# HG changeset patch
# User iuc
# Date 1676664283 0
# Node ID 9ee34ba73ebfe304496b06b00a3135e9ee62b31f
# Parent  79b885ce78d7a4b2d2842027a8644e8e94fbe90e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266

diff -r 79b885ce78d7 -r 9ee34ba73ebf macros.xml
--- a/macros.xml	Tue Nov 01 16:57:42 2022 +0000
+++ b/macros.xml	Fri Feb 17 20:04:43 2023 +0000
@@ -1,11 +1,12 @@
 <macros>
-    <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
-    whenever you make changes to the following two version tokens!
+    <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
+    whenever you make changes to the @TOOL_VERSION@ token!
     The data manager uses a symlink to this macro file to keep the STAR and
-    the index versions in sync, but you should manually adjust the +galaxy
-    version number. -->
+    the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
     <!-- STAR version to be used -->
-    <token name="@VERSION@">2.7.8a</token>
+    <token name="@TOOL_VERSION@">2.7.10b</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
     by the current version.
@@ -14,12 +15,14 @@
     or by looking for the versionGenome parameter in source/parametersDefault
     of STAR's source code -->
     <token name="@IDX_VERSION@">2.7.4a</token>
+    <token name="@IDX_VERSION_SUFFIX@">1</token>
     <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">star</requirement>
-            <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">star</requirement>
+            <requirement type="package" version="1.16.1">samtools</requirement>
+            <requirement type="package" version="1.12">gzip</requirement>
             <yield />
         </requirements>
     </xml>
@@ -35,7 +38,7 @@
     </xml>
 
     <xml name="index_selection" token_with_gene_model="0">
-        <param argument="--genomeDir" name="genomeDir" type="select"
+        <param argument="--genomeDir" type="select"
         label="Select reference genome"
         help="If your genome of interest is not listed, contact the Galaxy team">
             <options from_data_table="@IDX_DATA_TABLE@">
@@ -55,8 +58,8 @@
             <citation type="doi">10.1093/bioinformatics/bts635</citation>
         </citations>
     </xml>
-    <xml name="@SJDBOPTIONS@" token_optional="true">
-         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
+    <xml name="SJDBOPTIONS">
+         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
          <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
     </xml>
     <xml name="dbKeyActions">
@@ -81,11 +84,16 @@
     <token name="@TEMPINDEX@"><![CDATA[
     ## Create temporary index for custom reference
     #if str($refGenomeSource.geneSource) == 'history':
+        #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
+            ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
+        #else
+            gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
+        #end if
         mkdir -p tempstargenomedir &&
         STAR
             --runMode genomeGenerate
             --genomeDir 'tempstargenomedir'
-            --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
+            --genomeFastaFiles refgenome.fa
             ## Handle difference between indices with/without annotations
             #if 'GTFconditional' in $refGenomeSource:
                 ## GTFconditional exists only in STAR, but not STARsolo
@@ -109,6 +117,8 @@
                 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
             #end if
             --runThreadN \${GALAXY_SLOTS:-4}
+            ## in bytes
+            --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
         &&
     #end if
     ]]></token>
@@ -121,17 +131,15 @@
     #else:
         '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
         ## Handle difference between indices with/without annotations
-        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
-            #if $refGenomeSource.GTFconditional.sjdbGTFfile:
-                --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
-                --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
-                #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
-                    --sjdbGTFtagExonParentTranscript Parent
-                #end if
+        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
+            --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
+            --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
+            #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
+                --sjdbGTFtagExonParentTranscript Parent
             #end if
         #end if
-        #end if
-        ]]></token>
+    #end if
+    ]]></token>
     <token name="@READSHANDLING@" ><![CDATA[
     ## Check that the input pairs are of the same type
     ## otherwise STARsolo will run for a long time and then error out.
@@ -161,8 +169,13 @@
         @FASTQ_GZ_OPTION@
     #end if
     ]]></token>
+    <token name="@LIMITS@" ><![CDATA[
+        --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
+        --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
+        --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
+    ]]></token>
     <xml name="ref_selection">
-        <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
+        <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" />
           <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
     </xml>
     <xml name="stdio" >
@@ -245,4 +258,143 @@
             <option value="None" >No adapter clipping</option>
         </param>
     </xml>
+    <xml name="common_SAM_attributes">
+        <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
+        <option value="HI" selected="true">HI (query hit index)</option>
+        <option value="AS" selected="true">AS (local alignment score)</option>
+        <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
+        <option value="NM">NM (edit distance of the aligned read to the reference)</option>
+        <option value="MD">MD (string for mismatching positions)</option>
+        <option value="jM">jM (intron motifs for all junctions)</option>
+        <option value="jI">jI (1-based start and end of introns for all junctions)</option>
+    </xml>
+    <xml name="limits">
+        <section name="junction_limits" title="Junction Limits" expanded="false">
+            <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
+            <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
+            <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
+        </section>
+    </xml>
+    <xml name="outCountActions">
+        <actions>
+            <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
+        </actions>
+    </xml>
+    <xml name="outWig">
+        <conditional name="outWig">
+            <param name="outWigType" type="select" label="Compute coverage">
+                <option value="None">No coverage</option>
+                <option value="bedGraph">Yes in bedgraph format</option>
+                <option value="wiggle">Yes in wiggle format</option>
+            </param>
+            <when value="None">
+                <!-- This is necessary for the filtering of output -->
+                <param name="outWigStrand" type="hidden" value="false" />
+            </when>
+            <when value="bedGraph">
+                <expand macro="outWigParams"/>
+            </when>
+            <when value="wiggle">
+                <expand macro="outWigParams"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="outWigParams">
+        <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
+            <option value="">Default (everything that mapped)</option>
+            <option value="read_5p">signal from only 5’ of the 1st read</option>
+            <option value="read2">signal from only 2nd read</option>
+        </param>
+        <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="collapse strands (unstranded coverage)" help="By default, the strands are separated."/>
+        <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/>
+        <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
+    </xml>
+    <token name="@OUTWIG@"><![CDATA[
+        #if str($outWig.outWigType) != 'None':
+            --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
+            --outWigStrand '$outWig.outWigStrand'
+            --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
+            --outWigNorm '$outWig.outWigNorm'
+        #end if
+    ]]></token>
+    <token name="@OUTWIGOUTPUTS@"><![CDATA[
+        #if str($outWig.outWigType) == "bedGraph":
+            && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
+            && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
+            #if str($outWig.outWigStrand) == "Stranded":
+                && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
+                && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
+            #end if
+        #elif str($outWig.outWigType) == "wiggle":
+            && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
+            && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
+            #if str($outWig.outWigStrand) == "Stranded":
+                && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
+                && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
+            #end if
+        #end if
+    ]]></token>
+    <xml name="outWigOutputs">
+        <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
+            <filter>outWig['outWigType'] != "None"</filter>
+            <expand macro="dbKeyActions" />
+            <change_format>
+                <when input="outWig.outWigType" value="wiggle" format="wig" />
+            </change_format>
+        </data>
+        <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
+            <filter>outWig['outWigType'] != "None"</filter>
+            <expand macro="dbKeyActions" />
+            <change_format>
+                <when input="outWig.outWigType" value="wiggle" format="wig" />
+            </change_format>
+        </data>
+        <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
+            <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
+            <expand macro="dbKeyActions" />
+            <change_format>
+                <when input="outWig.outWigType" value="wiggle" format="wig" />
+            </change_format>
+        </data>
+        <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
+            <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
+            <expand macro="dbKeyActions" />
+            <change_format>
+                <when input="outWig.outWigType" value="wiggle" format="wig" />
+            </change_format>
+        </data>
+    </xml>
+    <xml name="quantMode">
+        <conditional name="quantmode_output">
+            <param argument="--quantMode" type="select"
+            label="Per gene/transcript output"
+            help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
+                <option value="-">No per gene or transcript output</option>
+                <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
+                <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
+                <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
+            </param>
+            <when value="-" />
+            <when value="GeneCounts" />
+            <when value="TranscriptomeSAM">
+                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
+                label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
+                help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
+            </when>
+            <when value="TranscriptomeSAM GeneCounts">
+                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
+                label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
+                help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="quantModeNoGTF">
+        <conditional name="quantmode_output">
+            <param argument="--quantMode" type="select"
+            label="Per gene/transcript output">
+                <option value="-">No per gene or transcript output as no GTF was provided</option>
+            </param>
+            <when value="-" />
+        </conditional>
+    </xml>
 </macros>
diff -r 79b885ce78d7 -r 9ee34ba73ebf rg_rnaStarSolo.xml
--- a/rg_rnaStarSolo.xml	Tue Nov 01 16:57:42 2022 +0000
+++ b/rg_rnaStarSolo.xml	Fri Feb 17 20:04:43 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="rna_starsolo" name="RNA STARSolo" version="@VERSION@" profile="20.01" license="MIT">
+<tool id="rna_starsolo" name="RNA STARSolo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
     <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description>
     <macros>
         <import>macros.xml</import>
@@ -22,16 +22,20 @@
 
     #if str($sc.solo_type) == "CB_UMI_Simple":
     @READSHANDLING@
-    --soloCBwhitelist '$sc.soloCBwhitelist'
+    #if $sc.soloCBwhitelist:
+        --soloCBwhitelist '$sc.soloCBwhitelist'
+    #else
+        --soloCBwhitelist None
+    #end if
     ## 1 - check length of barcode, 0 - do not check
     ## Good for checking custom chemistries
     --soloBarcodeReadLength $sc.soloBarcodeReadLength
-    #if str($sc.params.chemistry) == "CR2":
+    #if str($sc.params.chemistry) == "Cv2":
     --soloCBstart 1
     --soloCBlen 16
     --soloUMIstart 17
     --soloUMIlen 10
-    #else if str($sc.params.chemistry) == "CR3":
+    #else if str($sc.params.chemistry) == "Cv3":
     --soloCBstart 1
     --soloCBlen 16
     --soloUMIstart 17
@@ -90,12 +94,20 @@
     --soloCBwhitelist None
     #end if
 
-    --soloUMIfiltering $solo.soloUMIfiltering
     --soloStrand $solo.soloStrand
     --soloFeatures $solo.soloFeatures
-    --soloUMIdedup $sc.soloUMIdedup
-    --quantMode TranscriptomeSAM
-    --outSAMtype BAM Unsorted
+    --soloUMIdedup $sc.umidedup.soloUMIdedup
+    #if str($sc.umidedup.soloUMIdedup) == "1MM_CR":
+        --soloUMIfiltering $sc.umidedup.soloUMIfiltering
+    #end if
+    --quantMode TranscriptomeSAM $solo.quantModeGene
+    #set $tag_names = str($solo.outSAMattributes).replace(',', ' ')
+    --outSAMattributes $tag_names
+    #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != 'None':
+        --outSAMtype BAM SortedByCoordinate
+    #else:
+        --outSAMtype BAM Unsorted
+    #end if
 
     #if str($solo.filter.filter_type) == "cellranger2":
     --soloCellFilter CellRanger2.2 $solo.filter.n_expected $solo.filter.max_perc $solo.filter.max_min_ratio
@@ -109,24 +121,39 @@
     ## Splice junctions are always under "raw" directory
 
     --soloOutFormatFeaturesGeneField3 '${solo.soloOutFormatFeaturesGeneField3}'
+
+    ## Limits
+    @LIMITS@
+
+    ##outWig:
+    @OUTWIG@
     ## Rename the the selected features directory
     && mv Solo.out/${solo.soloFeatures} Solo.out/soloFeatures
     ## put the barcodes and features stats into a single file
     && cat <(echo "Barcodes:") Solo.out/Barcodes.stats <(echo "Genes:") Solo.out/soloFeatures/Features.stats > '${output_stats}'
 
-    ## BAM sorting (logic copied from samtools_sort wrapper)
-    ## choosing BAM SortedByCoord appeared once to give fewer reads
-    ## than BAM Unsorted followed by a samtools sort
-    ## so better go with the latter?
+
+    #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != 'None':
+        ## recompress BAM output for smaller file size
+        && samtools view -b -o '$output_BAM' Aligned.sortedByCoord.out.bam
+    #else:
+        ## BAM sorting (logic copied from samtools_sort wrapper)
+        ## choosing BAM SortedByCoord appeared once to give fewer reads
+        ## than BAM Unsorted followed by a samtools sort
+        ## so better go with the latter?
 
-    &&
-    ##compute the number of ADDITIONAL threads to be used by samtools (-@)
-    addthreads=\${GALAXY_SLOTS:-2} && (( addthreads-- )) &&
-    ##compute the number of memory available to samtools sort (-m)
-    ##use only 75% of available: https://github.com/samtools/samtools/issues/831
-    addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
-    ((addmemory=addmemory*75/100)) &&
-    samtools sort -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" -O bam -o '$output_BAM' Aligned.out.bam
+        &&
+        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
+        addthreads=\${GALAXY_SLOTS:-2} && (( addthreads-- )) &&
+        ##compute the number of memory available to samtools sort (-m)
+        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
+        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
+        ((addmemory=addmemory*75/100)) &&
+        samtools sort -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" -O bam -o '$output_BAM' Aligned.out.bam
+    #end if
+    ##outWig:
+    @OUTWIGOUTPUTS@
+
     ]]></command>
     <configfiles>
         <configfile name="manifest_file" >
@@ -170,13 +197,13 @@
                     </when>
                     <when value="without-gtf">
                         <expand macro="index_selection" with_gene_model="0" />
-                        <expand macro="@SJDBOPTIONS@" optional="false" />
+                        <expand macro="SJDBOPTIONS"/>
                     </when>
                 </conditional>
             </when>
             <when value="history">
                 <expand macro="ref_selection" />
-                <expand macro="@SJDBOPTIONS@" optional="false"/>
+                <expand macro="SJDBOPTIONS"/>
             </when>
         </conditional>
         <conditional name="sc" >
@@ -187,15 +214,15 @@
             </param>
             <when value="CB_UMI_Simple">
                 <expand macro="input_selection" />
-                <param format="txt,tsv" argument="--soloCBwhitelist" type="data" label="RNA-Seq Cell Barcode Whitelist"/>
+                <param format="txt,tsv" argument="--soloCBwhitelist" optional="True" type="data" label="RNA-Seq Cell Barcode Whitelist"/>
                 <conditional name="params" >
                     <param name="chemistry" type="select" label="Configure Chemistry Options">
-                        <option value="CR2" selected="true">Cell Ranger v2</option>
-                        <option value="CR3">Cell Ranger v3</option>
+                        <option value="Cv2" selected="true">Chromium chemistry v2</option>
+                        <option value="Cv3">Chromium chemistry v3</option>
                         <option value="custom">Custom</option>
                     </param>
-                    <when value="CR2" />
-                    <when value="CR3" />
+                    <when value="Cv2" />
+                    <when value="Cv3" />
                     <when value="custom" >
                         <param argument="--soloCBstart" type="integer" min="1" value="1" label="Cell Barcode Start Base" />
                         <param argument="--soloCBlen" type="integer" min="1" value="16" label="Cell Barcode Length" />
@@ -219,11 +246,25 @@
                     </when>
                 </conditional>
                 <param argument="--soloBarcodeReadLength" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Barcode Size is same size of the Read" help="Disable this if your R1 barcodes contain poly-T bases after the barcode sequence." />
-                <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
-                    <expand macro="umidedup_options" />
-                    <option value="Exact" >Exact</option>
-                    <option value="1MM_CR" >CellRanger2-4 algorithm</option>
-                </param>
+                <conditional name="umidedup">
+                    <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
+                        <expand macro="umidedup_options" />
+                        <option value="Exact" >Exact</option>
+                        <option value="1MM_CR" >CellRanger2-4 algorithm</option>
+                    </param>
+                    <when value="1MM_All"/>
+                    <when value="1MM_Directional_UMItools"/>
+                    <when value="1MM_Directional"/>
+                    <when value="Exact"/>
+                    <when value="1MM_CR">
+                        <param argument="--soloUMIfiltering" type="select" label="Type of UMI filtering" >
+                            <option value="-" selected="true">Remove UMIs with N and homopolymers (similar to CellRanger 2.2.0)</option>
+                            <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option>
+                            <option value="MultiGeneUMI_All" >Remove all UMIs that map to more than one gene</option>
+                            <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option>
+                        </param>                 
+                    </when>
+                </conditional>
                 <param argument="--soloCBmatchWLtype" type="select" label="Matching the Cell Barcodes to the WhiteList" help="Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed
     CBs have to have at least one read with exact match; 1MM_multi: multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches; 1MM_multi_pseudocounts: same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes.">
                     <expand macro="cb_match_wl_common" />
@@ -252,23 +293,46 @@
                 </param>
                 <param name="umi_end_anchor_pos" type="integer" value="0" label="0-based position of the UMI end with respect to the anchor base" />
                 <expand macro="solo_adapter_params" />
-                <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
-                    <expand macro="umidedup_options" />
-                    <option value="Exact" >Exact</option>
-                    <option value="1MM_CR" >CellRanger2-4 algorithm</option>
-                </param>
+                <conditional name="umidedup">
+                    <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
+                        <expand macro="umidedup_options" />
+                        <option value="Exact" >Exact</option>
+                        <option value="1MM_CR" >CellRanger2-4 algorithm</option>
+                    </param>
+                    <when value="1MM_All"/>
+                    <when value="1MM_Directional_UMItools"/>
+                    <when value="1MM_Directional"/>
+                    <when value="Exact"/>
+                    <when value="1MM_CR">
+                        <param argument="--soloUMIfiltering" type="select" label="Type of UMI filtering" >
+                            <option value="-" selected="true">Remove UMIs with N and homopolymers (similar to CellRanger 2.2.0)</option>
+                            <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option>
+                            <option value="MultiGeneUMI_All" >Remove all UMIs that map to more than one gene</option>
+                            <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option>
+                        </param>                 
+                    </when>
+                </conditional>
                 <param argument="--soloCBmatchWLtype" type="select" label="Matching the Cell Barcodes to the WhiteList" help="Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed
     CBs have to have at least one read with exact match; 1MM_multi: multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches; 1MM_multi_pseudocounts: same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes.">
                     <expand macro="cb_match_wl_common" />
+                    <!-- should we add EditDist_2? -->
                 </param>
             </when>
             <when value="SmartSeq">
                 <expand macro="input_selection_smart_seq" />
                 <param name="cell_ids" format="txt,tsv" type="data" label="File containing cell IDs of the samples. One ID per line in order of samples in the above collection."/>
-                <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
-                    <option value="Exact" >Exact</option>
-                    <option value="NoDedup">Do not deduplicate UMIs</option>
-                </param>
+                <conditional name="umidedup">
+                    <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.">
+                        <expand macro="umidedup_options" />
+                        <option value="Exact" >Exact</option>
+                        <option value="NoDedup" >CellRanger2-4 algorithm</option>
+                    </param>
+                    <when value="1MM_All"/>
+                    <when value="1MM_Directional_UMItools"/>
+                    <when value="1MM_Directional"/>
+                    <when value="Exact"/>
+                    <when value="NoDedup"/>
+                </conditional>
             </when>
         </conditional>
         <section name="solo" title="Advanced Settings" expanded="true">
@@ -281,11 +345,8 @@
                 <option value="Gene" selected="true">Gene: Count reads matching the Gene Transcript</option>
                 <option value="SJ" >Splice Junctions: Count reads at exon-intron junctions</option>
                 <option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option>
-            </param>
-            <param argument="--soloUMIfiltering" type="select" label="Type of UMI filtering" >
-                <option value="-" selected="true">Remove UMIs with N and homopolymers (similar to CellRanger 2.2.0)</option>
-                <option value="MultiGeneUMI" >Remove lower-count UMIs that map to more than one gene</option>
-                <option value="MultiGeneUMI_CR" >Remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0</option>
+                <option value="GeneFull_ExonOverIntron" >Full: Count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons</option>
+                <option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option>
             </param>
             <conditional name="filter" >
                 <param name="filter_type" type="select" label="Cell filtering type and parameters" >
@@ -298,6 +359,7 @@
                     <param name="n_expected" type="integer" min="1" value="3000" label="Number of expected cells" />
                     <param name="max_perc" type="float" min="0" max="1" value="0.99" label="Robust maximum percentile for UMI count" />
                     <param name="max_min_ratio" type="float" min="1" value="10" label="Maximum to minimum ratio for UMI count" />
+                    <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" />
                 </when>
                 <when value="emptydrops" >
                     <param name="nExpectedCells" type="integer" min="1" value="3000" label="Number of expected cells" />
@@ -310,14 +372,31 @@
                     <param name="candMaxN" type="integer" value="20000" label="Number of extra barcodes after initial cell calling" />
                     <param name="FDR" type="float" value="0.01" label="Maximum adjusted p-value for determining a barcode as non-ambient" />
                     <param name="simN" type="integer" value="10000" label="Number of log likelihood simulations" />
+                    <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" />
                 </when>
                 <when value="topcells" >
                     <param name="n_cells" type="integer" min="1" value="3000" label="Number of top cells to report sorted by UMI count" />
+                    <param name="output_raw" type="boolean" checked="false" label="Output raw matrix in addition to filtered one" />
                 </when>
-                <when value="no_filter" />
+                <when value="no_filter">
+                    <param name="output_raw" type="hidden" value="true" />
+                </when>
             </conditional>
             <param argument="--soloOutFormatFeaturesGeneField3" type="text" value="Gene Expression" label="Field 3 in the Genes output." help="Input '-' to remove the 3rd column from the output." />
+            <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true"
+            label="Read alignment tags to include in the BAM output">
+                <expand macro="common_SAM_attributes"/>
+                <option value="CR">CR Cellular barcode sequence bases (uncorrected)</option>
+                <option value="CY">CY Phred quality of the cellular barcode sequence in the CR tag</option>
+                <option value="GX">GX Gene ID</option>
+                <option value="GN">GN Gene name</option>
+                <option value="CB">CB Cell identifier (corrected)</option>
+                <option value="UB">UB UMI (corrected)</option>
+            </param>
+            <param name="quantModeGene" type="boolean" truevalue="GeneCounts" falsevalue="" checked="false" label="Output global gene count" help="Can be used by MultiQC" />
+            <expand macro="limits" />
         </section>
+        <expand macro="outWig"/>
     </inputs>
     <outputs>
         <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
@@ -333,7 +412,7 @@
         <!-- soloCellFilter set to None, if SJ is selected for soloFeatures -->
         <data format="tsv" name="output_genes" label="${tool.name} on ${on_string}: Genes raw"
               from_work_dir="Solo.out/soloFeatures/raw/features.tsv" >
-              <filter>solo['filter']['filter_type'] == "no_filter" or solo['soloFeatures'] == "SJ" </filter>
+              <filter>solo['filter']['output_raw'] or solo['soloFeatures'] == "SJ" </filter>
         </data>
         <data format="tsv" name="output_genes_filtered" label="${tool.name} on ${on_string}: Genes filtered"
               from_work_dir="Solo.out/soloFeatures/filtered/features.tsv" >
@@ -341,7 +420,7 @@
         </data>
         <data format="tsv" name="output_barcodes" label="${tool.name} on ${on_string}: Barcodes raw"
               from_work_dir="Solo.out/soloFeatures/raw/barcodes.tsv" >
-              <filter>solo['filter']['filter_type'] == "no_filter" or solo['soloFeatures'] == "SJ" </filter>
+              <filter>solo['filter']['output_raw'] or solo['soloFeatures'] == "SJ" </filter>
         </data>
         <data format="tsv" name="output_barcodes_filtered" label="${tool.name} on ${on_string}: Barcodes filtered"
               from_work_dir="Solo.out/soloFeatures/filtered/barcodes.tsv" >
@@ -349,7 +428,7 @@
         </data>
         <data format="mtx" name="output_matrix" label="${tool.name} on ${on_string}: Matrix Gene Counts raw"
               from_work_dir="Solo.out/soloFeatures/raw/matrix.mtx" >
-            <filter>solo['soloFeatures'] == "Gene" and solo['filter']['filter_type'] == "no_filter" </filter>
+            <filter>solo['soloFeatures'] == "Gene" and solo['filter']['output_raw'] </filter>
             <expand macro="dbKeyActions" />
         </data>
         <data format="mtx" name="output_matrix_filtered" label="${tool.name} on ${on_string}: Matrix Gene Counts filtered"
@@ -364,18 +443,24 @@
         </data>
         <data format="mtx" name="output_matrixGeneFull" label="${tool.name} on ${on_string}: Matrix Full Gene Counts raw"
               from_work_dir="Solo.out/soloFeatures/raw/matrix.mtx" >
-            <filter>solo['soloFeatures'] == "GeneFull" and solo['filter']['filter_type'] == "no_filter" </filter>
+            <filter>"GeneFull" in solo['soloFeatures'] and solo['filter']['output_raw'] </filter>
             <expand macro="dbKeyActions" />
         </data>
         <data format="mtx" name="output_matrixGeneFull_filtered" label="${tool.name} on ${on_string}: Matrix Full Gene Counts filtered"
               from_work_dir="Solo.out/soloFeatures/filtered/matrix.mtx" >
-            <filter>solo['soloFeatures'] == "GeneFull" and solo['filter']['filter_type'] != "no_filter" </filter>
+            <filter>"GeneFull" in solo['soloFeatures'] and solo['filter']['filter_type'] != "no_filter" </filter>
             <expand macro="dbKeyActions" />
         </data>
         <data format="bam" name="output_BAM" label="${tool.name} on ${on_string}: Alignments" >
             <expand macro="dbKeyActions" />
         </data>
         <data format="txt" name="output_stats" label="${tool.name} on ${on_string}: Barcode/Feature Statistic Summaries"/>
+        <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: combined reads per gene" from_work_dir="ReadsPerGene.out.tab">
+            <filter>solo['quantModeGene']</filter>
+            <expand macro="dbKeyActions" />
+            <expand macro="outCountActions" />
+        </data>
+        <expand macro="outWigOutputs"/>
     </outputs>
     <!-- Generating test data that is big enough for STARsolo to detect and small enough
          for Galaxy to test requires careful modification of input FASTA and GTF data,
@@ -386,7 +471,8 @@
          here: https://gist.github.com/mtekman/149a7c52fd73e5d8ebe49f5a27b0743d
     -->
     <tests>
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="7">
+            <!-- test 1 -->
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
                 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
@@ -403,9 +489,11 @@
                 </conditional>
                 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
                 <conditional name="params">
-                    <param name="chemistry" value="CR3" />
+                    <param name="chemistry" value="Cv3" />
                 </conditional>
-                <param name="soloUMIdedup" value="1MM_All" />
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="1MM_All" />
+                </conditional>
             </conditional>
             <section name="solo" >
                 <conditional name="filter">
@@ -413,35 +501,47 @@
                 </conditional>
                 <param name="soloStrand" value="Forward" />
                 <param name="soloFeatures" value="Gene" />
+                <param name="quantModeGene" value="true" />
             </section>
             <output name="output_barcodes" >
                 <assert_contents>
                     <!-- first and last line -->
                     <has_line line="AAACCTGAGCGCTCCA" />
                     <has_line line="TTTGGTTAGTGGGCTA" />
+                    <has_n_lines n="394" />
                 </assert_contents>
             </output>
             <output name="output_genes">
                 <assert_contents>
                     <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
                     <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
+                    <has_n_lines n="14" />
                 </assert_contents>
             </output>
             <output name="output_matrix" >
                 <assert_contents>
                     <has_line_matching expression="14\s+394\s+7" />
                     <has_line_matching expression="4\s+381\s+1" />
+                    <has_n_lines n="10" />
                 </assert_contents>
             </output>
             <output name="output_stats" >
                 <assert_contents>
-                    <has_line_matching expression="\s+nUnmapped\s+5823" />
-                    <has_line_matching expression="\s+nUMIs\s+8" />
+                    <has_line_matching expression="\s+noUnmapped\s+5823" />
+                    <has_line_matching expression="\s+yesUMIs\s+8" />
                 </assert_contents>
             </output>
             <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
+            <output name="reads_per_gene" >
+                <assert_contents>
+                    <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />
+                    <has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" />
+                </assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="6"><!-- same as above, but using custom -->
+        <test expect_num_outputs="6">
+            <!-- test 2 -->
+            <!-- same as above, but using custom and no reads_per_gene-->
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
                 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
@@ -471,31 +571,37 @@
             </section>
             <output name="output_barcodes_filtered" >
                 <assert_contents>
+                    <!-- first and last line -->
                     <has_line line="ACACCGGTCTAACGGT" />
                     <has_line line="TTCTCAATCCACGTTC" />
+                    <has_n_lines n="7" />
                 </assert_contents>
             </output>
             <output name="output_genes_filtered">
                 <assert_contents>
                     <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
                     <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
+                    <has_n_lines n="14" />
                 </assert_contents>
             </output>
             <output name="output_matrix_filtered" >
                 <assert_contents>
                     <has_line_matching expression="14\s+7\s+7" />
                     <has_line_matching expression="4\s+7\s+1" />
+                    <has_n_lines n="10" />
                 </assert_contents>
             </output>
             <output name="output_stats" >
                 <assert_contents>
-                    <has_line_matching expression="\s+nUnmapped\s+5823" />
-                    <has_line_matching expression="\s+nUMIs\s+8" />
+                    <has_line_matching expression="\s+noUnmapped\s+5823" />
+                    <has_line_matching expression="\s+yesUMIs\s+8" />
                 </assert_contents>
             </output>
             <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
         </test>
-        <test expect_num_outputs="6"><!-- Multiple repeats test -->
+        <test expect_num_outputs="6">
+            <!-- test 3 -->
+            <!-- Multiple repeats test -->
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
                 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
@@ -512,9 +618,11 @@
                 </conditional>
                 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
                 <conditional name="params">
-                    <param name="chemistry" value="CR3" />
+                    <param name="chemistry" value="Cv3" />
                 </conditional>
-                <param name="soloUMIdedup" value="1MM_All" />
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="1MM_All" />
+                </conditional>
             </conditional>
             <section name="solo" >
                 <param name="soloStrand" value="Forward" />
@@ -524,11 +632,17 @@
                 <assert_contents>
                     <has_line line="ACACCGGTCTAACGGT" />
                     <has_line line="TTCTCAATCCACGTTC" />
+                    <has_n_lines n="7" />
                 </assert_contents>
             </output>
-            <!-- BAM output is huge, we don't need to test here -->
+            <output name="output_BAM" >
+                <assert_contents>
+                    <has_size value="166147" delta="600" />
+                </assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="10">
+            <!-- test 4 -->
             <!-- Test with paired collection -->
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
@@ -550,24 +664,35 @@
                 </conditional>
                 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
                 <conditional name="params">
-                    <param name="chemistry" value="CR3" />
+                    <param name="chemistry" value="Cv3" />
                 </conditional>
-                <param name="soloUMIdedup" value="1MM_All" />
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="1MM_All" />
+                </conditional>
             </conditional>
             <section name="solo" >
                 <param name="soloStrand" value="Forward" />
                 <param name="soloFeatures" value="Gene" />
             </section>
+            <conditional name="outWig">
+                <param name="outWigType" value="bedGraph" />
+            </conditional>
             <output name="output_barcodes_filtered" >
                 <assert_contents>
                     <has_line line="ACACCGGTCTAACGGT" />
                     <has_line line="TTCTCAATCCACGTTC" />
+                    <has_n_lines n="7" />
                 </assert_contents>
             </output>
             <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
+            <output name="signal_unique_str1" file="Signal.Unique.str1.out.bg" />
+            <output name="signal_uniquemultiple_str1" file="Signal.UniqueMultiple.str1.out.bg" />
+            <output name="signal_unique_str2" file="Signal.Unique.str2.out.bg" />
+            <output name="signal_uniquemultiple_str2" file="Signal.UniqueMultiple.str2.out.bg" />
         </test>
-        <test expect_num_outputs="6">
-            <!-- Test soloFeatures, soloCBmatchWLtype, soloCellFilter, soloOutFormatFeaturesGeneField3, soloUMIfiltering -->
+        <test expect_num_outputs="9">
+            <!-- test 5 -->
+            <!-- Test soloFeatures, soloCBmatchWLtype, soloCellFilter, soloOutFormatFeaturesGeneField3 -->
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
                 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
@@ -585,17 +710,19 @@
                 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
                 <param name="soloCBmatchWLtype" value="1MM_multi_pseudocounts" />
                 <conditional name="params">
-                    <param name="chemistry" value="CR3" />
+                    <param name="chemistry" value="Cv3" />
                 </conditional>
-                <param name="soloUMIdedup" value="1MM_All" />
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="1MM_All" />
+                </conditional>
             </conditional>
             <section name="solo" >
-                <param name="soloUMIfiltering" value="MultiGeneUMI" />
                 <param name="soloStrand" value="Forward" />
                 <param name="soloFeatures" value="GeneFull" />
                 <conditional name="filter">
                     <param name="filter_type" value="topcells" />
                     <param name="n_cells" value="5" />
+                    <param name="output_raw" value="true" />
                 </conditional>
                 <param name="soloOutFormatFeaturesGeneField3" value="Dummy Text" />
             </section>
@@ -604,22 +731,48 @@
                     <!-- first and last line -->
                     <has_line line="AGACGTTCAAGGCTCC" />
                     <has_line line="TCAACGAAGCTAGTGG" />
+                    <has_n_lines n="6" />
                 </assert_contents>
             </output>
             <output name="output_genes_filtered" >
                 <assert_contents>
                     <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" />
                     <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" />
+                    <has_n_lines n="14" />
                 </assert_contents>
             </output>
             <output name="output_matrixGeneFull_filtered" >
                 <assert_contents>
                     <has_line_matching expression="14\s+6\s+14" />
                     <has_line_matching expression="10\s+6\s+1" />
+                    <has_n_lines n="17" />
+                </assert_contents>
+            </output>
+            <output name="output_barcodes" >
+                <assert_contents>
+                    <!-- first and last line -->
+                    <has_line line="AAACCTGAGCGCTCCA" />
+                    <has_line line="TTTGGTTAGTGGGCTA" />
+                    <has_n_lines n="394" />
+                </assert_contents>
+            </output>
+            <output name="output_genes">
+                <assert_contents>
+                    <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" />
+                    <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" />
+                    <has_n_lines n="14" />
+                </assert_contents>
+            </output>
+            <output name="output_matrix" >
+                <assert_contents>
+                    <has_line_matching expression="14\s+394\s+195" />
+                    <has_line_matching expression="3\s+1\s+1" />
+                    <has_n_lines n="198" />
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="6">
+            <!-- test 6 -->
             <!-- Emptydrops filtering -->
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
@@ -637,9 +790,11 @@
                 </conditional>
                 <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
                 <conditional name="params">
-                    <param name="chemistry" value="CR3" />
+                    <param name="chemistry" value="Cv3" />
                 </conditional>
-                <param name="soloUMIdedup" value="1MM_All" />
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="1MM_All" />
+                </conditional>
             </conditional>
             <section name="solo" >
                 <conditional name="filter">
@@ -663,29 +818,33 @@
                     <!-- first and last line -->
                     <has_line line="ACACCGGTCTAACGGT" />
                     <has_line line="TTCTCAATCCACGTTC" />
+                    <has_n_lines n="7" />
                 </assert_contents>
             </output>
             <output name="output_genes_filtered">
                 <assert_contents>
                     <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
                     <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
+                    <has_n_lines n="14" />
                 </assert_contents>
             </output>
             <output name="output_matrix_filtered" >
                 <assert_contents>
                     <has_line_matching expression="14\s+7\s+7" />
                     <has_line_matching expression="4\s+7\s+1" />
+                    <has_n_lines n="10" />
                 </assert_contents>
             </output>
             <output name="output_stats" >
                 <assert_contents>
-                    <has_line_matching expression="\s+nUnmapped\s+5823" />
-                    <has_line_matching expression="\s+nUMIs\s+8" />
+                    <has_line_matching expression="\s+noUnmapped\s+5823" />
+                    <has_line_matching expression="\s+yesUMIs\s+8" />
                 </assert_contents>
             </output>
             <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
         </test>
         <test expect_num_outputs="6">
+            <!-- test 7 -->
             <!-- Test soloType CB_UMI_Complex -->
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
@@ -722,7 +881,9 @@
                 <param name="soloAdapterSequence" value="GAGTGATTGCTTGTGACGCCTT"  />
                 <param name="soloAdapterMismatchesNmax" value="1" />
                 <param name="clipAdapterType" value="CellRanger4" />
-                <param name="soloUMIdedup" value="1MM_All" />
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="1MM_All" />
+                </conditional>
                 <param name="soloCBmatchWLtype" value="1MM" />
             </conditional>
             <output name="output_barcodes_filtered" >
@@ -730,28 +891,32 @@
                     <!-- first and last line -->
                     <has_line line="ACAACGTGG_AAACCTCC" />
                     <has_line line="ATTCCAGAC_TTCGCTGG" />
+                    <has_n_lines n="33" />
                 </assert_contents>
             </output>
             <output name="output_genes_filtered">
                 <assert_contents>
                     <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
                     <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
+                    <has_n_lines n="14" />
                 </assert_contents>
             </output>
             <output name="output_matrix_filtered" >
                 <assert_contents>
                     <has_line_matching expression="14\s+33\s+36" />
                     <has_line_matching expression="2\s+33\s+1" />
+                    <has_n_lines n="39" />
                 </assert_contents>
             </output>
             <output name="output_stats" >
                 <assert_contents>
-                    <has_line_matching expression="\s+nExactMatch\s+791" />
-                    <has_line_matching expression="\s+nUMIs\s+36" />
+                    <has_line_matching expression="\s+yesWLmatchExact\s+791" />
+                    <has_line_matching expression="\s+yesUMIs\s+36" />
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="6">
+            <!-- test 8 -->
             <!-- Test soloType SmartSeq -->
             <conditional name="refGenomeSource">
                 <param name="geneSource" value="history" />
@@ -824,7 +989,9 @@
                     </param>
                 </conditional>
                 <param name="cell_ids" value="smartseq.cellids.txt" />
-                <param name="soloUMIdedup" value="Exact" />
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="Exact" />
+                </conditional>
             </conditional>
             <section name="solo" >
                 <param name="soloStrand" value="Unstranded" />
@@ -837,24 +1004,152 @@
                 <assert_contents>
                     <has_line line="CSC6_D02" />
                     <not_has_text text="MGH26_A02" />
+                    <has_n_lines n="3" />
                 </assert_contents>
             </output>
             <output name="output_genes_filtered">
                 <assert_contents>
                     <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
                     <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
+                    <has_n_lines n="14" />
                 </assert_contents>
             </output>
             <output name="output_matrix_filtered" >
                 <assert_contents>
                     <has_line_matching expression="14\s+3\s+10" />
                     <has_line_matching expression="12\s+3\s+1" />
+                    <has_n_lines n="13" />
                 </assert_contents>
             </output>
             <output name="output_stats" >
                 <assert_contents>
-                    <has_line_matching expression="\s+nExactMatch\s+9000" />
-                    <has_line_matching expression="\s+nUMIs\s+32" />
+                    <has_line_matching expression="\s+yesWLmatchExact\s+9000" />
+                    <has_line_matching expression="\s+yesUMIs\s+32" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="6">
+            <!-- test 9 -->
+            <!-- Test outSAMattributes -->
+            <conditional name="refGenomeSource">
+                <param name="geneSource" value="history" />
+                <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
+                <param name="genomeSAindexNbases" value="4" />
+                <param name="sjdbOverhang" value="100" />
+                <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
+            </conditional>
+            <conditional name="sc" >
+                <param name="solo_type" value="CB_UMI_Simple" />
+                <conditional name="input_types">
+                    <param name="use" value="repeat" />
+                    <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
+                    <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
+                </conditional>
+                <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
+                <conditional name="params">
+                    <param name="chemistry" value="Cv3" />
+                </conditional>
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="1MM_All" />
+                </conditional>
+            </conditional>
+            <section name="solo" >
+                <conditional name="filter">
+                    <param name="filter_type" value="no_filter" />
+                </conditional>
+                <param name="soloStrand" value="Forward" />
+                <param name="soloFeatures" value="Gene" />
+                <param name="outSAMattributes" value="NH,HI,AS,nM,GX,GN,CB,UB" />
+            </section>
+            <output name="output_barcodes" >
+                <assert_contents>
+                    <!-- first and last line -->
+                    <has_line line="AAACCTGAGCGCTCCA" />
+                    <has_line line="TTTGGTTAGTGGGCTA" />
+                    <has_n_lines n="394" />
+                </assert_contents>
+            </output>
+            <output name="output_genes">
+                <assert_contents>
+                    <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
+                    <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
+                    <has_n_lines n="14" />
+                </assert_contents>
+            </output>
+            <output name="output_matrix" >
+                <assert_contents>
+                    <has_line_matching expression="14\s+394\s+7" />
+                    <has_line_matching expression="4\s+381\s+1" />
+                    <has_n_lines n="10" />
+                </assert_contents>
+            </output>
+            <output name="output_stats" >
+                <assert_contents>
+                    <has_line_matching expression="\s+noUnmapped\s+5823" />
+                    <has_line_matching expression="\s+yesUMIs\s+8" />
+                </assert_contents>
+            </output>
+            <output name="output_BAM" >
+                <assert_contents>
+                    <has_size value="153108" delta="600" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="6">
+            <!-- test 10 -->
+            <!-- Test soloFeatures -->
+            <conditional name="refGenomeSource">
+                <param name="geneSource" value="history" />
+                <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
+                <param name="genomeSAindexNbases" value="4" />
+                <param name="sjdbOverhang" value="100" />
+                <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
+            </conditional>
+            <conditional name="sc" >
+                <param name="solo_type" value="CB_UMI_Simple" />
+                <conditional name="input_types">
+                    <param name="use" value="repeat" />
+                    <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
+                    <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
+                </conditional>
+                <param name="soloCBwhitelist" value="filtered.barcodes.txt" />
+                <param name="soloCBmatchWLtype" value="1MM_multi_pseudocounts" />
+                <conditional name="params">
+                    <param name="chemistry" value="Cv3" />
+                </conditional>
+                <conditional name="umidedup">
+                    <param name="soloUMIdedup" value="1MM_CR" />
+                    <param name="soloUMIfiltering" value="MultiGeneUMI" />
+                </conditional>
+            </conditional>
+            <section name="solo" >
+                <param name="soloStrand" value="Forward" />
+                <param name="soloFeatures" value="GeneFull_ExonOverIntron" />
+                <conditional name="filter">
+                    <param name="filter_type" value="no_filter" />
+                </conditional>
+                <param name="soloOutFormatFeaturesGeneField3" value="Dummy Text" />
+            </section>
+            <output name="output_barcodes" >
+                <assert_contents>
+                    <!-- first and last line -->
+                    <has_line line="AAACCTGAGCGCTCCA" />
+                    <has_line line="TTTGGTTAGTGGGCTA" />
+                    <has_n_lines n="394" />
+                </assert_contents>
+            </output>
+            <output name="output_genes" >
+                <assert_contents>
+                    <has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Dummy\s+Text" />
+                    <has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Dummy\s+Text" />
+                    <has_n_lines n="14" />
+                </assert_contents>
+            </output>
+            <output name="output_matrixGeneFull" >
+                <assert_contents>
+                    <has_line_matching expression="14\s+394\s+104" />
+                    <has_line_matching expression="10\s+2\s+1" />
+                    <has_n_lines n="107" />
                 </assert_contents>
             </output>
         </test>
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/Signal.Unique.str1.out.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Signal.Unique.str1.out.bg	Fri Feb 17 20:04:43 2023 +0000
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diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/Signal.Unique.str2.out.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Signal.Unique.str2.out.bg	Fri Feb 17 20:04:43 2023 +0000
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diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/Signal.UniqueMultiple.str1.out.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Signal.UniqueMultiple.str1.out.bg	Fri Feb 17 20:04:43 2023 +0000
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diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/Signal.UniqueMultiple.str2.out.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Signal.UniqueMultiple.str2.out.bg	Fri Feb 17 20:04:43 2023 +0000
@@ -0,0 +1,1520 @@
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diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/filtered3.bam
Binary file test-data/filtered3.bam has changed
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/rnastar_test_mapped_reads_PE.bam
Binary file test-data/rnastar_test_mapped_reads_PE.bam has changed
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/rnastar_test_splicejunctions_PE.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_splicejunctions_PE.bed	Fri Feb 17 20:04:43 2023 +0000
@@ -0,0 +1,2 @@
+test_chromosome	251	350	1	1	0	51	0	37
+test_chromosome	401	500	1	1	0	41	0	36
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_Signal.Unique.both.read2.out.wig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_Signal.Unique.both.read2.out.wig	Fri Feb 17 20:04:43 2023 +0000
@@ -0,0 +1,290 @@
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diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_rev_Signal.Unique.str1.out.bg
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_rev_Signal.Unique.str2.out.bg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_rev_Signal.Unique.str2.out.bg	Fri Feb 17 20:04:43 2023 +0000
@@ -0,0 +1,124 @@
+test_chromosome	58	59	10416.66667
+test_chromosome	59	65	20833.33333
+test_chromosome	65	70	31250.00000
+test_chromosome	70	72	41666.66667
+test_chromosome	72	75	52083.33333
+test_chromosome	75	79	62500.00000
+test_chromosome	79	87	72916.66667
+test_chromosome	87	93	83333.33333
+test_chromosome	93	95	93750.00000
+test_chromosome	95	97	104166.66667
+test_chromosome	97	99	114583.33333
+test_chromosome	99	100	125000.00000
+test_chromosome	100	102	135416.66667
+test_chromosome	102	107	145833.33333
+test_chromosome	107	112	177083.33333
+test_chromosome	112	118	187500.00000
+test_chromosome	118	121	197916.66667
+test_chromosome	121	128	218750.00000
+test_chromosome	128	130	229166.66667
+test_chromosome	130	131	260416.66667
+test_chromosome	131	132	270833.33333
+test_chromosome	132	133	260416.66667
+test_chromosome	133	136	250000.00000
+test_chromosome	136	137	270833.33333
+test_chromosome	137	138	281250.00000
+test_chromosome	138	140	302083.33333
+test_chromosome	140	145	291666.66667
+test_chromosome	145	147	281250.00000
+test_chromosome	147	150	270833.33333
+test_chromosome	150	152	260416.66667
+test_chromosome	152	153	270833.33333
+test_chromosome	153	154	291666.66667
+test_chromosome	154	155	312500.00000
+test_chromosome	155	156	322916.66667
+test_chromosome	156	159	333333.33333
+test_chromosome	159	160	343750.00000
+test_chromosome	160	161	354166.66667
+test_chromosome	161	163	364583.33333
+test_chromosome	163	164	375000.00000
+test_chromosome	164	165	385416.66667
+test_chromosome	165	167	406250.00000
+test_chromosome	167	168	416666.66667
+test_chromosome	168	169	406250.00000
+test_chromosome	169	171	427083.33333
+test_chromosome	171	172	437500.00000
+test_chromosome	172	177	427083.33333
+test_chromosome	177	182	416666.66667
+test_chromosome	182	183	385416.66667
+test_chromosome	183	187	395833.33333
+test_chromosome	187	194	385416.66667
+test_chromosome	194	196	395833.33333
+test_chromosome	196	199	385416.66667
+test_chromosome	199	200	406250.00000
+test_chromosome	200	204	416666.66667
+test_chromosome	204	205	427083.33333
+test_chromosome	205	207	406250.00000
+test_chromosome	207	209	416666.66667
+test_chromosome	209	211	427083.33333
+test_chromosome	211	212	406250.00000
+test_chromosome	212	213	385416.66667
+test_chromosome	213	220	375000.00000
+test_chromosome	220	224	385416.66667
+test_chromosome	224	226	395833.33333
+test_chromosome	226	227	406250.00000
+test_chromosome	227	228	395833.33333
+test_chromosome	228	229	385416.66667
+test_chromosome	229	232	354166.66667
+test_chromosome	232	233	364583.33333
+test_chromosome	233	234	375000.00000
+test_chromosome	234	235	364583.33333
+test_chromosome	235	236	343750.00000
+test_chromosome	236	238	333333.33333
+test_chromosome	238	239	322916.66667
+test_chromosome	239	240	312500.00000
+test_chromosome	240	242	291666.66667
+test_chromosome	242	243	302083.33333
+test_chromosome	243	244	312500.00000
+test_chromosome	244	245	291666.66667
+test_chromosome	245	246	281250.00000
+test_chromosome	246	249	270833.33333
+test_chromosome	249	250	260416.66667
+test_chromosome	350	351	291666.66667
+test_chromosome	351	352	302083.33333
+test_chromosome	352	353	312500.00000
+test_chromosome	353	354	322916.66667
+test_chromosome	354	357	333333.33333
+test_chromosome	357	358	343750.00000
+test_chromosome	358	359	333333.33333
+test_chromosome	359	361	343750.00000
+test_chromosome	361	365	354166.66667
+test_chromosome	365	369	364583.33333
+test_chromosome	369	370	343750.00000
+test_chromosome	370	372	354166.66667
+test_chromosome	372	374	375000.00000
+test_chromosome	374	379	354166.66667
+test_chromosome	379	380	333333.33333
+test_chromosome	380	381	322916.66667
+test_chromosome	381	383	312500.00000
+test_chromosome	383	395	302083.33333
+test_chromosome	395	399	291666.66667
+test_chromosome	399	400	281250.00000
+test_chromosome	500	505	260416.66667
+test_chromosome	505	506	250000.00000
+test_chromosome	506	507	239583.33333
+test_chromosome	507	508	229166.66667
+test_chromosome	508	516	218750.00000
+test_chromosome	516	517	208333.33333
+test_chromosome	517	518	187500.00000
+test_chromosome	518	521	177083.33333
+test_chromosome	521	522	166666.66667
+test_chromosome	522	524	156250.00000
+test_chromosome	524	526	145833.33333
+test_chromosome	526	527	135416.66667
+test_chromosome	527	528	125000.00000
+test_chromosome	528	529	114583.33333
+test_chromosome	529	532	104166.66667
+test_chromosome	532	534	93750.00000
+test_chromosome	534	536	83333.33333
+test_chromosome	536	540	72916.66667
+test_chromosome	540	543	62500.00000
+test_chromosome	543	545	52083.33333
+test_chromosome	545	547	41666.66667
+test_chromosome	547	549	20833.33333
+test_chromosome	549	550	10416.66667
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_revlib_R1.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_revlib_R1.fastqsanger	Fri Feb 17 20:04:43 2023 +0000
@@ -0,0 +1,192 @@
+@test_mRNA_150_290_0/1
+TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_255_2/1
+GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_72_258_4/1
+GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_107_286_5/1
+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_122_299_6/1
+CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_234_7/1
+AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_155_9/1
+TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_230_b/1
+TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_276_c/1
+CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_268_d/1
+CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_118_297_f/1
+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_16_194_10/1
+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_266_13/1
+AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_218_16/1
+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_195_17/1
+ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_126_282_18/1
+AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_274_1c/1
+TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_225_1e/1
+CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_249_20/1
+GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_267_22/1
+CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_69_229_23/1
+ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_21_208_24/1
+GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_146_27/1
+ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_103_284_2a/1
+AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_271_2b/1
+ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_50_224_2d/1
+CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_26_189_30/1
+AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_79_256_31/1
+AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_267_32/1
+CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_145_300_37/1
+GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_228_3a/1
+CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_30_231_3c/1
+CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_220_3d/1
+GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_278_3e/1
+CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_23_186_42/1
+TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_106_253_45/1
+AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_47/1
+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_63_229_4c/1
+ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_245_4d/1
+CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_88_257_50/1
+TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_9_179_52/1
+TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_250_57/1
+AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_272_5a/1
+GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_114_277_5b/1
+GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_279_5f/1
+CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_293_60/1
+CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_297_61/1
+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_295_63/1
+TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_revlib_R2.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_revlib_R2.fastqsanger	Fri Feb 17 20:04:43 2023 +0000
@@ -0,0 +1,192 @@
+@test_mRNA_150_290_0/2
+TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_255_2/2
+GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_72_258_4/2
+ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_107_286_5/2
+TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_122_299_6/2
+GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_234_7/2
+GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_155_9/2
+TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_230_b/2
+AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_276_c/2
+ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_268_d/2
+CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_118_297_f/2
+GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_16_194_10/2
+GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_266_13/2
+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_218_16/2
+GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_195_17/2
+GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_126_282_18/2
+GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_274_1c/2
+GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_225_1e/2
+ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_249_20/2
+GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_267_22/2
+ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_69_229_23/2
+AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_21_208_24/2
+GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_146_27/2
+GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_103_284_2a/2
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_271_2b/2
+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_50_224_2d/2
+CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_26_189_30/2
+GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_79_256_31/2
+ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_267_32/2
+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_145_300_37/2
+GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_228_3a/2
+GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_30_231_3c/2
+GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_220_3d/2
+GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_278_3e/2
+GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_23_186_42/2
+GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_106_253_45/2
+CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_47/2
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_63_229_4c/2
+ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_245_4d/2
+GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_88_257_50/2
+GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_9_179_52/2
+CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_250_57/2
+AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_272_5a/2
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_114_277_5b/2
+TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_279_5f/2
+AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_293_60/2
+CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_297_61/2
+CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_295_63/2
+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_test.fa.gz
Binary file test-data/tophat_test.fa.gz has changed
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_test_reads_per_gene_PE.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_test_reads_per_gene_PE.txt	Fri Feb 17 20:04:43 2023 +0000
@@ -0,0 +1,5 @@
+N_unmapped	5	5	5
+N_multimapping	0	0	0
+N_noFeature	0	48	47
+N_ambiguous	0	0	0
+GENE1	95	47	48
diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_test_reads_per_gene_PE_rev.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_test_reads_per_gene_PE_rev.txt	Fri Feb 17 20:04:43 2023 +0000
@@ -0,0 +1,5 @@
+N_unmapped	0	0	0
+N_multimapping	0	0	0
+N_noFeature	0	48	0
+N_ambiguous	0	0	0
+GENE1	48	0	48