post_aligner_soft_stats.tabular" compare="sim_size" delta="25"/>
-                <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="10"/>
-                <element name="picard_AlignmentSummaryMetrics" file="picard_AlignmentSummaryMetrics_stats.tabular" compare="sim_size" delta="0"/>
-                <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/>
-                <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/>
-                <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/>
-                <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/>
-                <element name="prokka" file="prokka_stats.tabular" compare="sim_size" delta="0"/>
-                <element name="qualimap_bamqc_genome_results" file="qualimap_bamqc_genome_results.tabular" compare="sim_size" delta="0"/>
-                <element name="quast" file="quast_stats.tabular" compare="sim_size" delta="0"/>
-                <element name="samblaster" file="samblaster_stats.tabular" compare="sim_size" delta="0"/>
-                <element name="samtools_flagstat">
-                    <assert_contents>
-                        <has_text text="samtools_flagstat" />
-                        <has_text text="mapped_passed" />
-                        <has_text text="20689039" />
-                    </assert_contents>
-                </element>
-                <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/>
-                <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/>
+            <output_collection name="stats" type="list" count="21">
+                <expand macro="element_assert" name="bamtools_stats" columns="20" lines="2" text="bamtools_txt"/>
+                <expand macro="element_assert" name="bcftools_stats" columns="28" lines="2" text="Test1"/>
+                <expand macro="element_assert" name="busco" columns="8" lines="2" text="busco_txt"/>
+                <expand macro="element_assert" name="featureCounts" columns="14" lines="7" text="5: TopHat on data 1, data 14, and data 13"/>
+                <expand macro="element_assert" name="gatk_varianteval" columns="12" lines="2" text="gatk_varianteval_txt"/>
+                <expand macro="element_assert" name="general_stats" columns="44" lines="23" text="x_bam"/>
+                <expand macro="element_assert" name="htseq" columns="9" lines="2" text="htseq_txt"/>
+                <expand macro="element_assert" name="picard_AlignmentSummaryMetrics" columns="26" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>
+                <expand macro="element_assert" name="picard_RnaSeqMetrics" columns="27" lines="2" text="picard_CollectRnaSeqMetrics_bam"/>
+                <expand macro="element_assert" name="picard_baseContent" columns="11" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>
+                <expand macro="element_assert" name="picard_dups" columns="10" lines="2" text="dataset_114"/>
+                <expand macro="element_assert" name="picard_insertSize" columns="23" lines="2" text="dataset_197_FR"/>
+                <expand macro="element_assert" name="prokka" columns="11" lines="3" text="Sample2"/>
+                <expand macro="element_assert" name="qualimap_bamqc_genome_results" columns="12" lines="2" text="x_bam"/>
+                <expand macro="element_assert" name="quast" columns="50" lines="2" text="14892_1#15"/>
+                <expand macro="element_assert" name="samblaster" columns="5" lines="2" text="virtual-normal"/>
+                <expand macro="element_assert" name="samtools_flagstat" columns="34" lines="2" text="samtools_flagstat_txt">
+                    <has_text text="samtools_flagstat" />
+                    <has_text text="mapped_passed" />
+                    <has_text text="20689039" />
+                </expand>
+                <expand macro="element_assert" name="samtools_idxstats" columns="68" lines="2" text="samtools_idxstats_txt_idxstat"/>
+                <expand macro="element_assert" name="samtools_stats" columns="40" lines="2" text="samtools_stats_txt"/>
+                <expand macro="element_assert" name="snpeff" columns="169" lines="2" text="snpeff_csv"/>
+                <expand macro="element_assert" name="sources" columns="4" lines="33" text="Bamtools"/>
             </output_collection>
         </test>
         <test expect_num_outputs="2">
@@ -1297,8 +1311,12 @@
                     <has_text text="fastqc_seq_heatmap_key_t" />
                 </assert_contents>
             </output>
-	    <output_collection name="stats" type="list" count="1"/>
-            <output_collection name="plots" type="list" count="1">
+	        <output_collection name="stats" type="list" count="3">
+                <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_2"/>
+                <expand macro="element_assert" name="general_stats" columns="6" lines="3" text="poulet5_2"/>
+                <expand macro="element_assert" name="sources" columns="4" lines="3" text="FastQC"/>
+            </output_collection>
+            <output_collection name="plots" type="list" count="7">
                 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>
             </output_collection>
         </test>