Build branch main with version main (ce40a4a)

Build pipeline: viash-hub.rnaseq.main-b6jtr Source commit: ce40a4a6d9 Source message: add unit tests
2024-11-27 09:19:16 +00:00
parent 20fef7a87e
commit 14e0d12189
295 changed files with 8300 additions and 8134 deletions
--- a/src/multiqc_custom_biotype/config.vsh.yaml
+++ b/src/multiqc_custom_biotype/config.vsh.yaml
@@ -36,6 +36,10 @@ resources:
  # Include the header for the biotypes in the component
  - path: biotypes_header.txt

+test_resources:
+  - type: bash_script
+    path: test.sh
+
 engines:
  - type: docker
    image: python:latest
--- a/src/multiqc_custom_biotype/script.py
+++ b/src/multiqc_custom_biotype/script.py
@@ -82,7 +82,7 @@ if __name__ == "__main__":
                filtered_lines.append(filtered_line)

    # Concatenate the header and the processed lines
-    result = biotypes_header + '\n' + '\n'.join(filtered_lines) + '\n'
+    result = biotypes_header + '\n'.join(filtered_lines) + '\n'

    # Write the result to par_featurecounts_multiqc
    with open(par["featurecounts_multiqc"], 'w') as output_file:
--- a/src/multiqc_custom_biotype/test.sh
+++ b/src/multiqc_custom_biotype/test.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+set -e 
+
+echo "> Prepare test data"
+
+cat > "test.featurecounts.txt" << HERE
+# Program:featureCounts v2.0.1; Command:"featureCounts" "-t" "CDS" "-T" "2" "-a" "genome.gtf" "-s" "1" "-o" "test.featureCounts.txt" "test.single_end.bam"
+Geneid	Chr	Start	End	Strand	Length	test.single_end.bam
+orf1ab	MT192765.1;MT192765.1	259;13461	13461;21545	+;+	21287	38
+S	MT192765.1	21556	25374	+	3819	4
+ORF3a	MT192765.1	25386	26210	+	825	0
+E	MT192765.1	26238	26462	+	225	1
+M	MT192765.1	26516	27181	+	666	1
+ORF6	MT192765.1	27195	27377	+	183	0
+ORF7a	MT192765.1	27387	27749	+	363	0
+ORF7b	MT192765.1	27749	27877	+	129	0
+ORF8	MT192765.1	27887	28249	+	363	0
+N	MT192765.1	28267	29523	+	1257	2
+ORF10	MT192765.1	29551	29664	+	114	0
+HERE
+
+echo "> Run test"
+"$meta_executable" \
+    --biocounts "test.featurecounts.txt" \
+    --id "test" \
+    --featurecounts_multiqc "test.biotype_counts_mqc.tsv" \
+    --featurecounts_rrna_multiqc "test.biotype_counts_rrna_mqc.tsv"
+
+echo "> Check results"
+[ ! -f "test.biotype_counts_mqc.tsv" ] && echo "test.biotype_counts_mqc.tsv was not created" && exit 1
+[ ! -s "test.biotype_counts_mqc.tsv" ] && echo "test.biotype_counts_mqc.tsv is empty" && exit 1
+[ ! -f "test.biotype_counts_rrna_mqc.tsv" ] && echo "test.biotype_counts_rrna_mqc.tsv was not created" && exit 1
+[ ! -s "test.biotype_counts_rrna_mqc.tsv" ] && echo "test.biotype_counts_rrna_mqc.tsv is empty" && exit 1
+
+exit 0
--- a/src/tx2gene/config.vsh.yaml
+++ b/src/tx2gene/config.vsh.yaml
@@ -12,7 +12,7 @@ argument_groups:
  - name: "--quant_results"
    type: file
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - name: "--gtf"
    type: file
  - name: "--gtf_extra_attributes"
@@ -32,10 +32,6 @@ argument_groups:
    type: file
    direction: output
    default: tx2gene.tsv
-  - name: "--updated_versions"
-    type: file
-    default: versions.yml
-    direction: output

 resources:
  - type: bash_script
@@ -43,6 +39,10 @@ resources:
  # copied from https://github.com/nf-core/rnaseq/blob/3.14.0/bin/tx2gene.py
  - path: tx2gene.py

+test_resources:
+  - type: bash_script
+    path: test.sh
+    
 engines:
 - type: docker
  image: ubuntu:22.04
--- a/src/tx2gene/script.sh
+++ b/src/tx2gene/script.sh
@@ -3,13 +3,13 @@
 set -eo pipefail

 function clean_up {
-    rm -rf "$salmon_tmpdir"
+    rm -rf "$tmpdir"
 }
 trap clean_up EXIT

-tmpdir=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXXXX")
+tmpdir=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXXXX")

-IFS="," read -ra results <<< $par_quant_results
+IFS=";" read -ra results <<< $par_quant_results
 for result in ${results[*]}
 do
    cp -r $result $tmpdir
--- a/src/tx2gene/test.sh
+++ b/src/tx2gene/test.sh
@@ -0,0 +1,52 @@
+#!/bin/bash 
+
+set -e
+
+echo "> Prepare test data"
+
+cat > "sample1_quant_results.sf" << HERE
+Name	Length	EffectiveLength	TPM	NumReads
+ENSSASG00005000004	3822	3572	15216.8	753
+ENSSASG00005000003	13218	12968	1502.34	269.9
+ENSSASG00005000002	21290	21040	23916.3	6971.1
+HERE
+
+cat > "sample2_quant_results.sf" << HERE
+Name	Length	EffectiveLength	TPM	NumReads
+ENSSASG00005000004	3822	3572	23713.5	703
+ENSSASG00005000003	13218	12968	14280	1536.92
+ENSSASG00005000002	21290	21040	37447.4	6539.08
+HERE
+
+cat > "genes.gtf" << HERE
+MN908947.3	ensembl	transcript	266	21555	.	+	.	gene_id "ENSSASG00005000002"; gene_version "1"; transcript_id "ENSSAST00005000002"; transcript_version "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1ab"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+MN908947.3	ensembl	exon	266	21555	.	+	.	gene_id "ENSSASG00005000002"; gene_version "1"; transcript_id "ENSSAST00005000002"; transcript_version "1"; exon_number "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1ab"; transcript_source "ensembl"; transcript_biotype "protein_coding"; exon_id "ENSSASE00005000002"; exon_version "1";
+MN908947.3	ensembl	CDS	266	21552	.	+	0	gene_id "ENSSASG00005000002"; gene_version "1"; transcript_id "ENSSAST00005000002"; transcript_version "1"; exon_number "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1ab"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "ENSSASP00005000002"; protein_version "1";
+MN908947.3	ensembl	start_codon	266	268	.	+	0	gene_id "ENSSASG00005000002"; gene_version "1"; transcript_id "ENSSAST00005000002"; transcript_version "1"; exon_number "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1ab"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+MN908947.3	ensembl	stop_codon	21553	21555	.	+	0	gene_id "ENSSASG00005000002"; gene_version "1"; transcript_id "ENSSAST00005000002"; transcript_version "1"; exon_number "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1ab"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+MN908947.3	ensembl	transcript	266	13483	.	+	.	gene_id "ENSSASG00005000003"; gene_version "1"; transcript_id "ENSSAST00005000003"; transcript_version "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1a"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+MN908947.3	ensembl	exon	266	13483	.	+	.	gene_id "ENSSASG00005000003"; gene_version "1"; transcript_id "ENSSAST00005000003"; transcript_version "1"; exon_number "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1a"; transcript_source "ensembl"; transcript_biotype "protein_coding"; exon_id "ENSSASE00005000003"; exon_version "1";
+MN908947.3	ensembl	CDS	266	13480	.	+	0	gene_id "ENSSASG00005000003"; gene_version "1"; transcript_id "ENSSAST00005000003"; transcript_version "1"; exon_number "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1a"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "ENSSASP00005000003"; protein_version "1";
+MN908947.3	ensembl	start_codon	266	268	.	+	0	gene_id "ENSSASG00005000003"; gene_version "1"; transcript_id "ENSSAST00005000003"; transcript_version "1"; exon_number "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1a"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+MN908947.3	ensembl	stop_codon	13481	13483	.	+	0	gene_id "ENSSASG00005000003"; gene_version "1"; transcript_id "ENSSAST00005000003"; transcript_version "1"; exon_number "1"; gene_name "ORF1ab"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ORF1a"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+MN908947.3	ensembl	transcript	21563	25384	.	+	.	gene_id "ENSSASG00005000004"; gene_version "1"; transcript_id "ENSSAST00005000004"; transcript_version "1"; gene_name "S"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "S"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+MN908947.3	ensembl	exon	21563	25384	.	+	.	gene_id "ENSSASG00005000004"; gene_version "1"; transcript_id "ENSSAST00005000004"; transcript_version "1"; exon_number "1"; gene_name "S"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "S"; transcript_source "ensembl"; transcript_biotype "protein_coding"; exon_id "ENSSASE00005000004"; exon_version "1";
+MN908947.3	ensembl	CDS	21563	25381	.	+	0	gene_id "ENSSASG00005000004"; gene_version "1"; transcript_id "ENSSAST00005000004"; transcript_version "1"; exon_number "1"; gene_name "S"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "S"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "ENSSASP00005000004"; protein_version "1";
+MN908947.3	ensembl	start_codon	21563	21565	.	+	0	gene_id "ENSSASG00005000004"; gene_version "1"; transcript_id "ENSSAST00005000004"; transcript_version "1"; exon_number "1"; gene_name "S"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "S"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+MN908947.3	ensembl	stop_codon	25382	25384	.	+	0	gene_id "ENSSASG00005000004"; gene_version "1"; transcript_id "ENSSAST00005000004"; transcript_version "1"; exon_number "1"; gene_name "S"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "S"; transcript_source "ensembl"; transcript_biotype "protein_coding";
+HERE
+
+echo "> Run test"
+"$meta_executable" \
+    --quant_results "sample1_quant_results.sf;sample2_quant_results.sf" \
+    --gtf "genes.gtf" \
+    --quant_type "salmon" \
+    --gtf_extra_attributes "gene_name" \
+    --gtf_group_features "gene_id" \
+    --tsv "tx2gene.tsv" 
+
+echo "> Check results"
+[ ! -f "tx2gene.tsv" ] && echo "tx2gene.tsv was not created" && exit 1
+[ ! -s "tx2gene.tsv" ] && echo "tx2gene.tsv is empty" && exit 1
+
+exit 0
--- a/src/tximport/config.vsh.yaml
+++ b/src/tximport/config.vsh.yaml
@@ -12,7 +12,7 @@ argument_groups:
  - name: "--quant_results"
    type: file
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - name: "--tx2gene_tsv"
    type: file
  - name: "--quant_type"
@@ -41,7 +41,7 @@ argument_groups:
  - name: "--lengths_gene"
    type: file
    direction: output
-    default: merged.gene_length.tsv
+    default: merged.gene_lengths.tsv
  - name: "--tpm_transcript"
    type: file
    direction: output
@@ -53,7 +53,7 @@ argument_groups:
  - name: "--lengths_transcript"
    type: file
    direction: output
-    default: merged.transcript_length.tsv
+    default: merged.transcript_lengths.tsv

 resources:
  - type: bash_script
@@ -61,6 +61,10 @@ resources:
  # copied from https://github.com/nf-core/rnaseq/blob/3.14.0/bin/tximport.r
  - path: tximport.r
  
+test_resources: 
+  - type: bash_script
+    path: test.sh
+
 engines:
 - type: docker
  image: ubuntu:22.04
--- a/src/tximport/script.sh
+++ b/src/tximport/script.sh
@@ -3,13 +3,13 @@
 set -eo pipefail

 function clean_up {
-    rm -rf "$salmon_tmpdir"
+    rm -rf "$tmpdir"
 }
 trap clean_up EXIT

-tmpdir=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXXXX")
+tmpdir=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXXXX")

-IFS="," read -ra results <<< $par_quant_results
+IFS=";" read -ra results <<< $par_quant_results
 for result in ${results[*]}
 do 
    cp -r $result $tmpdir
--- a/src/tximport/test.sh
+++ b/src/tximport/test.sh
@@ -0,0 +1,59 @@
+#!/bin/bash 
+
+set -e
+
+echo "> Prepare test data"
+
+cat > "sample1_quant_results.sf" << HERE
+Name	Length	EffectiveLength	TPM	NumReads
+ENSSASG00005000004	3822	3572	15216.8	753
+ENSSASG00005000003	13218	12968	1502.34	269.9
+ENSSASG00005000002	21290	21040	23916.3	6971.1
+HERE
+
+cat > "sample2_quant_results.sf" << HERE
+Name	Length	EffectiveLength	TPM	NumReads
+ENSSASG00005000004	3822	3572	23713.5	703
+ENSSASG00005000003	13218	12968	14280	1536.92
+ENSSASG00005000002	21290	21040	37447.4	6539.08
+HERE
+
+cat > tx2gene.tsv << HERE
+ENSSASG00005000002      ENSSASG00005000002      ORF1ab
+ENSSASG00005000003      ENSSASG00005000003      ORF1ab
+ENSSASG00005000004      ENSSASG00005000004      S
+HERE
+
+echo "> Run test"
+"$meta_executable" \
+    --quant_results "sample1_quant_results.sf;sample2_quant_results.sf" \
+    --tx2gene_tsv "tx2gene.tsv" \
+    --quant_type "salmon" \
+    # --tpm_gene gene_tpm.tsv \
+    # --counts_gene gene_counts.tsv \
+    # --counts_gene_length_scaled gene_counts_length_scaled.tsv \
+    # --counts_gene_scaled gene_counts_scaled.tsv \
+    # --lengths_gene gene_length.tsv \
+    # --tpm_transcript transcript_tpm.tsv \
+    # --counts_transcript transcript_counts.tsv \
+    # --lengths_transcript transcript_length.tsv
+
+echo "> Check results"
+[ ! -f "merged.gene_tpm.tsv" ] && echo "merged.gene_tpm.tsv was not created" && exit 1
+[ ! -s "merged.gene_tpm.tsv" ] && echo "merged.gene_tpm.tsv is empty" && exit 1
+[ ! -f "merged.gene_counts.tsv" ] && echo "merged.gene_counts.tsv was not created" && exit 1
+[ ! -s "merged.gene_counts.tsv" ] && echo "merged.gene_counts.tsv is empty" && exit 1
+[ ! -f "merged.gene_counts_length_scaled.tsv" ] && echo "merged.gene_counts_length_scaled.tsv was not created" && exit 1
+[ ! -s "merged.gene_counts_length_scaled.tsv" ] && echo "merged.gene_counts_length_scaled.tsv is empty" && exit 1
+[ ! -f "merged.gene_counts_scaled.tsv" ] && echo "merged.gene_counts_scaled.tsv was not created" && exit 1
+[ ! -s "merged.gene_counts_scaled.tsv" ] && echo "merged.gene_counts_scaled.tsv is empty" && exit 1
+[ ! -f "merged.gene_lengths.tsv" ] && echo "merged.gene_lengths.tsv was not created" && exit 1
+[ ! -s "merged.gene_lengths.tsv" ] && echo "merged.gene_lengths.tsv is empty" && exit 1
+[ ! -f "merged.transcript_tpm.tsv" ] && echo "merged.transcript_tpm.tsv was not created" && exit 1
+[ ! -s "merged.transcript_tpm.tsv" ] && echo "merged.transcript_tpm.tsv is empty" && exit 1
+[ ! -f "merged.transcript_counts.tsv" ] && echo "merged.transcript_counts.tsv was not created" && exit 1
+[ ! -s "merged.transcript_counts.tsv" ] && echo "merged.transcript_counts.tsv is empty" && exit 1
+[ ! -f "merged.transcript_lengths.tsv" ] && echo "merged.transcript_lengths.tsv was not created" && exit 1
+[ ! -s "merged.transcript_lengths.tsv" ] && echo "merged.transcript_lengths.tsv is empty" && exit 1
+
+exit 0
--- a/src/workflows/genome_alignment_and_quant/config.vsh.yaml
+++ b/src/workflows/genome_alignment_and_quant/config.vsh.yaml
@@ -39,16 +39,9 @@ argument_groups:
    type: boolean
    default: false
    description: When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file 
-  - name: "--seq_platform"
+  - name: --star_sjdb_gtf_feature_exon
    type: string
-    description: Sequencing platform.
-  - name: "--seq_center"
-    type: string
-    description: Sequencing center.
-  - name: "--extra_star_align_args"
-    type: string
-    default: ''
-    description: Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline.
+    description: Feature type in GTF file to be used as exons for building transcripts
  - name: "--bam_csi_index"
    type: boolean
    default: false
--- a/src/workflows/genome_alignment_and_quant/main.nf
+++ b/src/workflows/genome_alignment_and_quant/main.nf
@@ -17,7 +17,8 @@ workflow run_wf {
            "input_r2": "fastq_2",
            "genome_dir": "star_index",
            "sjdb_gtf_file": "gtf",
-          "out_sam_attr_rg_line": "star_sam_attr_rg_line"
+            "out_sam_attr_rg_line": "star_sam_attr_rg_line",
+            "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
          ],
          toState: [
            "genome_bam": "aligned_reads",
--- a/src/workflows/prepare_genome/main.nf
+++ b/src/workflows/prepare_genome/main.nf
@@ -42,7 +42,9 @@ workflow run_wf {
                toState: [ "gtf": "outfile" ],
                args: [
                    outfile: "gene_annotation.gtf", 
-                gtf_output: true
+                    gtf_output: true,
+                    keep_attrs: true,
+                    keep_exon_attrs: true
                ] 
            )

@@ -126,7 +128,7 @@ workflow run_wf {
                    "gtf": "gtf"
                ], 
                toState: [ "make_transcript_fasta_output": "output" ], 
-            key: "make_transcript_fasta",\
+                key: "make_transcript_fasta",
                args: [reference_name: "genome"]
            )
            | map { id, state -> 
--- a/src/workflows/pseudo_alignment_and_quant/main.nf
+++ b/src/workflows/pseudo_alignment_and_quant/main.nf
@@ -4,6 +4,7 @@ workflow run_wf {

  main:
    output_ch = input_ch
+    
      | map { id, state ->
        def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
        def paired = input.size() == 2
--- a/src/workflows/quality_control/config.vsh.yaml
+++ b/src/workflows/quality_control/config.vsh.yaml
@@ -120,9 +120,9 @@ argument_groups:
      - name: "--rseqc_modules"
        type: string
        multiple: true
-        multiple_sep: ","
+        multiple_sep: ";"
        description: Specify the RSeQC modules to run_wf
-        default: bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
+        default: bam_stat;inner_distance;infer_experiment;junction_annotation;junction_saturation;read_distribution;read_duplication
        choices: [ "bam_stat", "inner_distance", "infer_experiment", "junction_annotation", "junction_saturation", "read_distribution", "read_duplication", "tin" ]
      - name: "--sample_size"
        type: integer
--- a/src/workflows/quality_control/main.nf
+++ b/src/workflows/quality_control/main.nf
@@ -7,6 +7,9 @@ workflow run_wf {

        qc_ch = input_ch

+            // temporary fix to force assignment when alignment in skipped
+            | map {it} 
+
            // Feature biotype QC using featureCounts
            | map { id, state -> 
                def biotype_in_gtf = biotypeInGtf(state.gtf, state.biotype)
@@ -215,7 +218,6 @@ workflow run_wf {
            ) 

        merged_ch = qc_ch
-        
            | toSortedList
            | map { list -> 
                def ids = list.collect { id, state -> id }
@@ -489,7 +491,7 @@ workflow run_wf {
                },
                args: [count_col: 3, id_col: 1, outprefix: "deseq2"], 
                toState: [
-                "deseq2_output": "deseq2_output", 
+                    "deseq2_output": "outdir", 
                    "deseq2_pca_multiqc": "pca_multiqc", 
                    "deseq2_dists_multiqc": "dists_multiqc" 
                ], 
@@ -530,9 +532,9 @@ workflow run_wf {
                ],
                args: [count_col: 3, id_col: 1, outprefix: "deseq2"], 
                toState: [
-                "deseq2_output": "deseq2_output", 
-                "deseq2_pca_multiqc": "pca_multiqc", 
-                "deseq2_dists_multiqc": "dists_multiqc" 
+                    "deseq2_output_pseudo": "outdir", 
+                    "deseq2_pca_multiqc_pseudo": "pca_multiqc", 
+                    "deseq2_dists_multiqc_pseudo": "dists_multiqc" 
                ],
                key: "deseq2_qc_pseuso_align_quant"
            )
--- a/src/workflows/rnaseq/config.vsh.yaml
+++ b/src/workflows/rnaseq/config.vsh.yaml
@@ -193,19 +193,6 @@ argument_groups:
      - name: "--bam_csi_index"
        type: boolean_true
        description: Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
-      # - name: "--extra_star_align_args"
-      #   type: string
-      #   default: '--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif'
-      #   description: Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline.
-      # - name: "--star_ignore_sjdbgtf"
-      #   type: boolean_true
-      #   description: When using pre-built STAR indices, do not re-extract and use splice junctions from the GTF file. 
-      # - name: "--seq_platform"
-      #   type: string
-      #   description: Sequencing platform.
-      # - name: "--seq_center"
-      #   type: string
-      #   description: Sequencing center information to be added to read group of BAM files.
      - name: "--salmon_quant_libtype"
        type: string
        description: Override Salmon library type inferred based on strandedness defined in meta object.
@@ -317,12 +304,12 @@ argument_groups:
      - name: "--rseqc_modules"
        type: string
        multiple: true
-        multiple_sep: ","
-        description: Specify the RSeQC modules to run_wf
-        default: bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
+        multiple_sep: ";"
+        description: Specify the RSeQC modules to run_wf (comma-separated list)
+        default: bam_stat;inner_distance;infer_experiment;junction_annotation;junction_saturation;read_distribution;read_duplication
        choices: [ "bam_stat", "inner_distance", "infer_experiment", "junction_annotation", "junction_saturation", "read_distribution", "read_duplication", "tin" ]

-  - name: Multiqc paramenters
+  - name: MultiQC paramenters
    arguments:
      - name: "--multiqc_custom_config"
        type: file
@@ -380,14 +367,14 @@ argument_groups:
        required: false
        must_exist: false
        description: Path to output directory
-        default: fastq/$id.read_1.fastq
+        default: fastq/$id.read_1.fastq.gz
      - name: "--output_fastq_2"
        type: file
        direction: output
        required: false
        must_exist: false
        description: Path to output directory
-        default: fastq/$id.read_2.fastq
+        default: fastq/$id.read_2.fastq.gz
      
      # FastQC
      - name: "--fastqc_html_1"
@@ -872,6 +859,10 @@ argument_groups:
        type: file
        direction: output
        default: deseq2_qc
+      - name: "--deseq2_output_pseudo"
+        type: file
+        direction: output
+        default: deseq2_qc_pseudo

      # MultiQC
      - name: "--multiqc_report"
@@ -903,6 +894,10 @@ argument_groups:
        type: file
        direction: output
        default: pseudo_alignment_quantification/gene_counts_scaled.tsv
+      - name: "--pseudo_tpm_gene"
+        type: file
+        direction: output
+        default: pseudo_alignment_quantification/gene_tpm.tsv
      - name: "--pseudo_tpm_transcript"
        type: file
        direction: output
--- a/src/workflows/rnaseq/main.nf
+++ b/src/workflows/rnaseq/main.nf
@@ -208,10 +208,8 @@ workflow run_wf {
            "aligner": "aligner",
            "rsem_index": "rsem_index",
            "star_index": "star_index", 
-          "extra_star_align_args": "extra_star_align_args", 
+            "star_sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon",
            "star_ignore_sjdbgtf": "star_ignore_sjdbgtf",
-          "seq_platform": "seq_platform", 
-          "seq_center": "seq_center",
            "with_umi": "with_umi", 
            "umi_dedup_stats": "umi_dedup_stats",
            "gtf_group_features": "gtf_group_features",
@@ -245,7 +243,7 @@ workflow run_wf {

      // Filter channels to get samples that passed STAR minimum mapping percentage
      | map { id, state -> 
-      def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0
+        def percent_mapped = (!state.skip_alignment && state.passed_trimmed_reads) ? getStarPercentMapped(state.star_multiqc) : 0.0
        def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false
        [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ]
      }
@@ -435,6 +433,16 @@ workflow run_wf {
            "counts_transcript": "counts_transcript", 
            "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment",
            "deseq2_output": "deseq2_output", 
+            "pseudo_tpm_gene": "pseudo_tpm_gene",
+            "pseudo_counts_gene": "pseudo_counts_gene",
+            "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled",
+            "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", 
+            "pseudo_tpm_transcript": "pseudo_tpm_transcript", 
+            "pseudo_counts_transcript": "pseudo_counts_transcript", 
+            "pseudo_lengths_gene": "pseudo_lengths_gene",
+            "pseudo_lengths_transcript": "pseudo_lengths_transcript",
+            "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment",
+            "deseq2_output_pseudo": "deseq2_output_pseudo",  
            "multiqc_report": "multiqc_report", 
            "multiqc_data": "multiqc_data", 
            "multiqc_plots": "multiqc_plots"
@@ -552,10 +560,8 @@ workflow run_wf {
        ]
      )

-    output_ch = analysis_ch
-
  emit:
-    output_ch
+    analysis_ch
 }

 import nextflow.Nextflow
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml
@@ -1083,9 +1083,9 @@ build_info:
  output: "target/nextflow/fastp"
  executable: "target/nextflow/fastp/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf
@@ -4023,9 +4023,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/fastp",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml
@@ -645,9 +645,9 @@ build_info:
  output: "target/nextflow/featurecounts"
  executable: "target/nextflow/featurecounts/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf
@@ -3549,9 +3549,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/featurecounts",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml
@@ -685,9 +685,9 @@ build_info:
  output: "target/nextflow/gffread"
  executable: "target/nextflow/gffread/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf
@@ -3606,9 +3606,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/gffread",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml
@@ -456,9 +456,9 @@ build_info:
  output: "target/nextflow/multiqc"
  executable: "target/nextflow/multiqc/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf
@@ -3366,9 +3366,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/multiqc",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
  output: "target/nextflow/rsem/rsem_prepare_reference"
  executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf
@@ -3245,9 +3245,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/rsem/rsem_prepare_reference",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml
@@ -277,9 +277,9 @@ build_info:
  output: "target/nextflow/salmon/salmon_index"
  executable: "target/nextflow/salmon/salmon_index/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf
@@ -3129,9 +3129,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/salmon/salmon_index",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,9 +1173,9 @@ build_info:
  output: "target/nextflow/salmon/salmon_quant"
  executable: "target/nextflow/salmon/salmon_quant/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf
@@ -3964,9 +3964,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/salmon/salmon_quant",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,9 +173,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_flagstat"
  executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf
@@ -3028,9 +3028,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_flagstat",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,9 +183,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_idxstats"
  executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf
@@ -3040,9 +3040,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_idxstats",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml
@@ -189,9 +189,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_index"
  executable: "target/nextflow/samtools/samtools_index/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf
@@ -3053,9 +3053,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_index",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml
@@ -332,9 +332,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_sort"
  executable: "target/nextflow/samtools/samtools_sort/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf
@@ -3225,9 +3225,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_sort",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml
@@ -401,9 +401,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_stats"
  executable: "target/nextflow/samtools/samtools_stats/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf
@@ -3295,9 +3295,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_stats",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml
@@ -2663,9 +2663,9 @@ build_info:
  output: "target/nextflow/star/star_align_reads"
  executable: "target/nextflow/star/star_align_reads/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf
@@ -5943,9 +5943,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/star/star_align_reads",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml
@@ -333,9 +333,9 @@ build_info:
  output: "target/nextflow/star/star_genome_generate"
  executable: "target/nextflow/star/star_genome_generate/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf
@@ -3195,9 +3195,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/star/star_genome_generate",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -434,9 +434,9 @@ build_info:
  output: "target/nextflow/umi_tools/umi_tools_extract"
  executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
  viash_version: "0.9.0"
-  git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
-  git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-25-g065297b"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf
@@ -3299,9 +3299,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/umi_tools/umi_tools_extract",
    "viash_version" : "0.9.0",
-    "git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
-    "git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-25-g065297b"
+    "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
+    "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-26-ga13b57d"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/executable/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml
@@ -238,8 +238,8 @@ build_info:
  output: "target/executable/bbmap_bbsplit"
  executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit
@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
 cp -r bbmap/* /usr/local/bin

 LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:07Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:31Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools_genomecov/.config.vsh.yaml
@@ -178,8 +178,8 @@ build_info:
  output: "target/executable/bedtools_genomecov"
  executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools_genomecov/bedtools_genomecov
@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
 chmod a+x /usr/local/bin/bedtools

 LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:05Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cat_additional_fasta/.config.vsh.yaml
+++ b/target/executable/cat_additional_fasta/.config.vsh.yaml
@@ -182,8 +182,8 @@ build_info:
  output: "target/executable/cat_additional_fasta"
  executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/cat_additional_fasta/cat_additional_fasta
+++ b/target/executable/cat_additional_fasta/cat_additional_fasta
@@ -480,9 +480,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:04Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cat_fastq/.config.vsh.yaml
+++ b/target/executable/cat_fastq/.config.vsh.yaml
@@ -169,8 +169,8 @@ build_info:
  output: "target/executable/cat_fastq"
  executable: "target/executable/cat_fastq/cat_fastq"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/cat_fastq/cat_fastq
+++ b/target/executable/cat_fastq/cat_fastq
@@ -472,9 +472,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:03Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:27Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/deseq2_qc/.config.vsh.yaml
+++ b/target/executable/deseq2_qc/.config.vsh.yaml
@@ -237,8 +237,8 @@ build_info:
  output: "target/executable/deseq2_qc"
  executable: "target/executable/deseq2_qc/deseq2_qc"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/deseq2_qc/deseq2_qc
+++ b/target/executable/deseq2_qc/deseq2_qc
@@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
  Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:05Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/dupradar/.config.vsh.yaml
+++ b/target/executable/dupradar/.config.vsh.yaml
@@ -266,8 +266,8 @@ build_info:
  output: "target/executable/dupradar"
  executable: "target/executable/dupradar/dupradar"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/dupradar/dupradar
+++ b/target/executable/dupradar/dupradar
@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
  Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'

 LABEL org.opencontainers.image.description="Companion container for running component dupradar"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:05Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -198,8 +198,8 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -490,9 +490,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:08Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:33Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -177,8 +177,8 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -485,9 +485,9 @@ cargo install --locked --path . && \
 mv /usr/local/fq/target/release/fq /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:32Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/getchromsizes/.config.vsh.yaml
+++ b/target/executable/getchromsizes/.config.vsh.yaml
@@ -167,8 +167,8 @@ build_info:
  output: "target/executable/getchromsizes"
  executable: "target/executable/getchromsizes/getchromsizes"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/getchromsizes/getchromsizes
+++ b/target/executable/getchromsizes/getchromsizes
@@ -480,9 +480,9 @@ make && \
 make install

 LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:04Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gtf2bed/.config.vsh.yaml
+++ b/target/executable/gtf2bed/.config.vsh.yaml
@@ -145,8 +145,8 @@ build_info:
  output: "target/executable/gtf2bed"
  executable: "target/executable/gtf2bed/gtf2bed"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/gtf2bed/gtf2bed
+++ b/target/executable/gtf2bed/gtf2bed
@@ -466,9 +466,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gtf_filter/.config.vsh.yaml
+++ b/target/executable/gtf_filter/.config.vsh.yaml
@@ -155,8 +155,8 @@ build_info:
  output: "target/executable/gtf_filter"
  executable: "target/executable/gtf_filter/gtf_filter"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/gtf_filter/gtf_filter
+++ b/target/executable/gtf_filter/gtf_filter
@@ -470,9 +470,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:04Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:29Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gunzip/.config.vsh.yaml
+++ b/target/executable/gunzip/.config.vsh.yaml
@@ -144,8 +144,8 @@ build_info:
  output: "target/executable/gunzip"
  executable: "target/executable/gunzip/gunzip"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/gunzip/gunzip
+++ b/target/executable/gunzip/gunzip
@@ -466,9 +466,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component gunzip"
-LABEL org.opencontainers.image.created="2024-11-21T08:05:59Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -155,8 +155,8 @@ build_info:
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:00Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -253,8 +253,8 @@ build_info:
  output: "target/executable/kallisto/kallisto_quant"
  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:00Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml
+++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml
@@ -64,6 +64,10 @@ resources:
 - type: "file"
  path: "biotypes_header.txt"
 description: "Calculate features percentage for biotype counts"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
 info: null
 status: "enabled"
 requirements:
@@ -161,8 +165,8 @@ build_info:
  output: "target/executable/multiqc_custom_biotype"
  executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
+++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
@@ -476,9 +476,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:03Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -1183,7 +1183,7 @@ if __name__ == "__main__":
                filtered_lines.append(filtered_line)

    # Concatenate the header and the processed lines
-    result = biotypes_header + '\\n' + '\\n'.join(filtered_lines) + '\\n'
+    result = biotypes_header + '\\n'.join(filtered_lines) + '\\n'

    # Write the result to par_featurecounts_multiqc
    with open(par["featurecounts_multiqc"], 'w') as output_file:
--- a/target/executable/picard_markduplicates/.config.vsh.yaml
+++ b/target/executable/picard_markduplicates/.config.vsh.yaml
@@ -207,8 +207,8 @@ build_info:
  output: "target/executable/picard_markduplicates"
  executable: "target/executable/picard_markduplicates/picard_markduplicates"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/picard_markduplicates/picard_markduplicates
+++ b/target/executable/picard_markduplicates/picard_markduplicates
@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
 mv picard.jar /usr/local/bin 

 LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:02Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:26Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/prepare_multiqc_input/.config.vsh.yaml
+++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml
@@ -409,8 +409,8 @@ build_info:
  output: "target/executable/prepare_multiqc_input"
  executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/prepare_multiqc_input/prepare_multiqc_input
+++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input
@@ -557,9 +557,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
-LABEL org.opencontainers.image.created="2024-11-21T08:05:57Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:22Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
+++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
@@ -138,8 +138,8 @@ build_info:
  output: "target/executable/preprocess_transcripts_fasta"
  executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
+++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
@@ -462,9 +462,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:02Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:27Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/preseq_lcextrap/.config.vsh.yaml
+++ b/target/executable/preseq_lcextrap/.config.vsh.yaml
@@ -191,8 +191,8 @@ build_info:
  output: "target/executable/preseq_lcextrap"
  executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/preseq_lcextrap/preseq_lcextrap
+++ b/target/executable/preseq_lcextrap/preseq_lcextrap
@@ -495,9 +495,9 @@ mkdir build && cd build && \
 make && make install && make HAVE_HTSLIB=1 all 

 LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:01Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:26Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/.config.vsh.yaml
+++ b/target/executable/qualimap/.config.vsh.yaml
@@ -271,8 +271,8 @@ build_info:
  output: "target/executable/qualimap"
  executable: "target/executable/qualimap/qualimap"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/qualimap/qualimap
+++ b/target/executable/qualimap/qualimap
@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
  Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component qualimap"
-LABEL org.opencontainers.image.created="2024-11-21T08:05:59Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -299,8 +299,8 @@ build_info:
  output: "target/executable/rsem/rsem_calculate_expression"
  executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
 /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"

 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
-LABEL org.opencontainers.image.created="2024-11-21T08:05:59Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
@@ -182,8 +182,8 @@ build_info:
  output: "target/executable/rsem/rsem_merge_counts"
  executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
+++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
@@ -483,9 +483,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
-LABEL org.opencontainers.image.created="2024-11-21T08:05:58Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
@@ -163,8 +163,8 @@ build_info:
  output: "target/executable/rseqc/rseqc_bamstat"
  executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
+++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:03Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
@@ -186,8 +186,8 @@ build_info:
  output: "target/executable/rseqc/rseqc_inferexperiment"
  executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
+++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:05Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:30Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
@@ -272,8 +272,8 @@ build_info:
  output: "target/executable/rseqc/rseqc_innerdistance"
  executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
+++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:03Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:27Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
@@ -260,8 +260,8 @@ build_info:
  output: "target/executable/rseqc/rseqc_junctionannotation"
  executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
+++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
-LABEL org.opencontainers.image.created="2024-11-21T08:06:03Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
+LABEL org.opencontainers.image.created="2024-11-27T08:42:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
@@ -249,8 +249,8 @@ build_info:
  output: "target/executable/rseqc/rseqc_junctionsaturation"
  executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
  viash_version: "0.9.0"
-  git_commit: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
-  git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
+  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
+  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/Show More
+++ b/Show More