Mercurial > repos > iuc > multiqc

--- a/generate_test_data.sh	Fri Apr 20 01:06:25 2018 -0400
+++ b/generate_test_data.sh	Wed Apr 25 07:59:52 2018 -0400
@@ -46,8 +46,9 @@
 cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2/hisat2_2.txt'

 mkdir -p 'multiqc_WDir/hicexplorer'
-cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/'
-cp 'test-data/hicexplorer2.log' 'multiqc_WDir/hicexplorer/'
+cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/hicexplorer1'
+cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/hicexplorer1_1'
+cp 'test-data/hicexplorer2.log' 'multiqc_WDir/hicexplorer/hicexplorer2'

 mkdir -p 'multiqc_WDir/kallisto'
 cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto/kallisto_1.txt'
--- a/multiqc.xml	Fri Apr 20 01:06:25 2018 -0400
+++ b/multiqc.xml	Wed Apr 25 07:59:52 2018 -0400
@@ -8,6 +8,10 @@
         ]]></token>
         <token name="@CHECK_LN_FILE@">
 <![CDATA[
+#if $file_path in $file_paths
+    #set $file_path += '_' + str($file_paths.count($file_path))
+#end if
+#set $file_paths += [$file_path]
 grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
 ln -s '$file' '$file_path'  &&
         ]]></token>
@@ -23,6 +27,7 @@
         ]]></token>
         <token name="@LN_FILES@">
 <![CDATA[
+#set file_paths = []
 #for $file in $repeat.software_cond.input
     @ESCAPE_IDENTIFIER@
     #set file_path = os.path.join($software_dir, str($identifier))
@@ -31,6 +36,7 @@
         ]]></token>
         <token name="@LN_2_FILES@">
 <![CDATA[
+#set file_paths = []
 @CREATE_REPEAT_DIR_1@
 #for $file in $repeat2.input
     #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
@@ -40,6 +46,7 @@
         ]]></token>
         <token name="@LN_3_FILES@">
 <![CDATA[
+#set file_paths = []
 #for $file in $repeat2.type.input
     #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
     #set file_path = os.path.join($repeat_dir, str($identifier))
@@ -868,7 +875,7 @@
             <repeat name="results">
                 <conditional name="software_cond">
                     <param name="software" value="hicexplorer" />
-                    <param name="input" value="hicexplorer1.log,hicexplorer2.log" />
+                    <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log" />
                 </conditional>
             </repeat>
             <repeat name="results">
@@ -910,7 +917,7 @@
                     <has_text text="star_alignment_plot" />
                     <has_text text="tophat_alignment" />
                     <has_text text="hicexplorer" />
-
+                    <has_text text="hicexplorer1_log_1" />
                 </assert_contents>
             </output>
             <output_collection name="stats" type="list">
--- a/test-data/aligner_soft_report.html	Fri Apr 20 01:06:25 2018 -0400
+++ b/test-data/aligner_soft_report.html	Wed Apr 25 07:59:52 2018 -0400
@@ -24,7 +24,7 @@

 <!-- JSON plot data -->
 <script type="text/javascript">
-mqc_compressed_plotdata = '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';
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';
 num_datasets_plot_limit = 50;
 mqc_sample_names_rename = [];
 </script>
@@ -4746,7 +4746,7 @@
 <div class="alert alert-warning mqc_loading_warning" style="display:none;"><span class="glyphicon glyphicon-time"></span> &nbsp;Loading report..</div>

 <div id="analysis_dirs_wrapper">
-  <p>Report generated on 2018-04-06, 16:47 based on data in:
+  <p>Report generated on 2018-04-23, 22:00 based on data in:
   <code class="mqc_analysis_path">/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_WDir</code>

 </div>
@@ -4788,12 +4788,12 @@
                 <span class="glyphicon glyphicon glyphicon-stats"></span> Plot
             </button>

-        <small id="general_stats_table_numrows_text" class="mqc_table_numrows_text">Showing <sup id="general_stats_table_numrows" class="mqc_table_numrows">15</sup>/<sub>15</sub> rows and <sup id="general_stats_table_numcols" class="mqc_table_numcols">14</sup>/<sub>15</sub> columns.</small>
+        <small id="general_stats_table_numrows_text" class="mqc_table_numrows_text">Showing <sup id="general_stats_table_numrows" class="mqc_table_numrows">16</sup>/<sub>16</sub> rows and <sup id="general_stats_table_numcols" class="mqc_table_numcols">14</sup>/<sub>15</sub> columns.</small>

         <div id="general_stats_table_container" class="mqc_table_container">
             <div class="table-responsive mqc-table-responsive mqc-table-collapse">
                 <table id="general_stats_table" class="table table-condensed mqc_table" data-title="General Statistics">
-        <thead><tr><th class="rowheader">Sample Name</th><th id="header_mqc-generalstats-aligned_reads" class="mqc-generalstats-aligned_reads hidden" data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="Bismark"  data-shared-key=read_count><span class="mqc_table_tooltip" title="Bismark: Total Aligned Sequences (millions)">M Aligned</span></th><th id="header_mqc-generalstats-percent_aligned" class="mqc-generalstats-percent_aligned " data-dmax="100.0" data-dmin="0.0" data-namespace="Kallisto" ><span class="mqc_table_tooltip" title="Kallisto: % processed reads that were pseudoaligned">% Aligned</span></th><th id="header_mqc-generalstats-Pairs_considered" class="mqc-generalstats-Pairs_considered " data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="HiCExplorer"  data-shared-key=read_count><span class="mqc_table_tooltip" title="HiCExplorer: Total number of read pairs (millions)">M Pairs</span></th><th id="header_mqc-generalstats-Pairs_used" class="mqc-generalstats-Pairs_used " data-dmax="100.0" data-dmin="0.0" data-namespace="HiCExplorer" ><span class="mqc_table_tooltip" title="HiCExplorer: % Used pairs">% Used pairs</span></th><th id="header_mqc-generalstats-Mapped" class="mqc-generalstats-Mapped " data-dmax="100.0" data-dmin="0.0" data-namespace="HiCExplorer" ><span class="mqc_table_tooltip" title="HiCExplorer: % Mapped">% Mapped</span></th><th id="header_mqc-generalstats-Min_rest_site_distance" class="mqc-generalstats-Min_rest_site_distance " data-dmax="303.0" data-dmin="0" data-namespace="HiCExplorer" ><span class="mqc_table_tooltip" title="HiCExplorer: Minimum restriction site distance (bp)">Min RE dist</span></th><th id="header_mqc-generalstats-Max_rest_site_distance" class="mqc-generalstats-Max_rest_site_distance " data-dmax="1500.0" data-dmin="0" data-namespace="HiCExplorer" ><span class="mqc_table_tooltip" title="HiCExplorer: Max rest. site distance (bp)">Max RE dist</span></th><th id="header_mqc-generalstats-fragment_length" class="mqc-generalstats-fragment_length " data-dmax="169.418" data-dmin="0.0" data-namespace="Kallisto" ><span class="mqc_table_tooltip" title="Kallisto: Estimated average fragment length">Frag Length</span></th><th id="header_mqc-generalstats-pseudoaligned_reads" class="mqc-generalstats-pseudoaligned_reads " data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="Kallisto"  data-shared-key=read_count><span class="mqc_table_tooltip" title="Kallisto: Pseudoaligned reads (millions)">M Aligned</span></th><th id="header_mqc-generalstats-uniquely_mapped_percent" class="mqc-generalstats-uniquely_mapped_percent " data-dmax="100.0" data-dmin="0.0" data-namespace="STAR" ><span class="mqc_table_tooltip" title="STAR: % Uniquely mapped reads">% Aligned</span></th><th id="header_mqc-generalstats-uniquely_mapped" class="mqc-generalstats-uniquely_mapped " data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="STAR"  data-shared-key=read_count><span class="mqc_table_tooltip" title="STAR: Uniquely mapped reads (millions)">M Aligned</span></th><th id="header_mqc-generalstats-overall_alignment_rate" class="mqc-generalstats-overall_alignment_rate " data-dmax="100.0" data-dmin="0.0" data-namespace="Bowtie 2" ><span class="mqc_table_tooltip" title="Bowtie 2: overall alignment rate">% Aligned</span></th><th id="header_mqc-generalstats-overall_aligned_percent" class="mqc-generalstats-overall_aligned_percent " data-dmax="100.0" data-dmin="0.0" data-namespace="Tophat" ><span class="mqc_table_tooltip" title="Tophat: overall read mapping rate">% Aligned</span></th><th id="header_mqc-generalstats-aligned_not_multimapped_discordant" class="mqc-generalstats-aligned_not_multimapped_discordant " data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="Tophat"  data-shared-key=read_count><span class="mqc_table_tooltip" title="Tophat: Aligned reads, not multimapped or discordant (millions)">M Aligned</span></th><th id="header_mqc-generalstats-percent_trimmed" class="mqc-generalstats-percent_trimmed " data-dmax="100.0" data-dmin="0.0" data-namespace="Cutadapt" ><span class="mqc_table_tooltip" title="Cutadapt: % Total Base Pairs trimmed">% Trimmed</span></th></tr></thead><tbody><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1">HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "><div class="wrapper"><span class="bar" style="width:5.880883098970165%; background-color:#c5cee5;"></span><span class="val">5.9%</span></div></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1">HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "><div class="wrapper"><span class="bar" style="width:83.65114569077758%; background-color:#b6d4c4;"></span><span class="val">83.7%</span></div></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "><div class="wrapper"><span class="bar" style="width:99.08392260562633%; background-color:#b3d3c4;"></span><span class="val">167.9bp</span></div></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "><div class="wrapper"><span class="bar" style="width:81.86628682550811%; background-color:#e7b5c9;"></span><span class="val">48.5</span></div></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2">HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "><div class="wrapper"><span class="bar" style="width:31.038195169381073%; background-color:#e7f4f9;"></span><span class="val">31.0%</span></div></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1">HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "><div class="wrapper"><span class="bar" style="width:7.7267901650356645%; background-color:#c6d1e6;"></span><span class="val">7.7%</span></div></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1">HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "><div class="wrapper"><span class="bar" style="width:84.50278473550448%; background-color:#b5d4c4;"></span><span class="val">84.5%</span></div></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#b3d2c3;"></span><span class="val">169.4bp</span></div></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#d1b3bc;"></span><span class="val">59.3</span></div></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2">HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "><div class="wrapper"><span class="bar" style="width:32.18485266309055%; background-color:#e9f5f9;"></span><span class="val">32.2%</span></div></td></tr><tr><th class="rowheader" data-original-sn="bismark_SE_report">bismark_SE_report</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"><div class="wrapper"><span class="bar" style="width:0.37205562936607595%; background-color:#fcfcfd;"></span><span class="val">0.2</span></div></td><td class="data-coloured mqc-generalstats-percent_aligned "><div class="wrapper"><span class="bar" style="width:69.71079996207212%; background-color:#c1dfca;"></span><span class="val">69.7%</span></div></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="bowtie2_1">bowtie2_1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "><div class="wrapper"><span class="bar" style="width:98.33%; background-color:#b3c9bf;"></span><span class="val">98.3%</span></div></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="bowtie2_2">bowtie2_2</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "><div class="wrapper"><span class="bar" style="width:98.31%; background-color:#b3c9bf;"></span><span class="val">98.3%</span></div></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hicexplorer_hicexplorer1_small_test">hicexplorer_hicexplorer1_small_test</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "><div class="wrapper"><span class="bar" style="width:0.16865966317661737%; background-color:#fdfefa;"></span><span class="val">0.1</span></div></td><td class="data-coloured mqc-generalstats-Pairs_used "><div class="wrapper"><span class="bar" style="width:37.32734564876029%; background-color:#e5f5e9;"></span><span class="val">37.3%</span></div></td><td class="data-coloured mqc-generalstats-Mapped "><div class="wrapper"><span class="bar" style="width:91.22150765630157%; background-color:#b9deca;"></span><span class="val">91.2%</span></div></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#b5c6d9;"></span><span class="val">303 bp</span></div></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "><div class="wrapper"><span class="bar" style="width:53.333333333333336%; background-color:#d4eeef;"></span><span class="val">800 bp</span></div></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hicexplorer_hicexplorer2_small_test_rf">hicexplorer_hicexplorer2_small_test_rf</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "><div class="wrapper"><span class="bar" style="width:0.16865966317661737%; background-color:#fdfefa;"></span><span class="val">0.1</span></div></td><td class="data-coloured mqc-generalstats-Pairs_used "><div class="wrapper"><span class="bar" style="width:35.94010981866917%; background-color:#e6f5e9;"></span><span class="val">35.9%</span></div></td><td class="data-coloured mqc-generalstats-Mapped "><div class="wrapper"><span class="bar" style="width:91.22150765630157%; background-color:#b9deca;"></span><span class="val">91.2%</span></div></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "><div class="wrapper"><span class="bar" style="width:50.165016501650165%; background-color:#d7f0ed;"></span><span class="val">152 bp</span></div></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#b5c6d9;"></span><span class="val">1500 bp</span></div></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hisat2_1">hisat2_1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "><div class="wrapper"><span class="bar" style="width:96.15%; background-color:#b3cac0;"></span><span class="val">96.2%</span></div></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hisat2_2">hisat2_2</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "><div class="wrapper"><span class="bar" style="width:96.15%; background-color:#b3cac0;"></span><span class="val">96.2%</span></div></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="star_log">star_log</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "><div class="wrapper"><span class="bar" style="width:89.0%; background-color:#b3d0c2;"></span><span class="val">89.0%</span></div></td><td class="data-coloured mqc-generalstats-uniquely_mapped "><div class="wrapper"><span class="bar" style="width:0.00015013262277306088%; background-color:#f7f4f9;"></span><span class="val">0.0</span></div></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="tophat_align">tophat_align</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "><div class="wrapper"><span class="bar" style="width:99.5%; background-color:#b3c8bf;"></span><span class="val">99.5%</span></div></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "><div class="wrapper"><span class="bar" style="width:0.5191096899305881%; background-color:#fcfbfd;"></span><span class="val">0.3</span></div></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr></tbody></table></div><div class="mqc-table-expand"><span class="glyphicon glyphicon-chevron-down" aria-hidden="true"></span></div></div>
+        <thead><tr><th class="rowheader">Sample Name</th><th id="header_mqc-generalstats-aligned_reads" class="mqc-generalstats-aligned_reads hidden" data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="Bismark"  data-shared-key=read_count><span class="mqc_table_tooltip" title="Bismark: Total Aligned Sequences (millions)">M Aligned</span></th><th id="header_mqc-generalstats-percent_aligned" class="mqc-generalstats-percent_aligned " data-dmax="100.0" data-dmin="0.0" data-namespace="Kallisto" ><span class="mqc_table_tooltip" title="Kallisto: % processed reads that were pseudoaligned">% Aligned</span></th><th id="header_mqc-generalstats-Pairs_considered" class="mqc-generalstats-Pairs_considered " data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="HiCExplorer"  data-shared-key=read_count><span class="mqc_table_tooltip" title="HiCExplorer: Total number of read pairs (millions)">M Pairs</span></th><th id="header_mqc-generalstats-Pairs_used" class="mqc-generalstats-Pairs_used " data-dmax="100.0" data-dmin="0.0" data-namespace="HiCExplorer" ><span class="mqc_table_tooltip" title="HiCExplorer: % Used pairs">% Used pairs</span></th><th id="header_mqc-generalstats-Mapped" class="mqc-generalstats-Mapped " data-dmax="100.0" data-dmin="0.0" data-namespace="HiCExplorer" ><span class="mqc_table_tooltip" title="HiCExplorer: % Mapped">% Mapped</span></th><th id="header_mqc-generalstats-Min_rest_site_distance" class="mqc-generalstats-Min_rest_site_distance " data-dmax="303.0" data-dmin="0" data-namespace="HiCExplorer" ><span class="mqc_table_tooltip" title="HiCExplorer: Minimum restriction site distance (bp)">Min RE dist</span></th><th id="header_mqc-generalstats-Max_rest_site_distance" class="mqc-generalstats-Max_rest_site_distance " data-dmax="1500.0" data-dmin="0" data-namespace="HiCExplorer" ><span class="mqc_table_tooltip" title="HiCExplorer: Max rest. site distance (bp)">Max RE dist</span></th><th id="header_mqc-generalstats-fragment_length" class="mqc-generalstats-fragment_length " data-dmax="169.418" data-dmin="0.0" data-namespace="Kallisto" ><span class="mqc_table_tooltip" title="Kallisto: Estimated average fragment length">Frag Length</span></th><th id="header_mqc-generalstats-pseudoaligned_reads" class="mqc-generalstats-pseudoaligned_reads " data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="Kallisto"  data-shared-key=read_count><span class="mqc_table_tooltip" title="Kallisto: Pseudoaligned reads (millions)">M Aligned</span></th><th id="header_mqc-generalstats-uniquely_mapped_percent" class="mqc-generalstats-uniquely_mapped_percent " data-dmax="100.0" data-dmin="0.0" data-namespace="STAR" ><span class="mqc_table_tooltip" title="STAR: % Uniquely mapped reads">% Aligned</span></th><th id="header_mqc-generalstats-uniquely_mapped" class="mqc-generalstats-uniquely_mapped " data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="STAR"  data-shared-key=read_count><span class="mqc_table_tooltip" title="STAR: Uniquely mapped reads (millions)">M Aligned</span></th><th id="header_mqc-generalstats-overall_alignment_rate" class="mqc-generalstats-overall_alignment_rate " data-dmax="100.0" data-dmin="0.0" data-namespace="Bowtie 2" ><span class="mqc_table_tooltip" title="Bowtie 2: overall alignment rate">% Aligned</span></th><th id="header_mqc-generalstats-overall_aligned_percent" class="mqc-generalstats-overall_aligned_percent " data-dmax="100.0" data-dmin="0.0" data-namespace="Tophat" ><span class="mqc_table_tooltip" title="Tophat: overall read mapping rate">% Aligned</span></th><th id="header_mqc-generalstats-aligned_not_multimapped_discordant" class="mqc-generalstats-aligned_not_multimapped_discordant " data-dmax="59.280919999999995" data-dmin="0.0" data-namespace="Tophat"  data-shared-key=read_count><span class="mqc_table_tooltip" title="Tophat: Aligned reads, not multimapped or discordant (millions)">M Aligned</span></th><th id="header_mqc-generalstats-percent_trimmed" class="mqc-generalstats-percent_trimmed " data-dmax="100.0" data-dmin="0.0" data-namespace="Cutadapt" ><span class="mqc_table_tooltip" title="Cutadapt: % Total Base Pairs trimmed">% Trimmed</span></th></tr></thead><tbody><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1">HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "><div class="wrapper"><span class="bar" style="width:5.880883098970165%; background-color:#c5cee5;"></span><span class="val">5.9%</span></div></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1">HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "><div class="wrapper"><span class="bar" style="width:83.65114569077758%; background-color:#b6d4c4;"></span><span class="val">83.7%</span></div></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "><div class="wrapper"><span class="bar" style="width:99.08392260562633%; background-color:#b3d3c4;"></span><span class="val">167.9bp</span></div></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "><div class="wrapper"><span class="bar" style="width:81.86628682550811%; background-color:#e7b5c9;"></span><span class="val">48.5</span></div></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2">HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "><div class="wrapper"><span class="bar" style="width:31.038195169381073%; background-color:#e7f4f9;"></span><span class="val">31.0%</span></div></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1">HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "><div class="wrapper"><span class="bar" style="width:7.7267901650356645%; background-color:#c6d1e6;"></span><span class="val">7.7%</span></div></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1">HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "><div class="wrapper"><span class="bar" style="width:84.50278473550448%; background-color:#b5d4c4;"></span><span class="val">84.5%</span></div></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#b3d2c3;"></span><span class="val">169.4bp</span></div></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#d1b3bc;"></span><span class="val">59.3</span></div></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2">HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "><div class="wrapper"><span class="bar" style="width:32.18485266309055%; background-color:#e9f5f9;"></span><span class="val">32.2%</span></div></td></tr><tr><th class="rowheader" data-original-sn="bismark_SE_report">bismark_SE_report</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"><div class="wrapper"><span class="bar" style="width:0.37205562936607595%; background-color:#fcfcfd;"></span><span class="val">0.2</span></div></td><td class="data-coloured mqc-generalstats-percent_aligned "><div class="wrapper"><span class="bar" style="width:69.71079996207212%; background-color:#c1dfca;"></span><span class="val">69.7%</span></div></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="bowtie2_1">bowtie2_1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "><div class="wrapper"><span class="bar" style="width:98.33%; background-color:#b3c9bf;"></span><span class="val">98.3%</span></div></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="bowtie2_2">bowtie2_2</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "><div class="wrapper"><span class="bar" style="width:98.31%; background-color:#b3c9bf;"></span><span class="val">98.3%</span></div></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hicexplorer_hicexplorer1_1_small_test">hicexplorer_hicexplorer1_1_small_test</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "><div class="wrapper"><span class="bar" style="width:0.16865966317661737%; background-color:#fdfefa;"></span><span class="val">0.1</span></div></td><td class="data-coloured mqc-generalstats-Pairs_used "><div class="wrapper"><span class="bar" style="width:37.32734564876029%; background-color:#e5f5e9;"></span><span class="val">37.3%</span></div></td><td class="data-coloured mqc-generalstats-Mapped "><div class="wrapper"><span class="bar" style="width:91.22150765630157%; background-color:#b9deca;"></span><span class="val">91.2%</span></div></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#b5c6d9;"></span><span class="val">303 bp</span></div></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "><div class="wrapper"><span class="bar" style="width:53.333333333333336%; background-color:#d4eeef;"></span><span class="val">800 bp</span></div></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hicexplorer_hicexplorer1_small_test">hicexplorer_hicexplorer1_small_test</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "><div class="wrapper"><span class="bar" style="width:0.16865966317661737%; background-color:#fdfefa;"></span><span class="val">0.1</span></div></td><td class="data-coloured mqc-generalstats-Pairs_used "><div class="wrapper"><span class="bar" style="width:37.32734564876029%; background-color:#e5f5e9;"></span><span class="val">37.3%</span></div></td><td class="data-coloured mqc-generalstats-Mapped "><div class="wrapper"><span class="bar" style="width:91.22150765630157%; background-color:#b9deca;"></span><span class="val">91.2%</span></div></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#b5c6d9;"></span><span class="val">303 bp</span></div></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "><div class="wrapper"><span class="bar" style="width:53.333333333333336%; background-color:#d4eeef;"></span><span class="val">800 bp</span></div></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hicexplorer_hicexplorer2_small_test_rf">hicexplorer_hicexplorer2_small_test_rf</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "><div class="wrapper"><span class="bar" style="width:0.16865966317661737%; background-color:#fdfefa;"></span><span class="val">0.1</span></div></td><td class="data-coloured mqc-generalstats-Pairs_used "><div class="wrapper"><span class="bar" style="width:35.94010981866917%; background-color:#e6f5e9;"></span><span class="val">35.9%</span></div></td><td class="data-coloured mqc-generalstats-Mapped "><div class="wrapper"><span class="bar" style="width:91.22150765630157%; background-color:#b9deca;"></span><span class="val">91.2%</span></div></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "><div class="wrapper"><span class="bar" style="width:50.165016501650165%; background-color:#d7f0ed;"></span><span class="val">152 bp</span></div></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "><div class="wrapper"><span class="bar" style="width:100.0%; background-color:#b5c6d9;"></span><span class="val">1500 bp</span></div></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hisat2_1">hisat2_1</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "><div class="wrapper"><span class="bar" style="width:96.15%; background-color:#b3cac0;"></span><span class="val">96.2%</span></div></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="hisat2_2">hisat2_2</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "><div class="wrapper"><span class="bar" style="width:96.15%; background-color:#b3cac0;"></span><span class="val">96.2%</span></div></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="star_log">star_log</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "><div class="wrapper"><span class="bar" style="width:89.0%; background-color:#b3d0c2;"></span><span class="val">89.0%</span></div></td><td class="data-coloured mqc-generalstats-uniquely_mapped "><div class="wrapper"><span class="bar" style="width:0.00015013262277306088%; background-color:#f7f4f9;"></span><span class="val">0.0</span></div></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr><tr><th class="rowheader" data-original-sn="tophat_align">tophat_align</th><td class="data-coloured mqc-generalstats-aligned_reads hidden"></td><td class="data-coloured mqc-generalstats-percent_aligned "></td><td class="data-coloured mqc-generalstats-Pairs_considered "></td><td class="data-coloured mqc-generalstats-Pairs_used "></td><td class="data-coloured mqc-generalstats-Mapped "></td><td class="data-coloured mqc-generalstats-Min_rest_site_distance "></td><td class="data-coloured mqc-generalstats-Max_rest_site_distance "></td><td class="data-coloured mqc-generalstats-fragment_length "></td><td class="data-coloured mqc-generalstats-pseudoaligned_reads "></td><td class="data-coloured mqc-generalstats-uniquely_mapped_percent "></td><td class="data-coloured mqc-generalstats-uniquely_mapped "></td><td class="data-coloured mqc-generalstats-overall_alignment_rate "></td><td class="data-coloured mqc-generalstats-overall_aligned_percent "><div class="wrapper"><span class="bar" style="width:99.5%; background-color:#b3c8bf;"></span><span class="val">99.5%</span></div></td><td class="data-coloured mqc-generalstats-aligned_not_multimapped_discordant "><div class="wrapper"><span class="bar" style="width:0.5191096899305881%; background-color:#fcfbfd;"></span><span class="val">0.3</span></div></td><td class="data-coloured mqc-generalstats-percent_trimmed "></td></tr></tbody></table></div><div class="mqc-table-expand"><span class="glyphicon glyphicon-chevron-down" aria-hidden="true"></span></div></div>
     <!-- MultiQC Table Columns Modal -->
     <div class="modal fade" id="general_stats_table_configModal" tabindex="-1">
       <div class="modal-dialog modal-lg">
--- a/test-data/aligner_soft_stats.tabular	Fri Apr 20 01:06:25 2018 -0400
+++ b/test-data/aligner_soft_stats.tabular	Wed Apr 25 07:59:52 2018 -0400
@@ -1,16 +1,17 @@
-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
+Sample	Cutadapt_mqc-generalstats-percent_trimmed	Kallisto_mqc-generalstats-percent_aligned	Kallisto_mqc-generalstats-fragment_length	Kallisto_mqc-generalstats-pseudoaligned_reads	Bismark_mqc-generalstats-percent_aligned	Bismark_mqc-generalstats-aligned_reads	Bowtie 2_mqc-generalstats-overall_alignment_rate	HiCExplorer_mqc-generalstats-Pairs_used	HiCExplorer_mqc-generalstats-Min_rest_site_distance	HiCExplorer_mqc-generalstats-Mapped	HiCExplorer_mqc-generalstats-Max_rest_site_distance	HiCExplorer_mqc-generalstats-Pairs_considered	HISAT2_mqc-generalstats-overall_alignment_rate	STAR_mqc-generalstats-uniquely_mapped	STAR_mqc-generalstats-uniquely_mapped_percent	Tophat_mqc-generalstats-aligned_not_multimapped_discordant	Tophat_mqc-generalstats-overall_aligned_percent
 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1	5.880883098970165
-HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1		48531088.0	167.866	83.65114569077758
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1		83.65114569077758	167.866	48531088.0
 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		59280920.0	169.418	84.50278473550448
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1		84.50278473550448	169.418	59280920.0
 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2	32.18485266309055
-bismark_SE_report					220558.0	69.71079996207212
+bismark_SE_report					69.71079996207212	220558.0
 bowtie2_1							98.33
 bowtie2_2							98.31
-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
+hicexplorer_hicexplorer1_1_small_test								0.3732734564876029	303.0	0.08778492343698428	800.0	99983.0
+hicexplorer_hicexplorer1_small_test								0.3732734564876029	303.0	0.08778492343698428	800.0	99983.0
+hicexplorer_hicexplorer2_small_test_rf								0.35940109818669175	152.0	0.08778492343698428	1500.0	99983.0
 hisat2_1													96.15
 hisat2_2													96.15
 star_log														89.0	89.0
-tophat_align																99.5	307733.0
+tophat_align																307733.0	99.5
--- a/test-data/bowtie2_stats.tabular	Fri Apr 20 01:06:25 2018 -0400
+++ b/test-data/bowtie2_stats.tabular	Wed Apr 25 07:59:52 2018 -0400
@@ -1,3 +1,3 @@
-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
+Sample	unpaired_total	total_reads	unpaired_aligned_one	unpaired_aligned_none	overall_alignment_rate	unpaired_aligned_multi
+bowtie2_1	21040602	21040602	13299463	351563	98.33	7389576
+bowtie2_2	16199126	16199126	10087714	274008	98.31	5837404
--- a/test-data/hisat2_stats.tabular	Fri Apr 20 01:06:25 2018 -0400
+++ b/test-data/hisat2_stats.tabular	Wed Apr 25 07:59:52 2018 -0400
@@ -1,3 +1,3 @@
-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
+Sample	unpaired_total	overall_alignment_rate	unpaired_aligned_one	unpaired_aligned_none	unpaired_aligned_multi
+hisat2_1	99978	96.15	86176	3849	9953
+hisat2_2	99978	96.15	86176	3849	9953
--- a/test-data/kallisto_stats.tabular	Fri Apr 20 01:06:25 2018 -0400
+++ b/test-data/kallisto_stats.tabular	Wed Apr 25 07:59:52 2018 -0400
@@ -1,3 +1,3 @@
-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
+Sample	percent_aligned	total_reads	not_pseudoaligned_reads	pseudoaligned_reads	fragment_length
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1	83.65114569077758	58016047.0	9484959.0	48531088.0	167.866
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1	84.50278473550448	70152623.0	10871703.0	59280920.0	169.418
--- a/test-data/star_stats.tabular	Fri Apr 20 01:06:25 2018 -0400
+++ b/test-data/star_stats.tabular	Wed Apr 25 07:59:52 2018 -0400
@@ -1,2 +1,2 @@
-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
+Sample	mismatch_rate	avg_input_read_length	num_annotated_splices	multimapped_toomany_percent	num_splices	uniquely_mapped	uniquely_mapped_percent	multimapped	multimapped_toomany	unmapped_tooshort	multimapped_percent	num_ATAC_splices	unmapped_tooshort_percent	total_reads	unmapped_mismatches	num_noncanonical_splices	insertion_rate	unmapped_other_percent	num_GTAG_splices	insertion_length	deletion_length	deletion_rate	unmapped_other	unmapped_mismatches_percent	num_GCAG_splices	avg_mapped_read_length
+star_log	1.73	75.0	0.0	0.0	47.0	89.0	89.0	1.0	0.0	10	1.0	0.0	10.0	100.0	0	0.0	0.0	0.0	47.0	0.0	0.0	0.0	0	0.0	0.0	74.8
--- a/test-data/tophat_stats.tabular	Fri Apr 20 01:06:25 2018 -0400
+++ b/test-data/tophat_stats.tabular	Wed Apr 25 07:59:52 2018 -0400
@@ -1,2 +1,2 @@
-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
+Sample	total_reads	concordant_aligned_percent	unaligned_total	aligned_total	aligned_multimap	aligned_discordant	overall_aligned_percent	aligned_not_multimapped_discordant
+tophat_align	316390.0	99.0	2985.0	313405.0	5638.0	34.0	99.5	307733.0