# HG changeset patch
# User iuc
# Date 1714477988 0
# Node ID 8eb8750070d48933470277b10a3e47cfdf2aabf6
# Parent  ae618321f34a874b7fced191a32a88696e276970
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 252f4cccd66513c985b3df9480d73c8b9f994520

diff -r ae618321f34a -r 8eb8750070d4 macros.xml
--- a/macros.xml	Mon Jan 30 12:01:28 2023 +0000
+++ b/macros.xml	Tue Apr 30 11:53:08 2024 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.2.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">2.2.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">stringtie</requirement>
-        <requirement type="package" version="1.16.1">samtools</requirement>
+        <requirement type="package" version="1.20">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
diff -r ae618321f34a -r 8eb8750070d4 stringtie.xml
--- a/stringtie.xml	Mon Jan 30 12:01:28 2023 +0000
+++ b/stringtie.xml	Tue Apr 30 11:53:08 2024 +0000
@@ -1,11 +1,11 @@
-<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>transcript assembly and quantification</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">stringtie</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
@@ -148,12 +148,12 @@
             </when>
             <when value="long_reads">
                 <param name="input_bam" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM file containing the long reads you want to assemble into transcripts"/>
-                <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
+                <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25"/>
             </when>
             <when value="mixed_reads">
                 <param name="input_bam_short" type="data" format="sam,bam,cram" label="Input short mapped reads" help="Input BAM/SAM/CRAM file containing the short reads you want to assemble into transcripts"/>
                 <param name="input_bam_long" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM file containing the long reads you want to assemble into transcripts"/>
-                <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
+                <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25"/>
             </when>
         </conditional>
         <param name="rna_strandness" type="select" label="Specify strand information"
@@ -177,13 +177,13 @@
                     <when value="cached">
                         <param name="ref_builtin" type="select" label="Use a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
                             <options from_data_table="gene_sets">
-                                <filter type="sort_by" column="2" />
-                                <validator type="no_options" message="No GTF file is available." />
+                                <filter type="sort_by" column="2"/>
+                                <validator type="no_options" message="No GTF file is available."/>
                             </options>
                         </param>
                     </when>
                     <when value="history">
-                        <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly" />
+                        <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly"/>
                     </when>
                 </conditional>
                 <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Use Reference transcripts only?" help="Limit the processing of read alignments to only estimate and output the assembled transcripts matching the reference transcripts given with the -G option. With this option, read bundles with no reference transcripts (novel transcripts) will be entirely skipped, which may provide a considerable speed boost when the given set of reference transcripts is limited to a set of target genes, for example. Default: No"/>
@@ -195,9 +195,9 @@
                     </param>
                     <when value="ballgown" />
                     <when value="deseq2">
-                        <param name="read_length" argument="--length" type="integer" min="0" value="75" label="Specify the average read length" help="Default: 75" />
-                        <param name="clustering" argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" checked="false" label="Cluster overlapping genes" help="Choose whether to cluster genes with different gene IDs that overlap. Transcripts containing the geneID prefix will be ignored. Default: No" />
-                        <param argument="--string" type="text" label="Prefix used for transcripts" help="If a different prefix was used for geneIDs assigned by StringTie than the default, specify it here. Only letters and numbers will be retained in this field. Default: MSTRG" >
+                        <param name="read_length" argument="--length" type="integer" min="0" value="75" label="Specify the average read length" help="Default: 75"/>
+                        <param name="clustering" argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" checked="false" label="Cluster overlapping genes" help="Choose whether to cluster genes with different gene IDs that overlap. Transcripts containing the geneID prefix will be ignored. Default: No"/>
+                        <param argument="--string" type="text" label="Prefix used for transcripts" help="If a different prefix was used for geneIDs assigned by StringTie than the default, specify it here. Only letters and numbers will be retained in this field. Default: MSTRG">
                             <sanitizer>
                                 <valid initial="string.letters,string.digits"></valid>
                             </sanitizer>
@@ -215,7 +215,7 @@
         </conditional>
         <section name="adv" title="Advanced Options">
             <param name="abundance_estimation" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Output gene abundance estimation file?" help="If selected, gene abundances will be reported in a tab-delimited file, see below for more information"/>
-            <param name="omit_sequences" argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="Ignore all read alignments (and thus do not attempt to perform transcript assembly) on the specified reference sequences. This parameter can be a single reference sequence name (e.g. chrM) or a comma-delimited list of sequence names (e.g. chrM,chrX,chrY). This can speed up StringTie especially in the case of excluding the mitochondrial genome, whose genes may have very high coverage in some cases, even though they may be of no interest for a particular RNA-Seq analysis. The reference sequence names are case sensitive, they must match identically the names of chromosomes/contigs of the target genome against which the RNA-Seq reads were aligned in the first place." />
+            <param name="omit_sequences" argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="Ignore all read alignments (and thus do not attempt to perform transcript assembly) on the specified reference sequences. This parameter can be a single reference sequence name (e.g. chrM) or a comma-delimited list of sequence names (e.g. chrM,chrX,chrY). This can speed up StringTie especially in the case of excluding the mitochondrial genome, whose genes may have very high coverage in some cases, even though they may be of no interest for a particular RNA-Seq analysis. The reference sequence names are case sensitive, they must match identically the names of chromosomes/contigs of the target genome against which the RNA-Seq reads were aligned in the first place."/>
             <param name="name_prefix" argument="-l" type="text" label="Name prefix for output transcripts" help="This prefix will be added to the name of the transcripts that are output. Only letters and numbers will be retained in this field. Default: STRG">
                 <sanitizer>
                     <valid initial="string.letters,string.digits"></valid>
@@ -223,18 +223,18 @@
             </param>
             <param name="fraction" argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum isoform fraction" help="Sets the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus. Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts. Default: 0.05"/>
             <param name="min_tlen" argument="-m" type="integer" min="0" value="200" label="Minimum assembled transcript length" help="Sets the minimum length allowed for the predicted transcripts. Default: 200"/>
-            <param name="min_anchor_len" argument="-a" type="integer" min="0" value="10" label="Minimum anchor length for junctions" help="Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10" />
-            <param name="min_anchor_cov" argument="-j" type="integer" min="0" value="1" label="Minimum junction coverage" help="There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1" />
+            <param name="min_anchor_len" argument="-a" type="integer" min="0" value="10" label="Minimum anchor length for junctions" help="Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10"/>
+            <param name="min_anchor_cov" argument="-j" type="integer" min="0" value="1" label="Minimum junction coverage" help="There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1"/>
             <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="1" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/>
             <param name="bdist" argument="-g" type="integer" min="0" value="50" label="Gap between read mappings triggering a new bundle" help="Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)"/>
             <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="1" label="Fraction of bundle allowed to be covered by multi-hit reads"  help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/>
-            <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" />
+            <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No"/>
             <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/>
             <param name="point_features" type="data" format="tabular" optional="true" label="Input point-features dataset" help="Loads a list of point-features from a text feature file to guide the transcriptome assembly. Accepted point features are transcription start sites (TSS) and polyadenylation sites (CPAS). There are four tab-delimited columns in the feature file. The first three define the location of the point feature on the cromosome (sequence name, coordinate and strand), and the last is the type of the feature (TSS or CPAS)."/>
         </section>
     </inputs>
     <outputs>
-        <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
+        <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts"/>
         <data name="gene_abundance_estimation" format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates">
             <filter>adv['abundance_estimation']</filter>
         </data>
@@ -276,146 +276,146 @@
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>
-            <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!--Ensure fraction option works -->
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="fraction" value="0.17" />
-            <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="fraction" value="0.17"/>
+            <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!--Ensure guide option works -->
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="guide_gff_select" value="history" />
+            <param name="use_guide" value="yes"/>
+            <param name="guide_gff_select" value="history"/>
             <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
-            <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!--Ensure guide with fraction works -->
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="guide_gff_select" value="history" />
-            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
-            <param name="fraction" value="0.17" />
-            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="use_guide" value="yes"/>
+            <param name="guide_gff_select" value="history"/>
+            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
+            <param name="fraction" value="0.17"/>
+            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!--Ensure coverage and output for Ballgown works -->
         <test expect_num_outputs="7">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="guide_gff_select" value="history" />
-            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
-            <param name="special_outputs_select" value="ballgown" />
-            <param name="coverage_file" value="true" />
-            <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
-            <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
-            <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
-            <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
-            <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
-            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" compare="re_match" sort="true"/>
-            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="use_guide" value="yes"/>
+            <param name="guide_gff_select" value="history"/>
+            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
+            <param name="special_outputs_select" value="ballgown"/>
+            <param name="coverage_file" value="true"/>
+            <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular"/>
+            <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular"/>
+            <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular"/>
+            <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular"/>
+            <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular"/>
+            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!--Ensure output for edgeR works -->
         <test expect_num_outputs="5">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="special_outputs_select" value="deseq2" />
-            <param name="input_estimation" value="true" />
+            <param name="use_guide" value="yes"/>
+            <param name="special_outputs_select" value="deseq2"/>
+            <param name="input_estimation" value="true"/>
             <param name="guide_gff_select" value="history" />
-            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
-            <param name="coverage_file" value="true" />
-            <param name="clustering" value="true" />
-            <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />
-            <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />
-            <output name="legend" file="legend.tsv" ftype="tabular" />
-            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" compare="re_match" sort="true"/>
-            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
+            <param name="coverage_file" value="true"/>
+            <param name="clustering" value="true"/>
+            <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular"/>
+            <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular"/>
+            <output name="legend" file="legend.tsv" ftype="tabular"/>
+            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2"/>
+            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!--Ensure gene abundances output works -->
         <test expect_num_outputs="2">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="guide_gff_select" value="history" />
-            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
-            <param name="fraction" value="0.17" />
-            <param name="abundance_estimation" value="true" />
-            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="use_guide" value="yes"/>
+            <param name="guide_gff_select" value="history"/>
+            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
+            <param name="fraction" value="0.17"/>
+            <param name="abundance_estimation" value="true"/>
+            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="2"/>
             <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
         </test>
         <!--Ensure another fraction value works -->
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="guide_gff_select" value="history" />
-            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
-            <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="use_guide" value="yes"/>
+            <param name="guide_gff_select" value="history"/>
+            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/>
+            <param name="fraction" value="0.15"/>
+            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!--Ensure built-in GTFs work -->
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="short_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="guide_gff_select" value="cached" />
-            <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="use_guide" value="yes"/>
+            <param name="guide_gff_select" value="cached"/>
+            <param name="fraction" value="0.15"/>
+            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!-- Test long reads input -->
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="long_reads"/>
-                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
+                <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="guide_gff_select" value="cached" />
-            <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="use_guide" value="yes"/>
+            <param name="guide_gff_select" value="cached"/>
+            <param name="fraction" value="0.15"/>
+            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!-- Test error splice option -->
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="long_reads"/>
-                <param name="input_bam" ftype="bam" value="long_reads.bam" />
-                <param name="error_splice" value="30" />
+                <param name="input_bam" ftype="bam" value="long_reads.bam"/>
+                <param name="error_splice" value="30"/>
             </conditional>            
-            <param name="use_guide" value="yes" />
-            <param name="guide_gff_select" value="cached" />
-            <param name="fraction" value="0.15" />
-            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="use_guide" value="yes"/>
+            <param name="guide_gff_select" value="cached"/>
+            <param name="fraction" value="0.15"/>
+            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <!-- Test mixed reads input -->
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="mixed_reads"/>
-                <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
-                <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
+                <param name="input_bam_short" ftype="bam" value="short_reads.bam"/>
+                <param name="input_bam_long" ftype="bam" value="long_reads.bam"/>
             </conditional>            
             <output name="output_gtf" ftype="gtf">
                 <assert_contents>
@@ -429,8 +429,8 @@
         <test expect_num_outputs="1">
             <conditional name="input_options">
                 <param name="input_mode" value="mixed_reads"/>
-                <param name="input_bam_short" ftype="cram" value="stringtie_in.cram" />
-                <param name="input_bam_long" ftype="cram" value="stringtie_in.cram" />
+                <param name="input_bam_short" ftype="cram" value="stringtie_in.cram"/>
+                <param name="input_bam_long" ftype="cram" value="stringtie_in.cram"/>
             </conditional>            
             <output name="output_gtf" ftype="gtf">
                 <assert_contents>
diff -r ae618321f34a -r 8eb8750070d4 stringtie_merge.xml
--- a/stringtie_merge.xml	Mon Jan 30 12:01:28 2023 +0000
+++ b/stringtie_merge.xml	Tue Apr 30 11:53:08 2024 +0000
@@ -1,11 +1,11 @@
 <tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>transcripts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">stringtie</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
@@ -26,35 +26,35 @@
         -o '$out_gtf' '$inputs'
     ]]></command>
     <inputs>
-        <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" />
-        <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" />
-        <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge" />
-        <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge" />
-        <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge" />
-        <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge" />
-        <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" />
-        <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" />
-        <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" />
+        <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format"/>
+        <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging"/>
+        <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge"/>
+        <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge"/>
+        <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge"/>
+        <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge"/>
+        <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction"/>
+        <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together"/>
+        <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them"/>
     </inputs>
     <outputs>
-        <data name="out_gtf" format="gtf" />
+        <data name="out_gtf" format="gtf"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
-            <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" />
-            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf"/>
+            <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf"/>
+            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <test>
-            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
+            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>
             <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
-            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true"/>
+            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="4"/>
         </test>
         <test>
-            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
+            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>
             <output name="out_gtf" ftype="gtf">
                 <assert_contents>
-                    <has_text text="stringtie --merge" />
+                    <has_text text="stringtie --merge"/>
                 </assert_contents>
             </output>
         </test>
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_merge_out1.gtf
--- a/test-data/stringtie_merge_out1.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_merge_out1.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; 
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; 
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; 
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; 
+# stringtie --merge -p 1 -G /tmp/tmpr8yl388j/files/d/8/3/dataset_d8325888-f757-4336-9e42-1101c6ec296d.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpr8yl388j/job_working_directory/000/6/outputs/dataset_51c0f399-1d26-44c7-a4fd-e6f8897fe843.dat /tmp/tmpr8yl388j/files/5/5/b/dataset_55be25a6-c7f0-474e-a011-bb4cd427cfa2.dat /tmp/tmpr8yl388j/files/b/2/e/dataset_b2ef2a9d-3640-4858-8424-b4a29c57164d.dat /tmp/tmpr8yl388j/files/d/9/b/dataset_d9be016a-da47-4ad1-89bd-e9781f2751db.dat /tmp/tmpr8yl388j/files/b/e/f/dataset_befee6d4-95fb-4ee9-83a4-9b1302e6a21a.dat
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; ref_gene_id "CUFF.1"; 
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "1"; ref_gene_id "CUFF.1"; 
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "2"; ref_gene_id "CUFF.1"; 
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "3"; ref_gene_id "CUFF.1"; 
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_merge_out2.gtf
--- a/test-data/stringtie_merge_out2.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_merge_out2.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,100 +1,100 @@
-# StringTie version 2\.2\.1
-# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat
-chr1\tStringTie\texon\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3204563\t3207049\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
-chr1\tStringTie\texon\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3411783\t3411982\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
-chr1\tStringTie\texon\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
-chr1\tStringTie\texon\t3660633\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
-chr1\tStringTie\ttranscript\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3204563\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; 
-chr1\tStringTie\ttranscript\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tStringTie\ttranscript\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
-chr1\tmm9_refFlat\texon\t4334224\t4340172\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4341991\t4342162\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4342283\t4342918\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4350281\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4481009\t4482749\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4483181\t4483547\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4483853\t4483944\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4485217\t4486023\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4486372\t4486494\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4763279\t4764597\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4763279\t4764597\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4763279\t4766882\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4774032\t4774186\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4774032\t4774186\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4797974\t4798063\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4798536\t4798567\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4818665\t4818730\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4820349\t4820396\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4822392\t4822462\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4827082\t4827155\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4829468\t4829569\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4831037\t4831213\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4835044\t4836816\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4847775\t4848057\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4847775\t4848057\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4857551\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4857551\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4868108\t4868213\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4876825\t4876912\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4879538\t4879683\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4880821\t4880877\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4881996\t4882150\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4883498\t4883644\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4885015\t4885086\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\texon\t4886437\t4887987\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
-chr1\tmm9_refFlat\ttranscript\t4334224\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";
-chr1\tmm9_refFlat\ttranscript\t4481009\t4486494\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";
-chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";
-chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";
-chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";
-chr1\tmm9_refFlat\ttranscript\t4797974\t4836816\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";
-chr1\tmm9_refFlat\ttranscript\t4847775\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";
-chr1\tmm9_refFlat\ttranscript\t4847775\t4887987\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";
\ No newline at end of file
+# stringtie --merge -p 1 -G /tmp/tmpr8yl388j/files/9/2/b/dataset_92bbbdee-6cfa-4cff-bab3-0d0836475341.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpr8yl388j/job_working_directory/000/10/outputs/dataset_81bd1351-3b74-4332-b789-a4f53357a8fa.dat /tmp/tmpr8yl388j/files/3/c/3/dataset_3c3b1fdc-0351-48ef-a6eb-6c226751f619.dat /tmp/tmpr8yl388j/files/2/a/4/dataset_2a44d87f-131b-4587-bf25-2527d7d89964.dat
+# StringTie version 2.2.2
+chr1	StringTie	transcript	3189811	3193042	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; 
+chr1	StringTie	exon	3189811	3193042	1000	.	.	gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; 
+chr1	StringTie	transcript	3200023	3200191	1000	.	.	gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; 
+chr1	StringTie	exon	3200023	3200191	1000	.	.	gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; 
+chr1	StringTie	transcript	3201078	3201809	1000	.	.	gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; 
+chr1	StringTie	exon	3201078	3201809	1000	.	.	gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; 
+chr1	StringTie	transcript	3204563	3661579	1000	-	.	gene_id "MSTRG.4"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; 
+chr1	StringTie	exon	3204563	3207049	1000	-	.	gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "1"; ref_gene_id "Xkr4"; 
+chr1	StringTie	exon	3411783	3411982	1000	-	.	gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "2"; ref_gene_id "Xkr4"; 
+chr1	StringTie	exon	3660633	3661579	1000	-	.	gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "3"; ref_gene_id "Xkr4"; 
+chr1	StringTie	transcript	3212214	3212439	1000	.	.	gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; 
+chr1	StringTie	exon	3212214	3212439	1000	.	.	gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; 
+chr1	StringTie	transcript	3212718	3212801	1000	.	.	gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; 
+chr1	StringTie	exon	3212718	3212801	1000	.	.	gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; 
+chr1	StringTie	transcript	3213096	3213242	1000	.	.	gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; 
+chr1	StringTie	exon	3213096	3213242	1000	.	.	gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; 
+chr1	StringTie	transcript	3242634	3243079	1000	.	.	gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; 
+chr1	StringTie	exon	3242634	3243079	1000	.	.	gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; 
+chr1	StringTie	transcript	3243348	3243401	1000	.	.	gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; 
+chr1	StringTie	exon	3243348	3243401	1000	.	.	gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; 
+chr1	StringTie	transcript	3277914	3278390	1000	.	.	gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; 
+chr1	StringTie	exon	3277914	3278390	1000	.	.	gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1"; 
+chr1	StringTie	transcript	3280687	3280741	1000	.	.	gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; 
+chr1	StringTie	exon	3280687	3280741	1000	.	.	gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1"; 
+chr1	StringTie	transcript	3282761	3282832	1000	.	.	gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; 
+chr1	StringTie	exon	3282761	3282832	1000	.	.	gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1"; 
+chr1	StringTie	transcript	3290489	3291273	1000	.	.	gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; 
+chr1	StringTie	exon	3290489	3291273	1000	.	.	gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1"; 
+chr1	StringTie	transcript	3299444	3299664	1000	.	.	gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; 
+chr1	StringTie	exon	3299444	3299664	1000	.	.	gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1"; 
+chr1	StringTie	transcript	3319000	3319051	1000	.	.	gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; 
+chr1	StringTie	exon	3319000	3319051	1000	.	.	gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1"; 
+chr1	StringTie	transcript	3351241	3351311	1000	.	.	gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; 
+chr1	StringTie	exon	3351241	3351311	1000	.	.	gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "1"; 
+chr1	StringTie	transcript	3355908	3356119	1000	.	.	gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; 
+chr1	StringTie	exon	3355908	3356119	1000	.	.	gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "1"; 
+chr1	StringTie	transcript	3363077	3363446	1000	.	.	gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; 
+chr1	StringTie	exon	3363077	3363446	1000	.	.	gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "1"; 
+chr1	StringTie	transcript	3363754	3363849	1000	.	.	gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; 
+chr1	StringTie	exon	3363754	3363849	1000	.	.	gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "1"; 
+chr1	StringTie	transcript	3377212	3377262	1000	.	.	gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; 
+chr1	StringTie	exon	3377212	3377262	1000	.	.	gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "1"; 
+chr1	StringTie	transcript	3386740	3386836	1000	.	.	gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; 
+chr1	StringTie	exon	3386740	3386836	1000	.	.	gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; exon_number "1"; 
+chr1	StringTie	transcript	3450907	3451109	1000	.	.	gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; 
+chr1	StringTie	exon	3450907	3451109	1000	.	.	gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; 
+chr1	mm9_refFlat	transcript	4334224	4350473	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";
+chr1	mm9_refFlat	exon	4334224	4340172	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "1";
+chr1	mm9_refFlat	exon	4341991	4342162	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "2";
+chr1	mm9_refFlat	exon	4342283	4342918	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "3";
+chr1	mm9_refFlat	exon	4350281	4350473	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "4";
+chr1	mm9_refFlat	transcript	4481009	4486494	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";
+chr1	mm9_refFlat	exon	4481009	4482749	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "1";
+chr1	mm9_refFlat	exon	4483181	4483547	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "2";
+chr1	mm9_refFlat	exon	4483853	4483944	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "3";
+chr1	mm9_refFlat	exon	4485217	4486023	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "4";
+chr1	mm9_refFlat	exon	4486372	4486494	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "5";
+chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";
+chr1	mm9_refFlat	exon	4763279	4766882	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1";
+chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2";
+chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3";
+chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4";
+chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5";
+chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";
+chr1	mm9_refFlat	exon	4763279	4764597	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1";
+chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2";
+chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3";
+chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4";
+chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5";
+chr1	mm9_refFlat	transcript	4763279	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";
+chr1	mm9_refFlat	exon	4763279	4764597	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1";
+chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2";
+chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3";
+chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4";
+chr1	mm9_refFlat	transcript	4797974	4836816	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";
+chr1	mm9_refFlat	exon	4797974	4798063	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1";
+chr1	mm9_refFlat	exon	4798536	4798567	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2";
+chr1	mm9_refFlat	exon	4818665	4818730	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3";
+chr1	mm9_refFlat	exon	4820349	4820396	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4";
+chr1	mm9_refFlat	exon	4822392	4822462	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5";
+chr1	mm9_refFlat	exon	4827082	4827155	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6";
+chr1	mm9_refFlat	exon	4829468	4829569	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7";
+chr1	mm9_refFlat	exon	4831037	4831213	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8";
+chr1	mm9_refFlat	exon	4835044	4836816	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9";
+chr1	mm9_refFlat	transcript	4847775	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";
+chr1	mm9_refFlat	exon	4847775	4848057	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1";
+chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2";
+chr1	mm9_refFlat	transcript	4847775	4887987	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";
+chr1	mm9_refFlat	exon	4847775	4848057	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1";
+chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2";
+chr1	mm9_refFlat	exon	4868108	4868213	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3";
+chr1	mm9_refFlat	exon	4876825	4876912	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4";
+chr1	mm9_refFlat	exon	4879538	4879683	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5";
+chr1	mm9_refFlat	exon	4880821	4880877	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6";
+chr1	mm9_refFlat	exon	4881996	4882150	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7";
+chr1	mm9_refFlat	exon	4883498	4883644	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8";
+chr1	mm9_refFlat	exon	4885015	4885086	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9";
+chr1	mm9_refFlat	exon	4886437	4887987	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out10.gtf
--- a/test-data/stringtie_out10.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out10.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "54\.160000";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.777779";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.795303"; FPKM "3354967\.250000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/8/4/7/dataset_84719807-dfbb-42a2-b1db-377469c94d05.dat -L -E 25 -o /tmp/tmpm2qmdax_/job_working_directory/000/26/outputs/dataset_4dfedf5d-98a8-4b6a-8f7d-1b6c2116bbd4.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.795303"; FPKM "3354967.250000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.777779";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "54.160000";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out11.gtf
--- a/test-data/stringtie_out11.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out11.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,58 +1,58 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 30 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-chr19\tStringTie\texon\t567221\t567648\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.815421";
-chr19\tStringTie\texon\t571310\t571579\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "4\.559259";
-chr19\tStringTie\texon\t571440\t571596\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.859873";
-chr19\tStringTie\texon\t571697\t571736\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "2\.550000";
-chr19\tStringTie\texon\t572567\t572701\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "3\.325926";
-chr19\tStringTie\texon\t577774\t578121\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.436781";
-chr19\tStringTie\texon\t579500\t579656\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000";
-chr19\tStringTie\texon\t580379\t580461\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142";
-chr19\tStringTie\texon\t580379\t580461\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.443858";
-chr19\tStringTie\texon\t580646\t580782\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.689962";
-chr19\tStringTie\texon\t580646\t580782\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.631207";
-chr19\tStringTie\texon\t581315\t581610\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142";
-chr19\tStringTie\texon\t581315\t581610\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.443858";
-chr19\tStringTie\texon\t582514\t582582\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142";
-chr19\tStringTie\texon\t582514\t582582\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.443858";
-chr19\tStringTie\texon\t582750\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.592226";
-chr19\tStringTie\texon\t582750\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.040156";
-chr19\tStringTie\texon\t589891\t590577\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "18\.537119";
-chr19\tStringTie\texon\t603544\t603967\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
-chr19\tStringTie\texon\t605061\t605222\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
-chr19\tStringTie\texon\t607964\t608182\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
-chr19\tStringTie\texon\t610259\t610405\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
-chr19\tStringTie\texon\t613248\t613488\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
-chr19\tStringTie\texon\t613852\t614016\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000";
-chr19\tStringTie\texon\t615795\t617159\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "19\.587545";
-chr19\tStringTie\texon\t617224\t617323\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "20\.289286";
-chr19\tStringTie\texon\t617224\t617323\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "1\.560714";
-chr19\tStringTie\texon\t617419\t617480\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "28\.788761";
-chr19\tStringTie\texon\t617419\t617480\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "1\.985432";
-chr19\tStringTie\texon\t617570\t617655\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "4\.996770";
-chr19\tStringTie\texon\t617570\t618586\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "30\.891500";
-chr19\tStringTie\texon\t617777\t617849\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.994817";
-chr19\tStringTie\texon\t618488\t618586\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.525252";
-chr19\tStringTie\texon\t618705\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "13\.750000";
-chr19\tStringTie\texon\t618705\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.875000";
-chr19\tStringTie\texon\t618997\t619110\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t619210\t619296\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t619586\t619765\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t619958\t620080\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000";
-chr19\tStringTie\texon\t620365\t620487\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000";
-chr19\tStringTie\texon\t621058\t621846\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.751584";
-chr19\tStringTie\texon\t622149\t622373\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t622582\t622752\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t622821\t622985\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t623454\t623603\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t624719\t624905\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t625124\t625254\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000";
-chr19\tStringTie\texon\t629540\t630168\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.941176";
-chr19\tStringTie\texon\t632834\t632938\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.000000";
-chr19\tStringTie\texon\t633425\t633601\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "3\.988701";
-chr19\tStringTie\ttranscript\t567221\t571736\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "5\.617600"; FPKM "37220\.644531"; TPM "77823\.132812";
-chr19\tStringTie\ttranscript\t571310\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "5\.416068"; FPKM "35885\.347656"; TPM "75031\.218750";
-chr19\tStringTie\ttranscript\t572567\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; cov "6\.175826"; FPKM "40919\.292969"; TPM "85556\.492188";
-chr19\tStringTie\ttranscript\t589891\t617159\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "19\.938414"; FPKM "132106\.343750"; TPM "276215\.781250";
-chr19\tStringTie\ttranscript\t617224\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "29\.150192"; FPKM "193141\.000000"; TPM "403830\.687500";
-chr19\tStringTie\ttranscript\t617224\t633601\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; cov "5\.886094"; FPKM "38999\.609375"; TPM "81542\.703125";
+# stringtie /tmp/tmpm2qmdax_/files/c/e/f/dataset_cefc5152-4ac0-4e7e-9223-1b55c7b7ac85.dat -L -E 30 -o /tmp/tmpm2qmdax_/job_working_directory/000/28/outputs/dataset_5597b8ed-94cb-4345-9b86-8ad715fbe328.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+chr19	StringTie	transcript	567221	571736	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.617600"; FPKM "37220.644531"; TPM "77823.132812";
+chr19	StringTie	exon	567221	567648	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421";
+chr19	StringTie	exon	571440	571596	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "5.859873";
+chr19	StringTie	exon	571697	571736	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "2.550000";
+chr19	StringTie	transcript	571310	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "5.416068"; FPKM "35885.347656"; TPM "75031.218750";
+chr19	StringTie	exon	571310	571579	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "4.559259";
+chr19	StringTie	exon	580379	580461	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "5.556142";
+chr19	StringTie	exon	580646	580782	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "5.689962";
+chr19	StringTie	exon	581315	581610	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "5.556142";
+chr19	StringTie	exon	582514	582582	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "5.556142";
+chr19	StringTie	exon	582750	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "5.592226";
+chr19	StringTie	transcript	572567	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; cov "6.175826"; FPKM "40919.292969"; TPM "85556.492188";
+chr19	StringTie	exon	572567	572701	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "3.325926";
+chr19	StringTie	exon	577774	578121	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "6.436781";
+chr19	StringTie	exon	579500	579656	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "7.000000";
+chr19	StringTie	exon	580379	580461	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "7.443858";
+chr19	StringTie	exon	580646	580782	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "6.631207";
+chr19	StringTie	exon	581315	581610	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "6.443858";
+chr19	StringTie	exon	582514	582582	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "6.443858";
+chr19	StringTie	exon	582750	583493	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "8"; cov "6.040156";
+chr19	StringTie	transcript	589891	617159	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "19.938414"; FPKM "132106.343750"; TPM "276215.781250";
+chr19	StringTie	exon	589891	590577	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "18.537119";
+chr19	StringTie	exon	603544	603967	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "21.000000";
+chr19	StringTie	exon	605061	605222	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "21.000000";
+chr19	StringTie	exon	607964	608182	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "21.000000";
+chr19	StringTie	exon	610259	610405	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "21.000000";
+chr19	StringTie	exon	613248	613488	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "6"; cov "21.000000";
+chr19	StringTie	exon	613852	614016	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "7"; cov "21.000000";
+chr19	StringTie	exon	615795	617159	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "8"; cov "19.587545";
+chr19	StringTie	transcript	617224	618760	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "29.150192"; FPKM "193141.000000"; TPM "403830.687500";
+chr19	StringTie	exon	617224	617323	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "20.289286";
+chr19	StringTie	exon	617419	617480	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "28.788761";
+chr19	StringTie	exon	617570	618586	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "3"; cov "30.891500";
+chr19	StringTie	exon	618705	618760	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "4"; cov "13.750000";
+chr19	StringTie	transcript	617224	633601	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; cov "5.886094"; FPKM "38999.609375"; TPM "81542.703125";
+chr19	StringTie	exon	617224	617323	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "1"; cov "1.560714";
+chr19	StringTie	exon	617419	617480	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "2"; cov "1.985432";
+chr19	StringTie	exon	617570	617655	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "3"; cov "4.996770";
+chr19	StringTie	exon	617777	617849	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "4"; cov "5.994817";
+chr19	StringTie	exon	618488	618586	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "5"; cov "5.525252";
+chr19	StringTie	exon	618705	618760	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "6"; cov "6.875000";
+chr19	StringTie	exon	618997	619110	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "7"; cov "6.000000";
+chr19	StringTie	exon	619210	619296	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "8"; cov "6.000000";
+chr19	StringTie	exon	619586	619765	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "9"; cov "6.000000";
+chr19	StringTie	exon	619958	620080	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "10"; cov "7.000000";
+chr19	StringTie	exon	620365	620487	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "11"; cov "7.000000";
+chr19	StringTie	exon	621058	621846	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "12"; cov "6.751584";
+chr19	StringTie	exon	622149	622373	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "13"; cov "6.000000";
+chr19	StringTie	exon	622582	622752	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "14"; cov "6.000000";
+chr19	StringTie	exon	622821	622985	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "15"; cov "6.000000";
+chr19	StringTie	exon	623454	623603	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "16"; cov "6.000000";
+chr19	StringTie	exon	624719	624905	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "17"; cov "6.000000";
+chr19	StringTie	exon	625124	625254	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "18"; cov "6.000000";
+chr19	StringTie	exon	629540	630168	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "19"; cov "5.941176";
+chr19	StringTie	exon	632834	632938	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "20"; cov "5.000000";
+chr19	StringTie	exon	633425	633601	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "21"; cov "3.988701";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out1_re.gtf
--- a/test-data/stringtie_out1_re.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out1_re.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/7/c/4/dataset_7c4559ac-1803-4156-86aa-a965c40579dd.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/2/outputs/dataset_628e00eb-c42b-4122-af6b-138d203e2288.dat -p 1 -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.237373";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "53.000004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out2_re.gtf
--- a/test-data/stringtie_out2_re.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out2_re.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/8/7/1/dataset_871b229a-6bb9-4fea-ad17-d71634870366.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/4/outputs/dataset_3a880427-cc94-440b-974f-61adfa148f55.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.237373";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "53.000004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out3_re.gtf
--- a/test-data/stringtie_out3_re.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out3_re.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/1/9/d/dataset_19d005b0-21af-4097-ba09-dcfd47a9639d.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/7/outputs/dataset_e7ff968a-b61b-4cce-900e-04fd85518371.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out4_re.gtf
--- a/test-data/stringtie_out4_re.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out4_re.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0( -A /[-_/a-zA-Z0-9]+\.dat)?
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/4/2/5/dataset_42595174-c98e-47c3-80d3-4e7f41bf639a.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/19/outputs/dataset_89f0738d-5fec-45ea-b655-2585a71d3d18.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 -A /tmp/tmpm2qmdax_/job_working_directory/000/19/outputs/dataset_793b9d71-4869-4258-a6a5-1d50bd53361f.dat
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out5.gtf
--- a/test-data/stringtie_out5.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out5.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/5/b/5/dataset_5b55cbd8-f515-46d6-b1d2-71201435248b.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/13/outputs/dataset_3b84d9d9-efe9-4d58-9f34-c6d3f5da763f.dat -p 1 -G guide.gff -C /tmp/tmpm2qmdax_/job_working_directory/000/13/outputs/dataset_8fb2eb9a-4a6c-4300-9639-0a39336f7dab.dat -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out6.gtf
--- a/test-data/stringtie_out6.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out6.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -e -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/5/f/e/dataset_5fe68ff0-f093-4d09-86ec-2e1a279bb301.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/16/outputs/dataset_821eef87-9397-4b49-8860-910104445af9.dat -p 1 -G guide.gff -C /tmp/tmpm2qmdax_/job_working_directory/000/16/outputs/dataset_5a1ac870-b1e8-4437-8b57-211b71557c52.dat -e -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; cov "49.237373";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; cov "53.000004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out8.gtf
--- a/test-data/stringtie_out8.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out8.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/1/d/b/dataset_1db0e632-3580-4045-9441-56a6e90bafea.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/22/outputs/dataset_2072a123-60b0-41ed-b4fc-9df0db87bff0.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out9.gtf
--- a/test-data/stringtie_out9.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out9.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,6 +1,6 @@
-# StringTie version 2\.2\.1
-# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1
-test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004";
-test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000";
-test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373";
-test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000";
+# stringtie /tmp/tmpm2qmdax_/files/c/8/7/dataset_c8776afe-26a8-48d2-bea6-b66d6a50a5ad.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/24/outputs/dataset_721fe1c9-4aea-4e2f-84d4-76e855eb610c.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.2
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000";
diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out_coverage.gtf
--- a/test-data/stringtie_out_coverage.gtf	Mon Jan 30 12:01:28 2023 +0000
+++ b/test-data/stringtie_out_coverage.gtf	Tue Apr 30 11:53:08 2024 +0000
@@ -1,4 +1,4 @@
-test_chromosome\tCufflinks\texon\t351\t400\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1
-test_chromosome\tCufflinks\texon\t501\t550\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1
-test_chromosome\tCufflinks\texon\t53\t250\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1
-test_chromosome\tCufflinks\ttranscript\t53\t550\t1000\t\+\t\.\tID=CUFF\.[0-9]+\.1;geneID=CUFF\.[0-9]+;coverage=60\.97
+test_chromosome	Cufflinks	transcript	53	550	1000	+	.	ID=CUFF.1.1;geneID=CUFF.1;coverage=60.97
+test_chromosome	Cufflinks	exon	53	250	1000	+	.	Parent=CUFF.1.1
+test_chromosome	Cufflinks	exon	351	400	1000	+	.	Parent=CUFF.1.1
+test_chromosome	Cufflinks	exon	501	550	1000	+	.	Parent=CUFF.1.1