Build branch main with version main (1d87dc7)

Build pipeline: viash-hub.rnaseq.main-g2rlq

Source commit: 1d87dc7c24

Source message: Multiple fixes (#23)

* multiple fixes

* update arguments and add test

* fix biobox module calls

* fix dependency

* add rsem merge counts

* exclude general stats in multiqc report

* output markduplicates metrics

* rename output reference files

assets/multiqc_config.yml

@@ -1,8 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/data-intuitive/rnaseq.vsh" </a>
+  This report has been generated by the <a href="https://github.com/viash-hub/rnaseq" </a>
   analysis pipeline. 
 report_section_order:
-  "rnaseq.vsh-methods-description":
+  "rnaseq-methods-description":
     order: -1000
   software_versions:
     order: -1001
@@ -10,6 +10,7 @@ report_section_order:
     order: -1002
 
 export_plots: true
+disable_version_detection: true
 
 # Run only these modules
 run_modules:
@@ -19,7 +20,6 @@ run_modules:
   - fastp
   - sortmerna
   - star
-  # - hisat2
   - rsem
   - salmon
   - kallisto
@@ -64,15 +64,13 @@ table_columns_visible:
   fastqc:
     percent_duplicates: False
 
-extra_fn_clean_exts:
+extra_fn_clean_extn:
-  - ".salmon_quant"
+  # - ".mapping_quality"
-  - ".mapping_quality"
+  # - ".MarkDuplicates_flagstat.output.flagstat"
-  - ".genome_sorted"
+  # - ".MarkDuplicates_idxstats.output.idxstats"
-  - ".MarkDuplicates"
+  # - ".MarkDuplicates_stats.output.txt"
-  - ".MarkDuplicates_flagstat"
+  # - ".genome_sorted_MarkDuplicates.output.bam"
-  - ".MarkDuplicates_stats"
+  # - ".genome_sorted_MarkDuplicates"
-  - ".genome_sorted_MarkDuplicates"
-  - ".star_aligned"  
   - ".read_1"  
   - ".read_2"  
 
@@ -117,32 +115,31 @@ sp:
     fn: "*.fastqc.zip"
 
   cutadapt:
-    fn: "*.trimming_report.txt"
+    fn: "*.trimming_report*.txt"
 
   fastp:
-    fn: "*.fastp.json"
+    fn: "*.fastp_out.json"
 
   sortmerna:
     fn: "*sortmerna*.log"
 
   star:
-    fn: "*.star_aligned.log.final.out"
+    fn: "*.star_align_reads.log.txt"
 
   # hisat2:
   #   fn: "*.hisat2.summary.log"
-
+  # salmon:
-  salmon/meta:
+  #   fn: "*meta_info.json"
-    fn: "*meta_info.json"
 
   preseq:
     fn: "*.lc_extrap.txt"
 
   samtools/stats:
-    fn: "*.stats"
+    fn: "*_stats.output.txt"
   samtools/flagstat:
-    fn: "*.flagstat"
+    fn: "*_flagstat.output.flagstat"
   samtools/idxstats:
-    fn: "*.idxstats*"
+    fn: "*_idxstats.output.idxstats"
 
   rseqc/bam_stat:
     fn: "*.mapping_quality.txt"

src/cat_fastq/config.vsh.yaml

@@ -25,13 +25,13 @@ argument_groups:
   - name: "--fastq_1"
     type: file
     direction: output
-    default: $id.read_1.merged.fastq
+    default: $id_r1.fastq
     description: Concatenated read 1 fastq
   - name: "--fastq_2"
     type: file
     direction: output
     must_exist: false
-    default: $id.read_2.merged.fastq
+    default: $id_r2.fastq
     description: Concatenated read 2 fastq
 
 resources:

src/fastqc/script.sh

@@ -30,10 +30,12 @@ fastqc -o $tmpdir ${input[*]}
 
 file1=$(basename -- "${input[0]}")
 read1="${file1%.fastq*}"
-file2=$(basename -- "${input[1]}")
-read2="${file2%.fastq*}"
-
 [[ -e "${tmpdir}/${read1}_fastqc.html" ]] && cp "${tmpdir}/${read1}_fastqc.html" $par_fastqc_html_1
-[[ -e "${tmpdir}/${read2}_fastqc.html" ]] && cp "${tmpdir}/${read2}_fastqc.html" $par_fastqc_html_2
 [[ -e "${tmpdir}/${read1}_fastqc.zip" ]] && cp "${tmpdir}/${read1}_fastqc.zip" $par_fastqc_zip_1
-[[ -e "${tmpdir}/${read2}_fastqc.zip" ]] && cp "${tmpdir}/${read2}_fastqc.zip" $par_fastqc_zip_2
+
+if $par_paired; then
+  file2=$(basename -- "${input[1]}")
+  read2="${file2%.fastq*}"
+  [[ -e "${tmpdir}/${read2}_fastqc.html" ]] && cp "${tmpdir}/${read2}_fastqc.html" $par_fastqc_html_2
+  [[ -e "${tmpdir}/${read2}_fastqc.zip" ]] && cp "${tmpdir}/${read2}_fastqc.zip" $par_fastqc_zip_2
+fi

src/kallisto/kallisto_quant/script.sh

@@ -23,16 +23,7 @@ if [[ "$par_extra_args" != *"--fr-stranded"* ]] && [[ "$par_extra_args" != *"--r
 fi
 
 mkdir -p $par_output
-echo "kallisto quant \
+
-    ${meta_cpus:+--threads $meta_cpus} \
-    --index $par_index \
-    ${par_gtf:+--gtf $par_gtf} \
-    ${par_chromosomes:+--chromosomes $par_chromosomes} \
-    $single_end_params \
-    $strandedness \
-    $par_extra_args \
-    -o $par_output \
-    ${input[*]} 2> >(tee -a ${par_output}/kallisto_quant.log >&2)"
 kallisto quant \
     ${meta_cpus:+--threads $meta_cpus} \
     --index $par_index \

src/prepare_multiqc_input/script.sh

@@ -24,6 +24,8 @@ IFS="," read -ra rsem_multiqc <<< $par_rsem_multiqc && for file in "${rsem_multi
 
 IFS="," read -ra salmon_multiqc <<< $par_salmon_multiqc && for file in "${salmon_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
 
+IFS="," read -ra pseudo_multiqc <<< $par_pseudo_multiqc && for file in "${pseudo_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
+
 IFS="," read -ra samtools_stats <<< $par_samtools_stats && for file in "${samtools_stats[@]}"; do [ -e "$file" ] && cp -r "$file" $par_output/; done
 
 IFS="," read -ra samtools_flagstat <<< $par_samtools_flagstat && for file in "${samtools_flagstat[@]}"; do [ -e "$file" ] && cp -r "$file" $par_output/; done
@@ -32,12 +34,9 @@ IFS="," read -ra samtools_idxstats <<< $par_samtools_idxstats && for file in "${
 
 IFS="," read -ra markduplicates_multiqc <<< $par_markduplicates_multiqc && for file in "${markduplicates_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
 
-IFS="," read -ra pseudo_multiqc <<< $par_pseudo_multiqc && for file in "${pseudo_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
-
-
 IFS="," read -ra featurecounts_multiqc <<< $par_featurecounts_multiqc && for file in "${featurecounts_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
 
-IFS="," read -ra featurecounts_rrna_multiqc <<< $par_featurecounts_rrna_multiqc&& for file in "${featurecounts_rrna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
+IFS="," read -ra featurecounts_rrna_multiqc <<< $par_featurecounts_rrna_multiqc && for file in "${featurecounts_rrna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
 
 [ -e "$par_aligner_pca_multiqc" ] && cp -r "$par_aligner_pca_multiqc" "$par_output/"
 

src/rsem/rsem_calculate_expression/config.vsh.yaml

@@ -33,9 +33,6 @@ argument_groups:
   - name: "--extra_args"
     type: string
     description: Extra rsem-calculate-expression arguments in addition to the defaults.
-  - name: "--versions"
-    type: file
-    must_exist: false
 
 - name: "Output"
   arguments:

src/rsem/rsem_calculate_expression/script.sh

@@ -19,10 +19,10 @@ fi
 
 IFS="," read -ra input <<< $par_input
 
-INDEX=`find -L $meta_resources_dir/ -name "*.grp" | sed 's/\.grp$//'`
+INDEX=`find -L $par_index/ -name "*.grp" | sed 's/\.grp$//'`
 
 rsem-calculate-expression \
-    ${meta_cpus:+--num-theads $meta_cpus} \
+    ${meta_cpus:+--num-threads $meta_cpus} \
     $strandedness \
     ${par_paired:+--paired-end} \
     $par_extra_args \
@@ -30,3 +30,10 @@ rsem-calculate-expression \
     $INDEX \
     $par_id
     
+[[ -e "${par_id}.genes.results" ]] && mv "${par_id}.genes.results" $par_counts_gene
+[[ -e "${par_id}id.isoforms.results" ]] && mv "${par_id}id.isoforms.results" $par_counts_transcripts
+[[ -e "${par_id}.stat" ]] && mv -r "${par_id}.stat" $par_stat
+# [[ -e "${par_id}.log" ]] && mv "${par_id}.log" $par_logs
+[[ -e "${par_id}.STAR.genome.bam" ]] && mv "${par_id}.STAR.genome.bam" $par_bam_star
+[[ -e "${par_id}.genome.bam" ]] && mv "${par_id}.genome.bam" $par_bam_genome
+[[ -e "${par_id}.transcript.bam" ]] && mv "${par_id}.transcript.bam" $par_bam_transcript

src/rsem/rsem_merge_counts/config.vsh.yaml

@@ -18,9 +18,6 @@ argument_groups:
   - name: "--counts_transcripts"
     type: file
     description: Expression counts on transcript level (isoforms)
-  - name: "--versions"
-    type: file
-    must_exist: false
 
 - name: "Output"
   arguments: 
@@ -44,10 +41,6 @@ argument_groups:
     description: File containing transcript TPM across all samples.
     default: rsem.merged.transcript_tpm.tsv
     direction: output
-  - name: "--updated_versions"
-    type: file
-    default: versions.yml
-    direction: output
 
 resources:
   - type: bash_script

src/trimgalore/config.vsh.yaml

@@ -232,13 +232,13 @@ argument_groups:
         required: false
         description: Output file for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists.
         direction: output
-        example: read_1.fastq
+        example: read_1.fastq.gz
       - name: --trimmed_r2
         type: file
         required: false
         description: Output file for read 2. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists.
         direction: output
-        example: read_2.fastq
+        example: read_2.fastq.gz
       - name: --trimming_report_r1
         type: file
         required: false

src/workflows/genome_alignment_and_quant/config.vsh.yaml

@@ -76,7 +76,7 @@ argument_groups:
     type: string
     default: 'gene_name'
     description: By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon.
-  - name: extra_rsem_calculate_expression_args
+  - name: --extra_rsem_calculate_expression_args
     type: string
     description: Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline.
   - name: "--aligner"
@@ -96,7 +96,7 @@ argument_groups:
   - name: "--star_multiqc"
     type: file
     direction: output
-    default: $id.star_align.log
+    default: $id_star.log
   - name: "--genome_bam_sorted"
     type: file
     direction: output
@@ -145,6 +145,39 @@ argument_groups:
     type: file
     direction: output
     default: $id.quant.sf
+  - name: "--salmon_multiqc"
+    type: file
+    direction: output
+  - name: "--rsem_counts_gene"
+    type: file
+    description: Expression counts on gene level
+    default: $id.genes.results
+    direction: output
+  - name: "--counts_transcripts"
+    type: file
+    description: Expression counts on transcript level
+    default: $id.isoforms.results
+    direction: output
+  - name: "--rsem_multiqc"
+    type: file
+    description: RSEM statistics
+    default: $id.stat
+    direction: output
+  - name: "--bam_star_rsem"
+    type: file
+    description: BAM file generated by STAR (optional)
+    default: $id.STAR.genome.bam
+    direction: output
+  - name: "--bam_genome_rsem"
+    type: file
+    description: Genome BAM file (optional)
+    default: $id.genome.bam
+    direction: output
+  - name: "--bam_transcript_rsem"
+    type: file
+    description: Transcript BAM file (optional)
+    default: $id.transcript.bam
+    direction: output
  
 resources:
   - type: nextflow_script
@@ -165,8 +198,10 @@ dependencies:
   - name: samtools/samtools_idxstats
     repository: biobox
   - name: umitools/umitools_dedup
+  # - name: umi_tools/umi_tools_dedup
     # repository: biobox
   - name: umitools_prepareforquant
+  # - name: umi_tools/umi_tools_prepareforquant
   #   repository: biobox
   - name: salmon/salmon_quant
     repository: biobox

src/workflows/genome_alignment_and_quant/main.nf

@@ -280,6 +280,11 @@ workflow run_wf {
         ]
     )
 
+    | map { id, state -> 
+      def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state
+      [ id, mod_state ]
+    }
+  
     | rsem_calculate_expression.run (
         runIf: { id, state -> state.aligner == 'star_rsem' },
         fromState: [
@@ -357,6 +362,7 @@ workflow run_wf {
       [ "star_alignment": "star_alignment", 
         "star_multiqc": "star_multiqc", 
         "rsem_multiqc": "rsem_multiqc",
+        "salmon_multiqc": "salmon_multiqc",
         "genome_bam_sorted": "genome_bam_sorted", 
         "genome_bam_index": "genome_bam_index",  
         "genome_bam_stats": "genome_bam_stats", 
@@ -368,7 +374,11 @@ workflow run_wf {
         "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", 
         "transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
         "quant_out_dir": "quant_out_dir",
-        "quant_results_file": "quant_results_file" ]
+        "quant_results_file": "quant_results_file",
+        "rsem_counts_gene": "rsem_counts_gene",
+        "rsem_counts_transcripts": "rsem_counts_transcripts",
+        "bam_genome_rsem": "bam_genome_rsem",
+        "bam_transcript_rsem": "bam_transcript_rsem" ]
     )
     
   emit:

src/workflows/genome_alignment_and_quant/test_run.sh

@@ -1,25 +1,43 @@
 #!/bin/bash
 
-viash ns build --setup cb --parallel
+# v;iash ns build --setup cb --parallel
 
 # Split error message from standard output
 # viash ns list > /dev/null 
 
-CURR=`pwd` 
+echo "> Preparing reference data files"
+gunzip --keep testData/minimal_test/reference/genes.gtf.gz
 
 cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
 id,fastq_1,fastq_2,strandedness
 WT_REP1,SRR6357070_1.fastq.gz,SRR6357070_2.fastq.gz,reverse
-WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
+RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
 HERE
 
+# echo "> Test 1: STAR Salmon"
+# nextflow run target/nextflow/workflows/genome_alignment_and_quant/main.nf \
+#   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
+#   --publish_dir test_results/genome_alignment_test1 \
+#   --fasta testData/minimal_test/reference/genome.fasta \
+#   --gtf testData/minimal_test/reference/genes.gtf \
+#   --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
+#   --star_index test_results/output_test1/STAR_index \
+#   --aligner star_salmon \
+#   -profile docker \
+#   -resume
+
+echo "> Test 2: STAR RSEM"
 nextflow run target/nextflow/workflows/genome_alignment_and_quant/main.nf \
   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
-  --publish_dir "test_results/genome_alignment_test" \
+  --publish_dir test_results/genome_alignment_test2 \
   --fasta testData/minimal_test/reference/genome.fasta \
-  --gtf testData/minimal_test/reference/genes.gtf.gz \
+  --gtf testData/minimal_test/reference/genes.gtf \
   --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
-  --star_index testData/test_output/star_index \
+  --rsem_index test_results/output_test1/RSEM_index \
-  --aligner "star_rsem" \
+  --aligner star_rsem \
+  --extra_rsem_calculate_expression_args "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" \
   -profile docker \
-  # -resume
+  -resume
+
+echo "Removing reference data files"
+rm testData/minimal_test/reference/genes.gtf

src/workflows/post_processing/config.vsh.yaml

@@ -79,27 +79,27 @@ argument_groups:
       - name: "--processed_genome_bam"
         type: file
         direction: output
-        default: $id.markdup.sorted.bam
+        default: $id.genome.bam
       - name: "--genome_bam_index"
         type: file
         direction: output
-        default: $id.markdup.sorted.bam
+        default: $id.genome.bam.bai
       - name: "--genome_bam_stats"
         type: file
         direction: output
-        default: $id.markdup.sorted.bam.stats
+        default: $id.genome.stats
       - name: "--genome_bam_flagstat"
         type: file
         direction: output
-        default: $id.markdup.sorted.bam.flagstat
+        default: $id.genome.flagstat
       - name: "--genome_bam_idxstats"
         type: file
         direction: output
-        default: $id.markdup.sorted.bam.idxstats
+        default: $id.genome.idxstats
       - name: "--markduplicates_metrics"
         type: file
         direction: output
-        default: $id.markdup.sorted.MarkDuplicates.metrics.txt
+        default: $id.MarkDuplicates.metrics.txt
       - name: "--stringtie_transcript_gtf"
         type: file
         direction: output
@@ -151,6 +151,8 @@ dependencies:
   - name: samtools/samtools_idxstats
     repository: biobox
   - name: stringtie
+  # - name: bedtools/bedtools_genomecov
+  #   repository: biobox
   - name: bedtools_genomecov
   - name: ucsc/bedclip
   - name: ucsc/bedgraphtobigwig

src/workflows/post_processing/main.nf

@@ -16,20 +16,20 @@ workflow run_wf {
                 "extra_picard_args": "extra_picard_args"
             ], 
             toState: [
-                "genome_bam": "output_bam",
+                "processed_genome_bam": "output_bam",
                 "markduplicates_metrics": "metrics"
             ]
         )
         | samtools_sort.run (
             runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
-            fromState: [ "input": "genome_bam" ],
+            fromState: [ "input": "processed_genome_bam" ],
-            toState: [ "genome_bam": "output" ],
+            toState: [ "processed_genome_bam": "output" ],
             key: "genome_sorted_MarkDuplicates" 
         )
         | samtools_index.run (
             runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
             fromState: [
-                "input": "genome_bam", 
+                "input": "processed_genome_bam", 
                 "csi": "bam_csi_index"
             ],
             toState: [ "genome_bam_index": "output" ],
@@ -38,7 +38,7 @@ workflow run_wf {
         | samtools_stats.run (
             runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, 
             fromState: [
-                "input": "genome_bam", 
+                "input": "processed_genome_bam", 
                 "bai": "genome_bam_index" 
             ],
             toState: [ "genome_bam_stats": "output" ],
@@ -47,7 +47,7 @@ workflow run_wf {
         | samtools_flagstat.run (
             runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, 
             fromState: [
-                "bam": "genome_bam", 
+                "bam": "processed_genome_bam", 
                 "bai": "genome_bam_index"
             ],
             toState: [ "genome_bam_flagstat": "output" ],
@@ -56,7 +56,7 @@ workflow run_wf {
         | samtools_idxstats.run(
             runIf: { id, state -> !state.skip_markduplicates && !state.with_umi }, 
             fromState: [
-            "bam": "genome_bam", 
+            "bam": "processed_genome_bam", 
             "bai": "genome_bam_index"
             ],
             toState: [ "genome_bam_idxstats": "output" ],
@@ -67,7 +67,7 @@ workflow run_wf {
             runIf: { id, state -> !state.skip_stringtie }, 
             fromState: [
                 "strandedness": "strandedness", 
-                "bam": "genome_bam",
+                "bam": "processed_genome_bam",
                 "annotation_gtf": "gtf",
                 "extra_stringtie_args": "extra_stringtie_args"
             ], 
@@ -85,7 +85,7 @@ workflow run_wf {
             runIf: { id, state -> !state.skip_bigwig },
             fromState: [
                 "strandedness": "strandedness", 
-                "bam": "genome_bam",
+                "bam": "processed_genome_bam",
                 "extra_bedtools_args": "extra_bedtools_args"
             ],
             toState: [
@@ -140,7 +140,7 @@ workflow run_wf {
         }
 
         | setState (
-            "processed_genome_bam": "genome_bam", 
+            "processed_genome_bam": "processed_genome_bam", 
             "genome_bam_index": "genome_bam_index",
             "genome_bam_stats": "genome_bam_stats",
             "genome_bam_flagstat": "genome_bam_flagstat", 

src/workflows/post_processing/test_run.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-viash ns build --setup cb --parallel
+# viash ns build --setup cb --parallel
 
 nextflow run target/nextflow/workflows/post_processing/main.nf \
   --publish_dir "testData/paired_end_test" \

src/workflows/pre_processing/config.vsh.yaml

@@ -139,13 +139,13 @@ argument_groups:
   - name: "Read filtering options"
     arguments: 
       - name: "--skip_bbsplit"
-        type: boolean
+        type: boolean_true
         description: Skip BBSplit for removal of non-reference genome reads.
-        default: true
+        # default: true
       - name: "--remove_ribo_rna"
-        type: boolean
+        type: boolean_true
         description: Enable the removal of reads derived from ribosomal RNA using SortMeRNA.
-        default: false
+        # default: false
   
   - name: "Other options"
     arguments: 
@@ -162,14 +162,14 @@ argument_groups:
         required: false
         must_exist: false
         description: Path to output directory
-        default: $id.$key.read_1.fastq
+        default: $id.read_1.fastq
       - name: "--qc_output2"
         type: file
         direction: output
         required: false
         must_exist: false
         description: Path to output directory
-        default: $id.$key.read_2.fastq
+        default: $id.read_2.fastq
       - name: "--fastqc_html_1"
         type: file
         direction: output
@@ -246,7 +246,20 @@ argument_groups:
         direction: output
         description: Results from Salmon quant
         default: $id.salmon_quant_output
-
+      - name: --trim_json
+        type: file
+        description: The fastp json format report file name
+        default: $id.fastp_out.json
+        direction: output
+      - name: --trim_html
+        type: file
+        description: The fastp html format report file name
+        default: $id.fastp_out.html
+        direction: output
+      - name: --merged_out
+        type: file
+        description: File name to store merged fastp output.
+        direction: output
 resources:
   - type: nextflow_script
     path: main.nf
@@ -256,14 +269,18 @@ dependencies:
   - name: fastqc
     # repository: biobox
   - name: umitools/umitools_extract
-    # repository: biobox
+  - name: umi_tools/umi_tools_extract
+    repository: biobox
   - name: trimgalore
     # repository: biobox
   - name: bbmap_bbsplit
+    # repository: biobox
   - name: sortmerna
+    # repository: biobox
   - name: fastp
     repository: biobox
   - name: fq_subsample
+    # repository: biobox
   - name: salmon/salmon_quant
     repository: biobox
    

src/workflows/pre_processing/main.nf

@@ -74,7 +74,8 @@ workflow run_wf {
         "trim_zip_2": "trimmed_fastqc_zip_2",
         "trim_html_1": "trimmed_fastqc_html_1",
         "trim_html_2": "trimmed_fastqc_html_2"
-      ]
+      ],
+      args: [gzip: true, fastqc: true]
     )
 
     // Trim reads using fastp
@@ -90,7 +91,7 @@ workflow run_wf {
       ],
       toState: [
         "fastq_1": "out1", 
-        // "fastq_2": "out2",
+        "fastq_2": "out2",
         "failed_trim": "failed_out",
         "failed_trim_unpaired1": "unpaired1",
         "failed_trim_unpaired2": "unpaired2",
@@ -154,8 +155,10 @@ workflow run_wf {
       runIf: { id, state -> state.strandedness == 'auto' }, 
       fromState: { id, state ->
         def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
-        [ input: input,
+        [ 
-          extra_args: state.extra_fq_subsample_args ] 
+          input: input,
+          extra_args: state.extra_fq_subsample_args
+        ]
       },
       toState: [
         "subsampled_fastq_1": "output_1",
@@ -189,9 +192,8 @@ workflow run_wf {
         def mates1 = state.paired ? state.subsampled_fastq_1 : null
         def mates2 = state.paired ? state.subsampled_fastq_2 : null
         [ unmated_reads: unmated_reads,
-          mates1: state.fastq1, 
+          mates1: mates1, 
-          mates2: state.fastq2, 
+          mates2: mates2, 
-          targets: state.transcript_fasta, 
           gene_map: state.gtf, 
           index: state.salmon_index,
           lib_type: state.lib_type ]

src/workflows/pre_processing/test_run.sh

@@ -2,30 +2,55 @@
 
 # viash ns build --parallel --setup cb 
 
-# nextflow run target/nextflow/workflows/pre_processing/main.nf \
+echo "> Preparing reference data files"
-#   --id RAP1_UNINDUCED_REP1 \
+gunzip --keep testData/minimal_test/reference/genes.gtf.gz
-#   --input 'testData/minimal_test/input_fastq/SRR6357073_1.fastq.gz' \
+mkdir -p testData/minimal_test/reference/salmon_index
-#   --publish_dir "test_results/preprocessing_no_samplesheet" \
+tar -C testData/minimal_test/reference/salmon_index --strip-components 1 -xavf testData/minimal_test/reference/salmon.tar.gz --no-same-owner
-#   --umitools_bc_pattern "NNNN" \
-#   -profile docker \
-#   -resume
 
 # Test paired-end data
 cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
 id,fastq_1,fastq_2,strandedness
-WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
+WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,auto
-RAP1_IAA_30M_REP1,SRR6357076_1.fastq.gz,SRR6357076_2.fastq.gz,reverse
+RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
 HERE
 
+echo "> Test 1: Running workflow with trimgalore"
 nextflow run target/nextflow/workflows/pre_processing/main.nf \
   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
-  --publish_dir "testData/paired_end_test" \
+  --publish_dir "test_results/pre_processing_test1" \
   --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
   --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
-  --gtf testData/minimal_test/reference/gene_annotation.gtf \
+  --gtf testData/minimal_test/reference/genes.gtf \
-  --salmon_index testData/minimal_test/reference/salmon.tar.gz \
+  --salmon_index testData/minimal_test/reference/salmon_index \
   --skip_trimming false \
   --trimmer trimgalore \
   --remove_ribo_rna false \
+  --ribo_database_manifest testData/minimal_test/reference/rrna-db-defaults.txt \
+  --skip_bbsplit false \
+  --bbsplit_index test_results/prepare_genome_test1/BBSplit_index \
   -profile docker \
   -resume
+
+# echo "> Test 2: Running workflow with fastp"
+# nextflow run target/nextflow/workflows/pre_processing/main.nf \
+#   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
+#   --publish_dir "test_results/pre_processing_test2" \
+#   --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
+#   --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
+#   --gtf testData/minimal_test/reference/genes.gtf \
+#   --salmon_index testData/minimal_test/reference/salmon_index \
+#   --skip_trimming false \
+#   --trimmer fastp \
+#   --remove_ribo_rna false \
+#   --ribo_database_manifest testData/minimal_test/reference/rrna-db-defaults.txt \
+#   --skip_bbsplit false \
+#   --bbsplit_index test_results/output_test1/BBSplit_index \
+#   -profile docker \
+#   -resume
+
+echo "Removing reference data files"
+rm testData/minimal_test/reference/genes.gtf
+rm -r testData/minimal_test/reference/salmon_index
+
+# TODO: Fix error while running sortmerna component
+# docker: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "/bin/bash": stat /bin/bash: no such file or directory: unknown.

src/workflows/prepare_genome/config.vsh.yaml

@@ -163,6 +163,7 @@ dependencies:
   - name: salmon/salmon_index
     repository: biobox
   - name: kallisto/kallisto_index
+    # repository: biobox
 
 runners: 
 - type: executable

src/workflows/prepare_genome/main.nf

@@ -35,9 +35,15 @@ workflow run_wf {
         // gff to gtf
         | gffread.run (
             runIf: {id, state -> !state.gtf && state.gff}, 
-            fromState: [ "input": "annotation" ], 
+            fromState: [ 
+                "input": "gff",
+                "genome": "fasta" 
+            ], 
             toState: [ "gtf": "outfile" ],
-            args: [output: "gene_annotation.gtf"] 
+            args: [
+                outfile: "gene_annotation.gtf", 
+                gtf_output: true
+            ] 
         )
 
         | gtf_filter.run(
@@ -116,13 +122,19 @@ workflow run_wf {
         | rsem_prepare_reference.run ( 
             runIf: {id, state -> !state.transcript_fasta}, 
             fromState: [
-                "fasta": "fasta", 
+                "reference_fasta_files": "fasta", 
                 "gtf": "gtf"
             ], 
-            toState: [ "transcript_fasta": "transcript_fasta" ], 
+            toState: [ "make_transcript_fasta_output": "output" ], 
-            key: "make_transcript_fasta",
+            key: "make_transcript_fasta",\
-            args: [transcript_fasta: "transcriptome.fasta"]
+            args: [reference_name: "genome"]
         )
+        | map { id, state -> 
+            def transcript_fasta = (!state.transcript_fasta) ?
+                state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} : 
+                state.transcript_fasta
+            [ id, state + [transcript_fasta: transcript_fasta] ]
+        }
 
         // chromosome size and fai index
         | getchromsizes.run (
@@ -195,11 +207,12 @@ workflow run_wf {
         | rsem_prepare_reference.run ( 
             runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'}, 
             fromState: [
-                "fasta": "fasta", 
+                "reference_fasta_files": "fasta", 
                 "gtf": "gtf"
             ], 
-            toState: [ "rsem_index": "rsem" ], 
+            toState: [ "rsem_index": "output" ], 
             key: "generate_rsem_index",
+            args: [reference_name: "genome"]
         )
         
         // TODO: Uncompress HISAT2 index or generate from scratch if required
@@ -229,10 +242,7 @@ workflow run_wf {
         // Uncompress Kallisto index or generate from scratch if required
         | untar.run (
             runIf: {id, state -> state.kallisto_index}, 
-            fromState: [
+            fromState: [ "input": "kallisto_index" ], 
-                "input": "kallisto_index", 
-                "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size"
-            ], 
             toState: [ "kallisto_index": "output" ], 
             key: "untar_kallisto_index",
             args: [output: "Kallisto_index"]

src/workflows/prepare_genome/test_run.sh

@@ -1,26 +1,50 @@
 #!/bin/bash
 
-viash ns build --setup cb --parallel
+# viash ns build --setup cb --parallel -q prepare_genome
 
+# echo "Test 1: Annotation file format - GTF"
+# nextflow run target/nextflow/workflows/prepare_genome/main.nf \
+#     --id test1 \
+#     --publish_dir "test_results/prepare_genome_test1" \
+#     --fasta testData/minimal_test/reference/genome.fasta \
+#     --gtf testData/minimal_test/reference/genes.gtf.gz \
+#     --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
+#     --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
+#     --genotype false \
+#     --biotype gene_biotype \
+#     --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
+#     --salmon_index testData/minimal_test/reference/salmon.tar.gz \
+#     --rsem_index testData/minimal_test/reference/rsem.tar.gz \
+#     -profile docker \
+#     -resume
+
+# echo "Test 2: Annotation file format - GFF"
+# nextflow run target/nextflow/workflows/prepare_genome/main.nf \
+#     --id test2 \
+#     --publish_dir "test_results/prepare_genome_test2" \
+#     --fasta testData/minimal_test/reference/genome.fasta \
+#     --gff testData/minimal_test/reference/genes.gff.gz \
+#     --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
+#     --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
+#     --genotype false \
+#     --biotype gene_biotype \
+#     --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
+#     --salmon_index testData/minimal_test/reference/salmon.tar.gz \
+#     --rsem_index testData/minimal_test/reference/rsem.tar.gz \
+#     -profile docker \
+#     -resume
+
+echo "Test 3: Annotation file format - GTF; Generate indices; Generate transcripts fasta"
 nextflow run target/nextflow/workflows/prepare_genome/main.nf \
-    --id ref \
+    --id test3 \
-    --publish_dir "testData/test_output" \
+    --publish_dir "test_results/prepare_genome_test3" \
-    --fasta testData/reference/genome.fasta \
+    --fasta testData/minimal_test/reference/genome.fasta \
-    --gtf testData/reference/genes.gtf.gz \
+    --gtf testData/minimal_test/reference/genes.gtf.gz \
-    --additional_fasta testData/reference/gfp.fa.gz \
+    --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
-    --transcript_fasta testData/reference/transcriptome.fasta \
     --genotype false \
     --biotype gene_biotype \
-    --bbsplit_fasta_list testData/reference/bbsplit_fasta_list.txt \
+    --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
-    --salmon_index testData/reference/salmon.tar.gz \
+    --pseudo_aligner kallisto \
-    # -profile docker \ 
+    --aligner star_rsem \
-    # -resume
+    -profile docker \
-    # --gff testData/reference/genes.gff.gz \
+    -resume
-    # --prepare_tools_indices a,b,c \
-    # --gene_bed "" \
-    # --splicesites "" \
-    # --star_index "" \
-    # --bbsplit_index "" \
-    # --rsem_index testData/reference/rsem.tar.gz \
-    # --salmon_index testData/reference/salmon.tar.gz \
-    # --hisat2_index testData/reference/hisat2.tar.gz \

src/workflows/pseudo_alignment_and_quant/config.vsh.yaml

@@ -59,11 +59,10 @@ argument_groups:
   - name: "--pseudo_multiqc"
     type: file
     direction: output
-    default: $id.quant.log
   - name: "--quant_out_dir"
     type: file
     direction: output
-    default: $id.salmon_quant
+    default: $id.quant
   - name: "--salmon_quant_results_file"
     type: file
     direction: output

src/workflows/pseudo_alignment_and_quant/main.nf

@@ -46,11 +46,16 @@ workflow run_wf {
             lib_type: state.lib_type ]
         },
         toState: [ 
-          "quant_results_dir": "output",
+          "quant_out_dir": "output",
           "salmon_quant_results_file": "quant_results" 
         ]
     )
 
+    | map { id, state -> 
+      def mod_state = (state.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state
+      [ id, mod_state ]
+    }
+
     | kallisto_quant.run ( 
         runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
         fromState: [

src/workflows/pseudo_alignment_and_quant/test_run.sh

@@ -1,26 +1,45 @@
 #!/bin/bash
 
-viash ns build --setup cb -q pseudo_alignment_and_quant
+# viash ns build --setup cb -q pseudo_alignment_and_quant
 
 # Split error message from standard output
 # viash ns list > /dev/null 
 
-CURR=`pwd` 
+echo "> Preparing reference data files"
+gunzip --keep testData/minimal_test/reference/genes.gtf.gz
+mkdir -p testData/minimal_test/reference/salmon_index
+tar -C testData/minimal_test/reference/salmon_index --strip-components 1 -xavf testData/minimal_test/reference/salmon.tar.gz 
 
-# Test paired-end data
 cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
 id,fastq_1,fastq_2,strandedness
 WT_REP1,SRR6357070_1.fastq.gz,SRR6357070_2.fastq.gz,reverse
-WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
+RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
 HERE
 
+echo "> Test 1: Salmon qunatification"
 nextflow run target/nextflow/workflows/pseudo_alignment_and_quant/main.nf \
   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
-  --publish_dir "test_results/psudo_alignment_test" \
+  --publish_dir "test_results/pseudo_alignment_test1" \
   --fasta testData/minimal_test/reference/genome.fasta \
   --gtf testData/minimal_test/reference/genes.gtf.gz \
   --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
-  --salmon_index testData/minimal_test/reference/salmon.tar.gz \
+  --salmon_index testData/minimal_test/reference/salmon_index \
   --pseudo_aligner salmon \
   -profile docker \
-  # -resume
+  -resume
+
+# echo "> Test 2: Kallisto qunatification"
+# nextflow run target/nextflow/workflows/pseudo_alignment_and_quant/main.nf \
+#   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
+#   --publish_dir "test_results/pseudo_alignment_test2" \
+#   --fasta testData/minimal_test/reference/genome.fasta \
+#   --gtf testData/minimal_test/reference/genes.gtf.gz \
+#   --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
+#   --kallisto_index test_results/prepare_genome_test3/Kallisto_index \
+#   --pseudo_aligner kallisto \
+#   -profile docker \
+#   -resume
+
+echo "Removing reference data files"
+rm testData/minimal_test/reference/genes.gtf
+rm -r testData/minimal_test/reference/salmon_index

src/workflows/quality_control/config.vsh.yaml

@@ -41,10 +41,10 @@ argument_groups:
         description: By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon.
       - name: "--quant_out_dir"
         type: file
-        description: Directory containing quantification results.
+        description: Directory containing Salmon quantification results.
       - name: "--quant_results_file"
         type: file
-        description: Quantification file.
+        description: Salmon quantification file.
       - name: "--pseudo_quant_out_dir"
         type: file
         description: Directory containing quantification results for pseudo alignment.
@@ -59,7 +59,13 @@ argument_groups:
         description: Method used for alognment and qqunatification.
       - name: "--pseudo_aligner"
         type: string
-        description: Method used for [seudo alignment and quantification.
+        description: Method used for pseudo alignment and quantification.
+      - name: "--rsem_counts_gene"
+        type: file
+        description: Expression counts on gene level
+      - name: "--rsem_counts_transcripts"
+        type: file
+        description: Expression counts on transcript level
 
       - name: "--skip_qc"
         type: boolean
@@ -258,11 +264,6 @@ argument_groups:
         type: string
       - name: "--multiqc_methods_description"
         type: file
-      - name: "--mqc_yml"
-        type: file
-        description: Software versions
-      - name: "--workflow_summary"
-        type: file
       - name: "--passed_trimmed_reads"
         type: boolean
       - name: "--num_trimmed_reads"
@@ -297,8 +298,8 @@ argument_groups:
         must_exist: false
       # - name: "--hisat2_multiqc"
       #   type: file
-      # - name: "--rsem_multiqc"
+      - name: "--rsem_multiqc"
-      #   type: file
+        type: file
       - name: "--genome_bam_stats"
         type: file
         must_exist: false
@@ -542,9 +543,6 @@ argument_groups:
         type: file
         direction: output
         default: multiqc_plots
-      - name: "--multiqc_versions"
-        type: file
-        direction: output
 
       # Biotype QC
       - name: "--featurecounts"
@@ -600,27 +598,27 @@ argument_groups:
       - name: "--pseudo_tpm_gene"
         type: file
         direction: output
-        default: salmon.merged.pseudo_gene_tpm.tsv
+        default: pseudo_gene_tpm.tsv
       - name: "--pseudo_counts_gene"
         type: file
         direction: output
-        default: salmon.merged.pseudo_gene_counts.tsv
+        default: pseudo_gene_counts.tsv
       - name: "--pseudo_counts_gene_length_scaled"
         type: file
         direction: output
-        default: salmon.merged.pseudo_gene_counts_length_scaled.tsv
+        default: pseudo_gene_counts_length_scaled.tsv
       - name: "--pseudo_counts_gene_scaled"
         type: file
         direction: output
-        default: salmon.merged.pseudo_gene_counts_scaled.tsv
+        default: pseudo_gene_counts_scaled.tsv
       - name: "--pseudo_tpm_transcript"
         type: file
         direction: output
-        default: salmon.merged.pseudo_transcript_tpm.tsv
+        default: pseudo_transcript_tpm.tsv
       - name: "--pseudo_counts_transcript"
         type: file
         direction: output
-        default: salmon.merged.pseudo_transcript_counts.tsv
+        default: pseudo_transcript_counts.tsv
       - name: "--pseudo_quant_merged_summarizedexperiment"
         type: file
         direction: output
@@ -642,6 +640,8 @@ dependencies:
   - name: rseqc/rseqc_tin
   - name: dupradar
   - name: qualimap
+  # - name: qualimap/qualimap_rnaseq
+  #   repository: biobox
   - name: preseq_lcextrap
   - name: featurecounts
     repository: biobox
@@ -650,6 +650,7 @@ dependencies:
   - name: prepare_multiqc_input
   - name: multiqc
     repository: biobox
+  - name: rsem/rsem_merge_counts
   - name: workflows/merge_quant_results
 
 runners: 

src/workflows/quality_control/main.nf

@@ -55,7 +55,7 @@ workflow run_wf {
                 "input": "genome_bam",
                 "extra_preseq_args": "extra_preseq_args"
             ],
-            toState: [ "preseq_output": "output" ],
+            toState: [ "preseq_output": "output" ]
         )
    
         | rseqc_bamstat.run (
@@ -214,10 +214,49 @@ workflow run_wf {
         merged_ch = qc_ch
         
         | toSortedList
-
         | map { list -> 
             def ids = list.collect { id, state -> state.id }
             def strandedness = list.collect { id, state -> state.strandedness }
+            def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
+            def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
+            def passed_mapping = list.collect { id, state -> state.passed_mapping }
+            def percent_mapped = list.collect { id, state -> state.percent_mapped }
+            def inferred_strand = list.collect { id, state -> state.inferred_strand }
+            def passed_strand_check = list.collect { id, state -> state.passed_strand_check }
+            def gtf = list.collect { id, state -> state.gtf }.unique()[0]
+            def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0]
+            def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0]
+            def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0]
+            def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0]
+            def aligner = list.collect { id, state -> state.aligner }.unique()[0]
+            def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0]
+            def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0]
+            def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0]
+            def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0]
+            def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] 
+            def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] 
+            def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] 
+            def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] 
+            def quant_results = list.collect { id, state -> 
+                (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? 
+                    state.quant_results_file : 
+                    null }
+            def rsem_counts_gene = list.collect { id, state -> 
+                (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? 
+                    state.rsem_counts_gene : 
+                    null }
+            def rsem_counts_transcripts = list.collect { id, state -> 
+                (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? 
+                    state.rsem_counts_transcripts : 
+                    null }
+            def pseudo_salmon_quant_results = list.collect { id, state -> 
+                (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? 
+                    state.pseudo_salmon_quant_results_file : 
+                    null }
+            def pseudo_kallisto_quant_results = list.collect { id, state -> 
+                (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? 
+                    state.pseudo_kallisto_quant_results_file : 
+                    null }
             def fastqc_zip_1 = list.collect { id, state -> 
                 (state.fastqc_zip_1 instanceof java.nio.file.Path && state.fastqc_zip_1.exists()) ? 
                     state.fastqc_zip_1 : 
@@ -242,26 +281,14 @@ workflow run_wf {
                 (state.trim_log_2 instanceof java.nio.file.Path && state.trim_log_2.exists()) ? 
                     state.trim_log_2 : 
                     null }
-            def sortmerna_log = list.collect { id, state -> 
+            def sortmerna_multiqc = list.collect { id, state -> 
-                (state.sortmerna_log instanceof java.nio.file.Path && state.sortmerna_log.exists()) ? 
+                (state.sortmerna_multiqc instanceof java.nio.file.Path && state.sortmerna_multiqc.exists()) ? 
-                    state.sortmerna_log : 
+                    state.sortmerna_multiqc : 
                     null }
             def star_multiqc = list.collect { id, state -> 
                 (state.star_multiqc instanceof java.nio.file.Path && state.star_multiqc.exists()) ? 
                     state.star_multiqc : 
                     null }
-            def quant_results = list.collect { id, state -> 
-                (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? 
-                    state.quant_results_file : 
-                    null }
-            def pseudo_salmon_quant_results = list.collect { id, state -> 
-                (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? 
-                    state.pseudo_salmon_quant_results_file : 
-                    null }
-            def pseudo_kallisto_quant_results = list.collect { id, state -> 
-                (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? 
-                    state.pseudo_kallisto_quant_results_file : 
-                    null }
             def genome_bam_stats = list.collect { id, state -> 
                 (state.genome_bam_stats instanceof java.nio.file.Path && state.genome_bam_stats.exists()) ? 
                     state.genome_bam_stats : 
@@ -278,6 +305,14 @@ workflow run_wf {
                 (state.markduplicates_multiqc instanceof java.nio.file.Path && state.markduplicates_multiqc.exists()) ? 
                     state.markduplicates_multiqc : 
                     null }
+            def salmon_multiqc = list.collect { id, state -> 
+                (state.salmon_multiqc instanceof java.nio.file.Path && state.salmon_multiqc.exists()) ? 
+                    state.salmon_multiqc : 
+                    null }
+            def rsem_multiqc = list.collect { id, state -> 
+                (state.rsem_multiqc instanceof java.nio.file.Path && state.rsem_multiqc.exists()) ? 
+                    state.rsem_multiqc : 
+                    null }
             def pseudo_multiqc = list.collect { id, state -> 
                 (state.pseudo_multiqc instanceof java.nio.file.Path && state.pseudo_multiqc.exists()) ? 
                     state.pseudo_multiqc : 
@@ -338,40 +373,45 @@ workflow run_wf {
                 (state.tin_output_summary instanceof java.nio.file.Path && state.tin_output_summary.exists()) ? 
                     state.tin_output_summary : 
                     null }
-            def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
-            def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
-            def passed_mapping = list.collect { id, state -> state.passed_mapping }
-            def percent_mapped = list.collect { id, state -> state.percent_mapped }
-            def inferred_strand = list.collect { id, state -> state.inferred_strand }
-            def passed_strand_check = list.collect { id, state -> state.passed_strand_check }
-            def gtf = list.collect { id, state -> state.gtf }.unique()[0]
-            def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0]
-            def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0]
-            def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0]
-            def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc } .unique()[0]
-            def aligner = list.collect { id, state -> state.aligner } .unique()[0]
-            def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner } .unique()[0]
-            def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0]
-            def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0]
-            def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0]
-            def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] 
             def multiqc_custom_config = list.collect { id, state -> state.multiqc_custom_config }.unique()[0] 
-            def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] 
-            def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] 
-            def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] 
             ["merged", [
                 ids: ids, 
                 strandedness: strandedness, 
+                num_trimmed_reads: num_trimmed_reads,
+                passed_trimmed_reads: passed_trimmed_reads,
+                passed_mapping: passed_mapping,
+                percent_mapped: percent_mapped,
+                inferred_strand: inferred_strand, 
+                passed_strand_check: passed_strand_check, 
+                skip_align: skip_align,
+                skip_pseudo_align: skip_pseudo_align,
+                quant_results: quant_results, 
+                rsem_counts_gene: rsem_counts_gene,
+                rsem_counts_transcripts: rsem_counts_transcripts,
+                pseudo_salmon_quant_results: pseudo_salmon_quant_results,
+                pseudo_kallisto_quant_results: pseudo_kallisto_quant_results,
+                gtf: gtf, 
+                gtf_extra_attributes: gtf_extra_attributes, 
+                gtf_group_features: gtf_group_features,
+                pca_header_multiqc: pca_header_multiqc, 
+                clustering_header_multiqc: clustering_header_multiqc,
+                aligner: aligner,
+                pseudo_aligner: pseudo_aligner,
+                deseq2_vst: deseq2_vst, 
+                extra_deseq2_args: extra_deseq2_args,
+                extra_deseq2_args2: extra_deseq2_args2,
+                skip_deseq2_qc: skip_deseq2_qc,
                 fastqc_zip: fastqc_zip_1 + fastqc_zip_2,
                 trim_zip: trim_zip_1 + trim_zip_2, 
                 trim_log: trim_log_1 + trim_log_2, 
-                sortmerna_log: sortmerna_log,
+                sortmerna_multiqc: sortmerna_multiqc,
                 star_multiqc: star_multiqc, 
-                salmon_multiqc: quant_results,
                 genome_bam_stats: genome_bam_stats,
                 genome_bam_flagstat: genome_bam_flagstat,
                 genome_bam_idxstats: genome_bam_idxstats,
                 markduplicates_multiqc: markduplicates_multiqc,
+                salmon_multiqc: salmon_multiqc,
+                rsem_multiqc: rsem_multiqc,
                 pseudo_multiqc: pseudo_multiqc,
                 featurecounts_multiqc: featurecounts_multiqc,
                 featurecounts_rrna_multiqc: featurecounts_rrna_multiqc,
@@ -387,32 +427,114 @@ workflow run_wf {
                 read_distribution_output: read_distribution_output,
                 read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping,
                 tin_output_summary: tin_output_summary, 
-                quant_results: quant_results, 
+                multiqc_custom_config: multiqc_custom_config
-                pseudo_salmon_quant_results: pseudo_salmon_quant_results,
-                pseudo_kallisto_quant_results: pseudo_kallisto_quant_results,
-                gtf: gtf, 
-                gtf_extra_attributes: gtf_extra_attributes, 
-                gtf_group_features: gtf_group_features,
-                pca_header_multiqc: pca_header_multiqc, 
-                clustering_header_multiqc: clustering_header_multiqc,
-                aligner: aligner,
-                pseudo_aligner: pseudo_aligner,
-                deseq2_vst: deseq2_vst, 
-                extra_deseq2_args: extra_deseq2_args,
-                extra_deseq2_args2: extra_deseq2_args2,
-                skip_deseq2_qc: skip_deseq2_qc,
-                num_trimmed_reads: num_trimmed_reads,
-                passed_trimmed_reads: passed_trimmed_reads,
-                passed_mapping: passed_mapping,
-                percent_mapped: percent_mapped,
-                inferred_strand: inferred_strand, 
-                passed_strand_check: passed_strand_check, 
-                multiqc_custom_config: multiqc_custom_config,
-                skip_align: skip_align,
-                skip_pseudo_align: skip_pseudo_align
             ] ]
         } 
 
+        // | map { list -> 
+        //     def ids = list.collect { id, state -> state.id }
+        //     def strandedness = list.collect { id, state -> state.strandedness }
+        //     def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
+        //     def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
+        //     def passed_mapping = list.collect { id, state -> state.passed_mapping }
+        //     def percent_mapped = list.collect { id, state -> state.percent_mapped }
+        //     def inferred_strand = list.collect { id, state -> state.inferred_strand }
+        //     def passed_strand_check = list.collect { id, state -> state.passed_strand_check }
+        //     def gtf = list.collect { id, state -> state.gtf }.unique()[0]
+        //     def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0]
+        //     def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0]
+        //     def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0]
+        //     def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0]
+        //     def aligner = list.collect { id, state -> state.aligner }.unique()[0]
+        //     def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0]
+        //     def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0]
+        //     def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0]
+        //     def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0]
+        //     def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0] 
+        //     def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0] 
+        //     def skip_align = list.collect { id, state -> state.skip_align }.unique()[0] 
+        //     def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0] 
+        //     def quant_results = list.collect { id, state -> 
+        //         (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ? 
+        //             state.quant_results_file : 
+        //             null }
+        //     def rsem_counts_gene = list.collect { id, state -> 
+        //         (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ? 
+        //             state.rsem_counts_gene : 
+        //             null }
+        //     def rsem_counts_transcripts = list.collect { id, state -> 
+        //         (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ? 
+        //             state.rsem_counts_transcripts : 
+        //             null }
+        //     def pseudo_salmon_quant_results = list.collect { id, state -> 
+        //         (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ? 
+        //             state.pseudo_salmon_quant_results_file : 
+        //             null }
+        //     def pseudo_kallisto_quant_results = list.collect { id, state -> 
+        //         (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ? 
+        //             state.pseudo_kallisto_quant_results_file : 
+        //             null }
+        //     def fastqc_zip_1_dirs = list.collect{it[1].fastqc_zip_1.getParent()}
+        //     def fastqc_zip_2_dirs = list.collect{it[1].fastqc_zip_2.getParent()}
+        //     def trim_zip_1_dirs = list.collect{it[1].trim_zip_1.getParent()}
+        //     def trim_zip_2_dirs = list.collect{it[1].trim_zip_2.getParent()}
+        //     def trim_log_1_dirs = list.collect{it[1].trim_log_1.getParent()}
+        //     def trim_log_2_dirs = list.collect{it[1].trim_log_2.getParent()}
+        //     def sortmerna_multiqc_dirs = list.collect{it[1].sortmerna_multiqc.getParent()}
+        //     def star_multiqc_dirs = list.collect{it[1].star_multiqc.getParent()}
+        //     def genome_bam_stats_dirs = list.collect{it[1].genome_bam_stats.getParent()}
+        //     def genome_bam_flagstat_dirs = list.collect{it[1].genome_bam_flagstat.getParent()}
+        //     def genome_bam_idxstats_dirs = list.collect{it[1].genome_bam_idxstats}
+        //     def markduplicates_multiqc_dirs = list.collect{it[1].markduplicates_multiqc.getParent()}
+        //     def salmon_multiqc_dirs = list.collect{it[1].salmon_multiqc}
+        //     def rsem_multiqc_dirs = list.collect{it[1].rsem_multiqc.getParent()}
+        //     def pseudo_multiqc_dirs = list.collect{it[1].pseudo_multiqc.getParent()}
+        //     def featurecounts_multiqc_dirs = list.collect{it[1].featurecounts_multiqc.getParent()}
+        //     def featurecounts_rrna_multiqc_dirs = list.collect{it[1].featurecounts_rrna_multiqc.getParent()}
+        //     def preseq_output_dirs = list.collect{it[1].preseq_output.getParent()}
+        //     def qualimap_output_dirs = list.collect{it[1].qualimap_output_dir}
+        //     def dupradar_output_dup_intercept_mqc_dirs = list.collect{it[1].dupradar_output_dup_intercept_mqc.getParent()}
+        //     def dupradar_output_duprate_exp_denscurve_mqc_dirs = list.collect{it[1].dupradar_output_duprate_exp_denscurve_mqc.getParent()}
+        //     def bamstat_output_dirs = list.collect{it[1].bamstat_output.getParent()}
+        //     def strandedness_output_dirs = list.collect{it[1].strandedness_output.getParent()}
+        //     def inner_dist_output_freq_dirs = list.collect{it[1].inner_dist_output_freq.getParent()}
+        //     def junction_annotation_output_log_dirs = list.collect{it[1].junction_annotation_output_log.getParent()}
+        //     def junction_saturation_output_plot_r_dirs = list.collect{it[1].junction_saturation_output_plot_r.getParent()}
+        //     def read_distribution_output_dirs = list.collect{it[1].read_distribution_output.getParent()}
+        //     def read_duplication_output_duplication_rate_mapping_dirs = list.collect{it[1].read_duplication_output_duplication_rate_mapping.getParent()}
+        //     def tin_output_summary_dirs = list.collect{it[1].tin_output_summary.getParent()}
+        //     def multiqc_custom_config_dirs = list.collect{it[1].multiqc_custom_config.getParent()}
+        //     ["merged", [
+        //         ids: ids, 
+        //         strandedness: strandedness, 
+        //         num_trimmed_reads: num_trimmed_reads,
+        //         passed_trimmed_reads: passed_trimmed_reads,
+        //         passed_mapping: passed_mapping,
+        //         percent_mapped: percent_mapped,
+        //         inferred_strand: inferred_strand, 
+        //         passed_strand_check: passed_strand_check, 
+        //         skip_align: skip_align,
+        //         skip_pseudo_align: skip_pseudo_align,
+        //         quant_results: quant_results, 
+        //         rsem_counts_gene: rsem_counts_gene,
+        //         rsem_counts_transcripts: rsem_counts_transcripts,
+        //         pseudo_salmon_quant_results: pseudo_salmon_quant_results,
+        //         pseudo_kallisto_quant_results: pseudo_kallisto_quant_results,
+        //         gtf: gtf, 
+        //         gtf_extra_attributes: gtf_extra_attributes, 
+        //         gtf_group_features: gtf_group_features,
+        //         pca_header_multiqc: pca_header_multiqc, 
+        //         clustering_header_multiqc: clustering_header_multiqc,
+        //         aligner: aligner,
+        //         pseudo_aligner: pseudo_aligner,
+        //         deseq2_vst: deseq2_vst, 
+        //         extra_deseq2_args: extra_deseq2_args,
+        //         extra_deseq2_args2: extra_deseq2_args2,
+        //         skip_deseq2_qc: skip_deseq2_qc,
+        //         multiqc_input: fastqc_zip_1_dirs + fastqc_zip_2_dirs + trim_zip_1_dirs + trim_zip_2_dirs + trim_log_1_dirs + trim_log_2_dirs + sortmerna_multiqc_dirs + star_multiqc_dirs + genome_bam_stats_dirs + genome_bam_flagstat_dirs + genome_bam_idxstats_dirs + markduplicates_multiqc_dirs + salmon_multiqc_dirs + rsem_multiqc_dirs + pseudo_multiqc_dirs + featurecounts_multiqc_dirs + featurecounts_rrna_multiqc_dirs + preseq_output_dirs + qualimap_output_dirs + dupradar_output_dup_intercept_mqc_dirs + dupradar_output_duprate_exp_denscurve_mqc_dirs + bamstat_output_dirs + strandedness_output_dirs + inner_dist_output_freq_dirs + junction_annotation_output_log_dirs + junction_saturation_output_plot_r_dirs + read_distribution_output_dirs + read_duplication_output_duplication_rate_mapping_dirs + tin_output_summary_dirs + multiqc_custom_config_dirs
+        //     ] ]
+        // } 
+
         // Merge quantification results of alignment
         | merge_quant_results.run (
             runIf: { id, state -> !state.skip_align && state.aligner == 'star_salmon' },
@@ -434,19 +556,36 @@ workflow run_wf {
                 "lengths_transcript": "lengths_transcript",
                 "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment"
             ], 
-            key: "merge_qunat_results"
+            key: "merge_quant_results"
+        )
+
+        | rsem_merge_counts.run (
+            runIf: { id, state -> state.aligner == 'star_rsem' }, 
+            fromState: [
+                "counts_gene": "rsem_counts_gene",
+                "counts_transcripts": "rsem_counts_transcripts"
+            ],
+            toState: [
+                "tpm_gene": "merged_gene_tpm",
+                "counts_gene": "merged_gene_counts",
+                "tpm_transcript": "merged_transcript_tpm", 
+                "counts_transcript": "merged_transcript_counts"
+            ]
         )
 
         | deseq2_qc.run (
             runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_align },
-            fromState: [
+            fromState: { id, state ->
-                "counts": "counts_gene_length_scaled",
+                def counts = (state.aligner == "star_rsem") ? state.counts_gene : state.counts_gene_length_scaled
-                "pca_header_multiqc": "pca_header_multiqc", 
+                [
-                "clustering_header_multiqc": "clustering_header_multiqc",
+                    counts: counts,
-                "deseq2_vst": "deseq2_vst", 
+                    pca_header_multiqc: state.pca_header_multiqc, 
-                "extra_deseq2_args": "extra_deseq2_args",
+                    clustering_header_multiqc: state.clustering_header_multiqc,
-                "extra_deseq2_args2": "extra_deseq2_args2" 
+                    deseq2_vst: state.deseq2_vst, 
-            ], 
+                    extra_deseq2_args: state.extra_deseq2_args,
+                    extra_deseq2_args2: state.extra_deseq2_args2 
+                ]
+            }, 
             toState: [
                 "deseq2_output": "deseq2_output", 
                 "deseq2_pca_multiqc": "pca_multiqc", 
@@ -547,14 +686,15 @@ workflow run_wf {
                 "fastqc_raw_multiqc": "fastqc_zip",
                 "fastqc_trim_multiqc": "trim_zip",
                 "trim_log_multiqc": "trim_log",
-                "sortmerna_multiqc": "sortmerna_log", 
+                "sortmerna_multiqc": "sortmerna_multiqc", 
                 "star_multiqc": "star_multiqc", 
                 "salmon_multiqc": "salmon_multiqc", 
+                "rsem_multiqc": "rsem_multiqc", 
+                "pseudo_multiqc": "pseudo_multiqc",
                 "samtools_stats": "genome_bam_stats", 
                 "samtools_flagstat": "genome_bam_flagstat", 
                 "samtools_idxstats": "genome_bam_idxstats", 
                 "markduplicates_multiqc": "markduplicates_multiqc",
-                "pseudo_multiqc": "pseudo_multiqc",
                 "featurecounts_multiqc": "featurecounts_multiqc",
                 "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", 
                 "aligner_pca_multiqc": "deseq2_pca_multiqc", 
@@ -583,10 +723,11 @@ workflow run_wf {
                 "title": "multiqc_title", 
                 "input": "multiqc_input", 
             ], 
+            args: [exclude_modules: "general_stats"],
             toState: [
                 "multiqc_report": "output_report", 
                 "multiqc_data": "output_data",
-                "multiqc_plots": "output_plots", 
+                "multiqc_plots": "output_plots"
             ]
         )
 
@@ -688,8 +829,7 @@ workflow run_wf {
                 "deseq2_output_pseudo": "deseq2_output_pseudo", 
                 "multiqc_report": "multiqc_report", 
                 "multiqc_data": "multiqc_data", 
-                "multiqc_plots": "multiqc_plots",
+                "multiqc_plots": "multiqc_plots"
-                "multiqc_versions": "multiqc_versions"
             ]
         )
 
@@ -749,3 +889,5 @@ def getInferexperimentStrandedness(inferexperiment_file, cutoff=30) {
     return [ strandedness, sense, antisense, undetermined ]
 }
 
+
+

src/workflows/rnaseq/config.vsh.yaml

@@ -233,11 +233,7 @@ argument_groups:
       - name: "--skip_pseudo_alignment"
         type: boolean_true
         description: Skip all of the pseudo-alignment-based processes within the pipeline.  
-      - name: extra_rsem_prepare_reference_args
+      - name: --extra_rsem_calculate_expression_args
-        type: string
-        description: Extra arguments to pass to rsem-prepare-reference command in addition to defaults defined by the pipeline.
-        default: '--star'
-      - name: extra_rsem_calculate_expression_args
         type: string
         description: Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline.
         default: '--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1'
@@ -349,42 +345,45 @@ argument_groups:
     
   - name: Output
     arguments:
+      # Reference files
       - name: "--output_fasta"
         type: file
         direction: output
-        default: genome/reference_genome.fasta
+        default: reference/genome.fasta
       - name: "--output_gtf"
         type: file
         direction: output
-        default: genome/gene_annotation.gtf
+        default: reference/gene_annotation.gtf
       - name: "--output_transcript_fasta"
         type: file
         direction: output
-        default: genome/transcriptome.fasta
+        default: reference/transcriptome.fasta
       - name: "--output_gene_bed"
         type: file
         direction: output
-        default: genome/gene_annotation.bed
+        default: reference/gene_annotation.bed
       - name: "--output_star_index"
         type: file
         direction: output
         description: Path to STAR index.
-        default: genome/index/STAR
+        default: reference/index/STAR
       - name: "--output_salmon_index"
         type: file
         direction: output
         description: Path to Salmon index.
-        default: genome/index/Salmon
+        default: reference/index/Salmon
       - name: "--output_bbsplit_index"
         type: file
         direction: output
         description: Path to BBSplit index.
-        default: genome/index/BBSplit
+        default: reference/index/BBSplit
       - name: "--output_kallisto_index"
         type: file
         direction: output
         description: Path to Kallisto index.
-        default: genome/index/Kallisto
+        default: reference/index/Kallisto
+      
+      # fastq
       - name: "--output_fastq_1"
         type: file
         direction: output
@@ -399,6 +398,8 @@ argument_groups:
         must_exist: false
         description: Path to output directory
         default: fastq/$id.read_2.fastq
+      
+      # FastQC
       - name: "--fastqc_html_1"
         type: file
         direction: output
@@ -427,18 +428,6 @@ argument_groups:
         required: false
         must_exist: false
         default: fastqc_raw/$id.read_2.fastqc.zip
-      - name: "--trim_log_1"
-        type: file
-        direction: output
-        required: false
-        must_exist: false
-        default: trimgalore/$id.read_1.trimming_report.txt
-      - name: "--trim_log_2"
-        type: file
-        direction: output
-        required: false
-        must_exist: false
-        default: trimgalore/$id.read_2.trimming_report.txt
       - name: "--trim_html_1"
         type: file
         direction: output
@@ -463,6 +452,34 @@ argument_groups:
         required: false
         must_exist: false
         default: fastqc_trim/$id.read_2.trimmed_fastqc.zip
+
+      # TrimGalore
+      - name: "--trim_log_1"
+        type: file
+        direction: output
+        required: false
+        must_exist: false
+        default: trimgalore/$id.read_1.trimming_report.txt
+      - name: "--trim_log_2"
+        type: file
+        direction: output
+        required: false
+        must_exist: false
+        default: trimgalore/$id.read_2.trimming_report.txt
+      
+      # fastp
+      - name: --fastp_trim_json
+        type: file
+        description: The fastp json format report file name
+        default: fastp/$id_out.json
+        direction: output
+      - name: --fastp_trim_html
+        type: file
+        description: The fastp html format report file name
+        default: fastp/$id_out.html
+        direction: output
+      
+      # SortMeRNA
       - name: "--sortmerna_log"
         type: file
         direction: output
@@ -470,18 +487,30 @@ argument_groups:
         required: false
         must_exist: false
         description: Sortmerna log file.
+      
+      # STAR
       - name: "--star_alignment"
         type: file
         direction: output
-        default: STAR_alignment/$id
+        default: STAR/$id
       - name: "--genome_bam_sorted"
         type: file
         direction: output
-        default: STAR_alignment/genome_processed/$id.genome.bam
+        default: STAR/genome_processed/$id.genome.bam
       - name: "--genome_bam_index"
         type: file
         direction: output
-        default: STAR_alignment/genome_processed/$id.genome.bam.bai
+        default: STAR/genome_processed/$id.genome.bam.bai
+      - name: "--transcriptome_bam"
+        type: file
+        direction: output
+        default: STAR/transcriptome_processed/$id.transcriptome.bam
+      - name: "--transcriptome_bam_index"
+        type: file
+        direction: output
+        default: STAR/transcriptome_processed/$id.transcriptome.bam.bai
+
+      # samtools
       - name: "--genome_bam_stats"
         type: file
         direction: output
@@ -494,14 +523,6 @@ argument_groups:
         type: file
         direction: output
         default: samtools_stats/$id.genome.idxstats
-      - name: "--transcriptome_bam"
-        type: file
-        direction: output
-        default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam
-      - name: "--transcriptome_bam_index"
-        type: file
-        direction: output
-        default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai
       - name: "--transcriptome_bam_stats"
         type: file
         direction: output
@@ -514,42 +535,85 @@ argument_groups:
         type: file
         direction: output
         default: samtools_stats/$id.transcriptome.idxstats
+      
+      # Transcript quantification
       - name: "--salmon_quant_results"
         type: file
         direction: output
-        default: salmon/$id
+        default: STAR_Salmon/$id
+      - name: "--salmon_quant_results_file"
+        type: file
+        direction: output
+        default: STAR_Salmon/$id/quant.sf
+      - name: "--pseudo_quant_results"
+        type: file
+        direction: output
+        default: Pseudo_align_quant/$id
+
+      # RSEM
+      - name: "--rsem_counts_gene"
+        type: file
+        description: Expression counts on gene level
+        default: RSEM/$id.genes.results
+        direction: output
+      - name: "--rsem_counts_transcripts"
+        type: file
+        description: Expression counts on transcript level
+        default: RSEM/$id.isoforms.results
+        direction: output
+      - name: "--bam_star_rsem"
+        type: file
+        description: BAM file generated by STAR (from RSEM)
+        default: RSEM/$id.STAR.genome.bam
+        direction: output
+      - name: "--bam_genome_rsem"
+        type: file
+        description: Genome BAM file (from RSEM)
+        default: RSEM/$id.genome.bam
+        direction: output
+      - name: "--bam_transcript_rsem"
+        type: file
+        description: Transcript BAM file (from RSEM)
+        default: RSEM/$id.transcript.bam
+        direction: output
+
+      # Quantification (alignment)
       - name: "--tpm_gene"
         type: file
         direction: output
-        default: salmon/gene_tpm.tsv
+        default: transcript_quantification/gene_tpm.tsv
       - name: "--counts_gene"
         type: file
         direction: output
-        default: salmon/gene_counts.tsv
+        default: transcript_quantification/gene_counts.tsv
       - name: "--counts_gene_length_scaled"
         type: file
         direction: output
-        default: salmon/gene_counts_length_scaled.tsv
+        default: transcript_quantification/gene_counts_length_scaled.tsv
       - name: "--counts_gene_scaled"
         type: file
         direction: output
-        default: salmon/gene_counts_scaled.tsv
+        default: transcript_quantification/gene_counts_scaled.tsv
       - name: "--tpm_transcript"
         type: file
         direction: output
-        default: salmon/transcript_tpm.tsv
+        default: transcript_quantification/transcript_tpm.tsv
       - name: "--counts_transcript"
         type: file
         direction: output
-        default: salmon/transcript_counts.tsv
+        default: transcript_quantification/transcript_counts.tsv
-      - name: "--salmon_merged_summarizedexperiment"
+      - name: "--quant_merged_summarizedexperiment"
         type: file
         direction: output
-        default: salmon/summarizedexperiment
+        default: transcript_quantification/summarizedexperiment
+
+      # MarkDuplicates
       - name: "--markduplicates_metrics"
         type: file
         direction: output
-        default: picard/$id.sorted.MarkDuplicates.metrics.txt
+        default: picard/$id.MarkDuplicates.metrics.txt
+
+      # StringTie
       - name: "--stringtie_transcript_gtf"
         type: file
         direction: output
@@ -566,6 +630,8 @@ argument_groups:
         type: file
         direction: output
         default: stringtie/$id.ballgown
+
+      # featureCounts
       - name: "--featurecounts"
         type: file
         direction: output
@@ -584,6 +650,8 @@ argument_groups:
         direction: output
         must_exist: false
         default: featurecounts/$id.featureCounts_rrna_mqc.tsv
+
+      # bedGraph
       - name: "--bedgraph_forward"
         type: file
         direction: output
@@ -592,6 +660,8 @@ argument_groups:
         type: file
         direction: output
         default: bedgraph/$id.reverse.bedgraph
+
+      # bigWig
       - name: "--bigwig_forward"
         type: file
         direction: output
@@ -600,10 +670,14 @@ argument_groups:
         type: file
         direction: output
         default: bigwig/$id.reverse.bigwig
+
+      # preseq lc_extrap
       - name: "--preseq_output"
         type: file
         direction: output
         default: preseq/$id.lc_extrap.txt
+
+      # RSeQC
       - name: "--bamstat_output"
         type: file
         direction: output
@@ -742,6 +816,8 @@ argument_groups:
         required: false
         default: RSeQC/tin/xls/$id.tin.xls
         description: file with TIN metrics (xls)
+
+      # DupRadar
       - name: "--dupradar_output_dupmatrix"
         type: file
         direction: output
@@ -783,6 +859,8 @@ argument_groups:
         direction: output
         required: false
         default: dupradar/intercept_slope/$id.intercept_slope.txt
+      
+      # Qualimap
       - name: "--qualimap_output_pdf"
         type: file
         direction: output
@@ -794,10 +872,14 @@ argument_groups:
         direction: output
         required: false
         default: qualimap/$id
+
+      # DESeq2
       - name: "--deseq2_output"
         type: file
         direction: output
         default: deseq2_qc
+
+      # MultiQC
       - name: "--multiqc_report"
         type: file
         direction: output
@@ -813,10 +895,32 @@ argument_groups:
       - name: "--multiqc_versions"
         type: file
         direction: output
-      - name: "--versions"
+      
+      # Quantification (pseudo alignment)
+      - name: "--pseudo_counts_gene"
         type: file
-        must_exist: false
         direction: output
+        default: pseudo_alignment_quantification/gene_counts.tsv
+      - name: "--pseudo_counts_gene_length_scaled"
+        type: file
+        direction: output
+        default: pseudo_alignment_quantification/gene_counts_length_scaled.tsv
+      - name: "--pseudo_counts_gene_scaled"
+        type: file
+        direction: output
+        default: pseudo_alignment_quantification/gene_counts_scaled.tsv
+      - name: "--pseudo_tpm_transcript"
+        type: file
+        direction: output
+        default: pseudo_alignment_quantification/transcript_tpm.tsv
+      - name: "--pseudo_counts_transcript"
+        type: file
+        direction: output
+        default: pseudo_alignment_quantification/transcript_counts.tsv
+      - name: "--pseudo_quant_merged_summarizedexperiment"
+        type: file
+        direction: output
+        default: pseudo_alignment_quantification/quant_merged_summarizedexperiment
         
 resources:
   - type: nextflow_script

src/workflows/rnaseq/main.nf

@@ -22,27 +22,27 @@ workflow run_wf {
     
     | map { list -> 
         [ "ref",  
-          [ fasta: list[1][-1].fasta,
+          [ fasta: list.collect { id, state -> state.fasta }.unique()[0],
-          gtf: list[1][-1].gtf, 
+          gtf: list.collect { id, state -> state.gtf }.unique()[0], 
-          gff: list[1][-1].gff, 
+          gff: list.collect { id, state -> state.gff }.unique()[0], 
-          additional_fasta: list[1][-1].additional_fasta,
+          additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0],
-          transcript_fasta: list[1][-1].transcript_fasta, 
+          transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], 
-          gene_bed: list[1][-1].gene_bed,
+          gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0],
-          bbsplit_fasta_list: list[1][-1].bbsplit_fasta_list,
+          bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0],
-          aligner: list[1][-1].aligner,
+          aligner: list.collect { id, state -> state.aligner }.unique()[0],
-          pseudo_aligner: list[1][-1].pseudo_aligner,
+          pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0],
-          star_index: list[1][-1].star_index,
+          star_index: list.collect { id, state -> state.star_index }.unique()[0],
-          rsem_index: list[1][-1].rsem_index,
+          rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0],
-          salmon_index: list[1][-1].salmon_index,
+          salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0],
-          kallisto_index: list[1][-1].kallisto_index,
+          kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0],
-          // splicesites: list[1][-1].splicesites,
+          // splicesites: list.collect { id, state -> state.splicesites }.unique()[0],
-          // hisat2_index: list[1][-1].hisat2_index,
+          // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0],
-          bbsplit_index: list[1][-1].bbsplit_index,
+          bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0],
-          skip_bbsplit: list[1][-1].skip_bbsplit,
+          skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0],
-          gencode: list[1][-1].gencode,
+          gencode: list.collect { id, state -> state.gencode }.unique()[0],
-          biotype: list[1][-1].biotype, 
+          biotype: list.collect { id, state -> state.biotype }.unique()[0], 
-          filter_gtf: list[1][-1].filter_gtf,
+          filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0],
-          pseudo_aligner_kmer_size: list[1][-1].pseudo_aligner_kmer_size ]
+          pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ]
         ]
     } 
 
@@ -213,11 +213,14 @@ workflow run_wf {
           "gtf_group_features": "gtf_group_features",
           "gtf_extra_attributes": "gtf_extra_attributes",
           "salmon_quant_libtype": "salmon_quant_libtype",
-          "salmon_index": "salmon_index" 
+          "salmon_index": "salmon_index",
+          "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" 
         ],
         toState: [
           "star_alignment": "star_alignment", 
           "star_multiqc": "star_multiqc", 
+          "rsem_multiqc": "rsem_multiqc",
+          "salmon_multiqc": "salmon_multiqc",
           "genome_bam_sorted": "genome_bam_sorted",
           "genome_bam_index": "genome_bam_index", 
           "genome_bam_stats": "genome_bam_stats", 
@@ -229,7 +232,11 @@ workflow run_wf {
           "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", 
           "transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
           "quant_out_dir": "quant_out_dir",
-          "quant_results_file": "quant_results_file"
+          "quant_results_file": "quant_results_file",
+          "rsem_counts_gene": "rsem_counts_gene",
+          "rsem_counts_transcripts": "rsem_counts_transcripts",
+          "bam_genome_rsem": "bam_genome_rsem",
+          "bam_transcript_rsem": "bam_transcript_rsem"
         ]
     )
 
@@ -331,16 +338,23 @@ workflow run_wf {
           "skip_align": "skip_alignment",
           "skip_pseudo_align": "skip_pseudo_alignment",
           "gtf": "gtf", 
+          "num_trimmed_reads": "num_trimmed_reads",
+          "passed_trimmed_reads": "passed_trimmed_reads",
+          "passed_mapping": "passed_mapping",
+          "percent_mapped": "percent_mapped",
           "genome_bam": "genome_bam_sorted", 
           "genome_bam_index": "genome_bam_index",
-          "quant_out_dir": "quant_out_dir",
+          "salmon_multiqc": "salmon_multiqc",
           "quant_results_file": "quant_results_file",
+          "rsem_multiqc": "rsem_multiqc",
+          "rsem_counts_gene": "rsem_counts_gene",
+          "rsem_counts_transcripts": "rsem_counts_transcripts",
+          "pseudo_multiqc": "pseudo_multiqc",
           "pseudo_quant_out_dir": "pseudo_quant_out_dir",
           "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", 
           "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", 
           "aligner": "aligner",
           "pseudo_aligner": "pseudo_aligner",
-          "pseudo_multiqc": "pseudo_multiqc",
           "gene_bed": "gene_bed",
           "extra_preseq_args": "extra_preseq_args",
           "extra_featurecounts_args": "extra_featurecounts_args", 
@@ -368,11 +382,7 @@ workflow run_wf {
           "genome_bam_flagstat": "genome_bam_flagstat", 
           "genome_bam_idxstats": "genome_bam_idxstats", 
           "markduplicates_multiqc": "markduplicates_metrics", 
-          "rseqc_modules": "rseqc_modules",
+          "rseqc_modules": "rseqc_modules"
-          "num_trimmed_reads": "num_trimmed_reads",
-          "passed_trimmed_reads": "passed_trimmed_reads",
-          "passed_mapping": "passed_mapping",
-          "percent_mapped": "percent_mapped"
         ], 
         toState: [
           "preseq_output": "preseq_output",
@@ -418,7 +428,7 @@ workflow run_wf {
           "counts_gene_scaled": "counts_gene_scaled", 
           "tpm_transcript": "tpm_transcript", 
           "counts_transcript": "counts_transcript", 
-          "salmon_merged_summarizedexperiment": "salmon_merged_summarizedexperiment",
+          "qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment",
           "deseq2_output": "deseq2_output", 
           "multiqc_report": "multiqc_report", 
           "multiqc_data": "multiqc_data", 
@@ -457,15 +467,17 @@ workflow run_wf {
         "star_alignment": "star_alignment", 
         "genome_bam_sorted": "genome_bam_sorted",
         "genome_bam_index": "genome_bam_index", 
-        "genome_bam_stats": "samtools_stats", 
+        "genome_bam_stats": "genome_bam_stats", 
-        "genome_bam_flagstat": "samtools_flagstat", 
+        "genome_bam_flagstat": "genome_bam_flagstat", 
-        "genome_bam_idxstats": "samtools_idxstats", 
+        "genome_bam_idxstats": "genome_bam_idxstats", 
         "transcriptome_bam": "transcriptome_bam", 
         "transcriptome_bam_index": "transcriptome_bam_index", 
         "transcriptome_bam_stats": "transcriptome_bam_stats", 
         "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", 
         "transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
-        "salmon_quant_results": "salmon_quant_results",
+        "salmon_quant_results": "quant_out_dir",
+        "pseudo_quant_results": "pseudo_quant_out_dir",
+        "markduplicates_metrics": "markduplicates_metrics",
         "stringtie_transcript_gtf": "stringtie_transcript_gtf",
         "stringtie_coverage_gtf": "stringtie_coverage_gtf",
         "stringtie_abundance": "stringtie_abundance",
@@ -531,8 +543,7 @@ workflow run_wf {
         "deseq2_output_pseudo": "deseq2_output_pseudo",  
         "multiqc_report": "multiqc_report", 
         "multiqc_data": "multiqc_data", 
-        "multiqc_plots": "multiqc_plots",
+        "multiqc_plots": "multiqc_plots"
-        "multiqc_versions": "multiqc_versions"
       ]
     )
 
@@ -611,7 +622,7 @@ def getFastpReadsAfterFiltering(json_file) {
 }
 
 //
-// Function that parses and returns the alignment rate from the STAR log output
+// Function that parses and returns the alignment rate from the STAR log outputs
 //
 def getStarPercentMapped(align_log) {
   def percent_aligned = 0

src/workflows/rnaseq/test_run.sh

@@ -1,30 +1,34 @@
 #!/bin/bash
 
-viash ns build --setup cb --parallel 
+# viash ns build --setup cb --parallel
 
 cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
 id,fastq_1,fastq_2,strandedness
 WT_REP1,SRR6357070_1.fastq.gz;SRR6357071_1.fastq.gz,SRR6357070_2.fastq.gz;SRR6357071_2.fastq.gz,reverse
+WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
+RAP1_IAA_30M_REP1,SRR6357076_1.fastq.gz,SRR6357076_2.fastq.gz,reverse
 RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
+RAP1_UNINDUCED_REP2,SRR6357074_1.fastq.gz;SRR6357075_1.fastq.gz,,reverse
 HERE
 
 echo ">> Test 1: Trimming reads with Trim galore; alignment with STAR and quantification with Salmon"
 nextflow run target/nextflow/workflows/rnaseq/main.nf \
   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
-  --publish_dir "test_results/full_pipeline_test1" \
+  --publish_dir test_results/full_pipeline_test1 \
   --fasta testData/minimal_test/reference/genome.fasta \
   --gtf testData/minimal_test/reference/genes.gtf.gz \
   --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
   --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
   --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
   --skip_pseudo_alignment \
-  -profile docker --resume
+  -profile docker \
+  --resume
 
 
 # echo ">> Test 2: Trimming reads with Trim galore; alignment with STAR and quantification with Salmon; pseudo-alignment and quantification with Kallisto"
 # nextflow run target/nextflow/workflows/rnaseq/main.nf \
 #   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
-#   --publish_dir "test_results/full_pipeline_test2" \
+#   --publish_dir test_results/full_pipeline_test2 \
 #   --fasta testData/minimal_test/reference/genome.fasta \
 #   --gtf testData/minimal_test/reference/genes.gtf.gz \
 #   --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
@@ -35,10 +39,11 @@ nextflow run target/nextflow/workflows/rnaseq/main.nf \
 #   --kallisto_quant_fragment_length_sd 10 \
 #   -profile docker --resume
 
+
 # echo ">> Test 3: Trimming reads with fastp; skip alignment; pseudo alignment and quantification with Salmon"
 # nextflow run target/nextflow/workflows/rnaseq/main.nf \
 #   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
-#   --publish_dir "test_results/full_pipeline_test3" \
+#   --publish_dir test_results/full_pipeline_test3 \
 #   --fasta testData/minimal_test/reference/genome.fasta \
 #   --gtf testData/minimal_test/reference/genes.gtf.gz \
 #   --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
@@ -47,3 +52,18 @@ nextflow run target/nextflow/workflows/rnaseq/main.nf \
 #   --trimmer fastp \
 #   --skip_alignment \
 #   -profile docker --resume
+
+
+# echo ">> Test 4: Trimming reads with Trim galore; alignment and quantification with RSEM (STAR)"
+# nextflow run target/nextflow/workflows/rnaseq/main.nf \
+#   --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
+#   --publish_dir test_results/full_pipeline_test4 \
+#   --fasta testData/minimal_test/reference/genome.fasta \
+#   --gtf testData/minimal_test/reference/genes.gtf.gz \
+#   --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
+#   --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
+#   --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
+#   --aligner star_rsem \
+#   --skip_pseudo_alignment \
+#   -profile docker \
+#   --resume

target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml

@@ -0,0 +1,475 @@
+name: "umi_tools_extract"
+namespace: "umi_tools"
+version: "v0.2.0"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "File containing the input data."
+    info: null
+    example:
+    - "sample.fastq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--read2_in"
+    description: "File containing the input data for the R2 reads (if paired). If\
+      \ provided, a <list of other required arguments> need to be provided."
+    info: null
+    example:
+    - "sample_R2.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--bc_pattern"
+    alternatives:
+    - "-p"
+    description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\
+      \ first 6 nucleotides \nof the read are from the UMI.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--bc_pattern2"
+    description: "The UMI barcode pattern to use for read 2."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output file for read 1."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--read2_out"
+    description: "Output file for read 2."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--filtered_out"
+    description: "Write out reads not matching regex pattern or cell barcode whitelist\
+      \ to this file.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--filtered_out2"
+    description: "Write out read pairs not matching regex pattern or cell barcode\
+      \ whitelist to this file.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Extract Options"
+  arguments:
+  - type: "string"
+    name: "--extract_method"
+    description: "UMI pattern to use. Default: `string`.\n"
+    info: null
+    example:
+    - "string"
+    required: false
+    choices:
+    - "string"
+    - "regex"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--error_correct_cell"
+    description: "Error correct cell barcodes to the whitelist."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--whitelist"
+    description: "Whitelist of accepted cell barcodes tab-separated format, where\
+      \ column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated)\
+      \ of other cell barcodes which should \nbe corrected to the barcode in column\
+      \ 1. If the --error_correct_cell option is not used, this\ncolumn will be ignored.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--blacklist"
+    description: "BlackWhitelist of cell barcodes to discard."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--subset_reads"
+    description: "Only parse the first N reads."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--quality_filter_threshold"
+    description: "Remove reads where any UMI base quality score falls below this threshold."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quality_filter_mask"
+    description: "If a UMI base has a quality below this threshold, replace the base\
+      \ with 'N'.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quality_encoding"
+    description: "Quality score encoding. Choose from:\n  * phred33 [33-77]\n  * phred64\
+      \ [64-106]\n  * solexa [59-106]\n"
+    info: null
+    required: false
+    choices:
+    - "phred33"
+    - "phred64"
+    - "solexa"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--reconcile_pairs"
+    description: "Allow read 2 infile to contain reads not in read 1 infile. This\
+      \ enables support for upstream protocols\nwhere read one contains cell barcodes,\
+      \ and the read pairs have been filtered and corrected without regard\nto the\
+      \ read2.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--three_prime"
+    alternatives:
+    - "--3prime"
+    description: "By default the barcode is assumed to be on the 5' end of the read,\
+      \ but use this option to sepecify that it is\non the 3' end instead. This option\
+      \ only works with --extract_method=string since 3' encoding can be specified\n\
+      explicitly with a regex, e.g `.*(?P<umi_1>.{5})$`.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--ignore_read_pair_suffixes"
+    description: "Ignore \"/1\" and \"/2\" read name suffixes. Note that this options\
+      \ is required if the suffixes are not whitespace\nseparated from the rest of\
+      \ the read name.\narguments:\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--umi_separator"
+    description: "The character that separates the UMI in the read name. Most likely\
+      \ a colon if you skipped the extraction with\nUMI-tools and used other software.\
+      \ Default: `_`\n"
+    info: null
+    example:
+    - "_"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--grouping_method"
+    description: "Method to use to determine read groups by subsuming those with similar\
+      \ UMIs. All methods start by identifying\nthe reads with the same mapping position,\
+      \ but treat similar yet nonidentical UMIs differently. Default: `directional`\n"
+    info: null
+    example:
+    - "directional"
+    required: false
+    choices:
+    - "unique"
+    - "percentile"
+    - "cluster"
+    - "adjacency"
+    - "directional"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--umi_discard_read"
+    description: "After UMI barcode extraction discard either R1 or R2 by setting\
+      \ this parameter to 1 or 2, respectively. Default: `0`\n"
+    info: null
+    example:
+    - 0
+    required: false
+    choices:
+    - 0
+    - 1
+    - 2
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Common Options"
+  arguments:
+  - type: "file"
+    name: "--log"
+    description: "File with logging information."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--log2stderr"
+    description: "Send logging information to stderr."
+    info: null
+    direction: "output"
+  - type: "integer"
+    name: "--verbose"
+    description: "Log level. The higher, the more output."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--error"
+    description: "File with error information."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--temp_dir"
+    description: "Directory for temporary files. If not set, the bash environmental\
+      \ variable TMPDIR is used.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--compresslevel"
+    description: "Level of Gzip compression to use. Default=6 matches GNU gzip rather\
+      \ than python gzip default (which is 9).\nDefault `6`.\n"
+    info: null
+    example:
+    - 6
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--timeit"
+    description: "Store timing information in file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--timeit_name"
+    description: "Name in timing file for this class of jobs."
+    info: null
+    default:
+    - "all"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--timeit_header"
+    description: "Add header for timing information."
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--random_seed"
+    description: "Random seed to initialize number generator with."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Flexible removal of UMI sequences from fastq reads.\nUMIs are removed\
+  \ and appended to the read name. Any other barcode, for example a library barcode,\n\
+  is left on the read. Can also filter reads by quality or against a whitelist.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "extract"
+- "umi-tools"
+- "umi"
+- "fastq"
+license: "MIT"
+references:
+  doi:
+  - "10.1101/gr.209601.116"
+links:
+  repository: "https://github.com/CGATOxford/UMI-tools"
+  homepage: "https://umi-tools.readthedocs.io/en/latest/"
+  documentation: "https://umi-tools.readthedocs.io/en/latest/reference/extract.html"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.2.0"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "umi_tools -v | sed 's/ version//g' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/umi_tools/umi_tools_extract/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  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: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
+package_config:
+  name: "biobox"
+  version: "v0.2.0"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"

target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'umi_tools/umi_tools_extract'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.2.0'
+  description = 'Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json

@@ -0,0 +1,442 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "umi_tools_extract",
+"description": "Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input" : {
+    "title": "Input",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, example: `sample.fastq`. File containing the input data",
+                "help_text": "Type: `file`, required, example: `sample.fastq`. File containing the input data."
+            
+            }
+    
+
+        ,
+                "read2_in": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `sample_R2.fastq`. File containing the input data for the R2 reads (if paired)",
+                "help_text": "Type: `file`, example: `sample_R2.fastq`. File containing the input data for the R2 reads (if paired). If provided, a \u003clist of other required arguments\u003e need to be provided."
+            
+            }
+    
+
+        ,
+                "bc_pattern": {
+                "type":
+                "string",
+                "description": "Type: `string`. The UMI barcode pattern to use e",
+                "help_text": "Type: `string`. The UMI barcode pattern to use e.g. \u0027NNNNNN\u0027 indicates that the first 6 nucleotides \nof the read are from the UMI.\n"
+            
+            }
+    
+
+        ,
+                "bc_pattern2": {
+                "type":
+                "string",
+                "description": "Type: `string`. The UMI barcode pattern to use for read 2",
+                "help_text": "Type: `string`. The UMI barcode pattern to use for read 2."
+            
+            }
+    
+
+}
+},
+    
+    
+    "output" : {
+    "title": "Output",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1",
+                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1."
+            ,
+                "default": "$id.$key.output.output"
+            }
+    
+
+        ,
+                "read2_out": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2",
+                "help_text": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2."
+            ,
+                "default": "$id.$key.read2_out.read2_out"
+            }
+    
+
+        ,
+                "filtered_out": {
+                "type":
+                "string",
+                "description": "Type: `file`. Write out reads not matching regex pattern or cell barcode whitelist to this file",
+                "help_text": "Type: `file`. Write out reads not matching regex pattern or cell barcode whitelist to this file.\n"
+            
+            }
+    
+
+        ,
+                "filtered_out2": {
+                "type":
+                "string",
+                "description": "Type: `file`. Write out read pairs not matching regex pattern or cell barcode whitelist to this file",
+                "help_text": "Type: `file`. Write out read pairs not matching regex pattern or cell barcode whitelist to this file.\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "extract options" : {
+    "title": "Extract Options",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "extract_method": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `string`, choices: ``string`, `regex``. UMI pattern to use",
+                "help_text": "Type: `string`, example: `string`, choices: ``string`, `regex``. UMI pattern to use. Default: `string`.\n",
+                "enum": ["string", "regex"]
+            
+            
+            }
+    
+
+        ,
+                "error_correct_cell": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Error correct cell barcodes to the whitelist",
+                "help_text": "Type: `boolean_true`, default: `false`. Error correct cell barcodes to the whitelist."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "whitelist": {
+                "type":
+                "string",
+                "description": "Type: `file`. Whitelist of accepted cell barcodes tab-separated format, where column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should \nbe corrected to the barcode in column 1",
+                "help_text": "Type: `file`. Whitelist of accepted cell barcodes tab-separated format, where column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should \nbe corrected to the barcode in column 1. If the --error_correct_cell option is not used, this\ncolumn will be ignored.\n"
+            
+            }
+    
+
+        ,
+                "blacklist": {
+                "type":
+                "string",
+                "description": "Type: `file`. BlackWhitelist of cell barcodes to discard",
+                "help_text": "Type: `file`. BlackWhitelist of cell barcodes to discard."
+            
+            }
+    
+
+        ,
+                "subset_reads": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Only parse the first N reads",
+                "help_text": "Type: `integer`. Only parse the first N reads."
+            
+            }
+    
+
+        ,
+                "quality_filter_threshold": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Remove reads where any UMI base quality score falls below this threshold",
+                "help_text": "Type: `integer`. Remove reads where any UMI base quality score falls below this threshold."
+            
+            }
+    
+
+        ,
+                "quality_filter_mask": {
+                "type":
+                "string",
+                "description": "Type: `string`. If a UMI base has a quality below this threshold, replace the base with \u0027N\u0027",
+                "help_text": "Type: `string`. If a UMI base has a quality below this threshold, replace the base with \u0027N\u0027.\n"
+            
+            }
+    
+
+        ,
+                "quality_encoding": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``phred33`, `phred64`, `solexa``. Quality score encoding",
+                "help_text": "Type: `string`, choices: ``phred33`, `phred64`, `solexa``. Quality score encoding. Choose from:\n  * phred33 [33-77]\n  * phred64 [64-106]\n  * solexa [59-106]\n",
+                "enum": ["phred33", "phred64", "solexa"]
+            
+            
+            }
+    
+
+        ,
+                "reconcile_pairs": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Allow read 2 infile to contain reads not in read 1 infile",
+                "help_text": "Type: `boolean_true`, default: `false`. Allow read 2 infile to contain reads not in read 1 infile. This enables support for upstream protocols\nwhere read one contains cell barcodes, and the read pairs have been filtered and corrected without regard\nto the read2.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "three_prime": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. By default the barcode is assumed to be on the 5\u0027 end of the read, but use this option to sepecify that it is\non the 3\u0027 end instead",
+                "help_text": "Type: `boolean_true`, default: `false`. By default the barcode is assumed to be on the 5\u0027 end of the read, but use this option to sepecify that it is\non the 3\u0027 end instead. This option only works with --extract_method=string since 3\u0027 encoding can be specified\nexplicitly with a regex, e.g `.*(?P\u003cumi_1\u003e.{5})$`.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "ignore_read_pair_suffixes": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Ignore \"/1\" and \"/2\" read name suffixes",
+                "help_text": "Type: `boolean_true`, default: `false`. Ignore \"/1\" and \"/2\" read name suffixes. Note that this options is required if the suffixes are not whitespace\nseparated from the rest of the read name.\narguments:\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "umi_separator": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `_`. The character that separates the UMI in the read name",
+                "help_text": "Type: `string`, example: `_`. The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with\nUMI-tools and used other software. Default: `_`\n"
+            
+            }
+    
+
+        ,
+                "grouping_method": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. Method to use to determine read groups by subsuming those with similar UMIs",
+                "help_text": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying\nthe reads with the same mapping position, but treat similar yet nonidentical UMIs differently. Default: `directional`\n",
+                "enum": ["unique", "percentile", "cluster", "adjacency", "directional"]
+            
+            
+            }
+    
+
+        ,
+                "umi_discard_read": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively",
+                "help_text": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively. Default: `0`\n",
+                "enum": [0, 1, 2]
+            
+            
+            }
+    
+
+}
+},
+    
+    
+    "common options" : {
+    "title": "Common Options",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "log": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.log.log`. File with logging information",
+                "help_text": "Type: `file`, default: `$id.$key.log.log`. File with logging information."
+            ,
+                "default": "$id.$key.log.log"
+            }
+    
+
+        ,
+                "log2stderr": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Send logging information to stderr",
+                "help_text": "Type: `boolean_true`, default: `false`. Send logging information to stderr."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "verbose": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Log level",
+                "help_text": "Type: `integer`. Log level. The higher, the more output."
+            
+            }
+    
+
+        ,
+                "error": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.error.error`. File with error information",
+                "help_text": "Type: `file`, default: `$id.$key.error.error`. File with error information."
+            ,
+                "default": "$id.$key.error.error"
+            }
+    
+
+        ,
+                "temp_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`. Directory for temporary files",
+                "help_text": "Type: `string`. Directory for temporary files. If not set, the bash environmental variable TMPDIR is used.\n"
+            
+            }
+    
+
+        ,
+                "compresslevel": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `6`. Level of Gzip compression to use",
+                "help_text": "Type: `integer`, example: `6`. Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default (which is 9).\nDefault `6`.\n"
+            
+            }
+    
+
+        ,
+                "timeit": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file",
+                "help_text": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file."
+            ,
+                "default": "$id.$key.timeit.timeit"
+            }
+    
+
+        ,
+                "timeit_name": {
+                "type":
+                "string",
+                "description": "Type: `string`, default: `all`. Name in timing file for this class of jobs",
+                "help_text": "Type: `string`, default: `all`. Name in timing file for this class of jobs."
+            ,
+                "default": "all"
+            }
+    
+
+        ,
+                "timeit_header": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Add header for timing information",
+                "help_text": "Type: `boolean_true`, default: `false`. Add header for timing information."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "random_seed": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Random seed to initialize number generator with",
+                "help_text": "Type: `integer`. Random seed to initialize number generator with."
+            
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input"
+    },
+
+    {
+    "$ref": "#/definitions/output"
+    },
+
+    {
+    "$ref": "#/definitions/extract options"
+    },
+
+    {
+    "$ref": "#/definitions/common options"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:03Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:50Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:03Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:10Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/cat_fastq/.config.vsh.yaml

@@ -30,7 +30,7 @@ argument_groups:
     description: "Concatenated read 1 fastq"
     info: null
     default:
-    - "$id.read_1.merged.fastq"
+    - "$id_r1.fastq"
     must_exist: true
     create_parent: true
     required: false
@@ -42,7 +42,7 @@ argument_groups:
     description: "Concatenated read 2 fastq"
     info: null
     default:
-    - "$id.read_2.merged.fastq"
+    - "$id_r2.fastq"
     must_exist: false
     create_parent: true
     required: false
@@ -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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/cat_fastq/cat_fastq

@@ -187,12 +187,12 @@ function ViashHelp {
   echo "Output:"
   echo "    --fastq_1"
   echo "        type: file, output, file must exist"
-  echo "        default: \$id.read_1.merged.fastq"
+  echo "        default: \$id_r1.fastq"
   echo "        Concatenated read 1 fastq"
   echo ""
   echo "    --fastq_2"
   echo "        type: file, output"
-  echo "        default: \$id.read_2.merged.fastq"
+  echo "        default: \$id_r2.fastq"
   echo "        Concatenated read 2 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="2024-09-14T08:49:11Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -869,10 +869,10 @@ fi
 
 # filling in defaults
 if [ -z ${VIASH_PAR_FASTQ_1+x} ]; then
-  VIASH_PAR_FASTQ_1="\$id.read_1.merged.fastq"
+  VIASH_PAR_FASTQ_1="\$id_r1.fastq"
 fi
 if [ -z ${VIASH_PAR_FASTQ_2+x} ]; then
-  VIASH_PAR_FASTQ_2="\$id.read_2.merged.fastq"
+  VIASH_PAR_FASTQ_2="\$id_r2.fastq"
 fi
 
 # check whether required files exist

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/deseq2_qc/deseq2_qc

@@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
   Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'
 
 LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:21Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:10Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:12Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:04Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -1200,13 +1200,15 @@ fastqc -o \$tmpdir \${input[*]}
 
 file1=\$(basename -- "\${input[0]}")
 read1="\${file1%.fastq*}"
-file2=\$(basename -- "\${input[1]}")
-read2="\${file2%.fastq*}"
-
 [[ -e "\${tmpdir}/\${read1}_fastqc.html" ]] && cp "\${tmpdir}/\${read1}_fastqc.html" \$par_fastqc_html_1
-[[ -e "\${tmpdir}/\${read2}_fastqc.html" ]] && cp "\${tmpdir}/\${read2}_fastqc.html" \$par_fastqc_html_2
 [[ -e "\${tmpdir}/\${read1}_fastqc.zip" ]] && cp "\${tmpdir}/\${read1}_fastqc.zip" \$par_fastqc_zip_1
-[[ -e "\${tmpdir}/\${read2}_fastqc.zip" ]] && cp "\${tmpdir}/\${read2}_fastqc.zip" \$par_fastqc_zip_2
+
+if \$par_paired; then
+  file2=\$(basename -- "\${input[1]}")
+  read2="\${file2%.fastq*}"
+  [[ -e "\${tmpdir}/\${read2}_fastqc.html" ]] && cp "\${tmpdir}/\${read2}_fastqc.html" \$par_fastqc_html_2
+  [[ -e "\${tmpdir}/\${read2}_fastqc.zip" ]] && cp "\${tmpdir}/\${read2}_fastqc.zip" \$par_fastqc_zip_2
+fi
 VIASHMAIN
 bash "\$tempscript" &
 wait "\$!"

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:04Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:04Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:16Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:19Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:05Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:18Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:07Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:17Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:07Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -1319,16 +1319,7 @@ if [[ "\$par_extra_args" != *"--fr-stranded"* ]] && [[ "\$par_extra_args" != *"-
 fi
 
 mkdir -p \$par_output
-echo "kallisto quant \\
+
-    \${meta_cpus:+--threads \$meta_cpus} \\
-    --index \$par_index \\
-    \${par_gtf:+--gtf \$par_gtf} \\
-    \${par_chromosomes:+--chromosomes \$par_chromosomes} \\
-    \$single_end_params \\
-    \$strandedness \\
-    \$par_extra_args \\
-    -o \$par_output \\
-    \${input[*]} 2> >(tee -a \${par_output}/kallisto_quant.log >&2)"
 kallisto quant \\
     \${meta_cpus:+--threads \$meta_cpus} \\
     --index \$par_index \\

target/executable/multiqc_custom_biotype/.config.vsh.yaml

@@ -170,8 +170,8 @@ build_info:
   output: "target/executable/multiqc_custom_biotype"
   executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
   viash_version: "0.9.0"
-  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/multiqc_custom_biotype/multiqc_custom_biotype

@@ -481,9 +481,9 @@ RUN apt-get update && \
 RUN pip install --upgrade pip
 
 LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:12Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:20Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:16Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:05Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -2287,6 +2287,8 @@ IFS="," read -ra rsem_multiqc <<< \$par_rsem_multiqc && for file in "\${rsem_mul
 
 IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
 
+IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseudo_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
+
 IFS="," read -ra samtools_stats <<< \$par_samtools_stats && for file in "\${samtools_stats[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done
 
 IFS="," read -ra samtools_flagstat <<< \$par_samtools_flagstat && for file in "\${samtools_flagstat[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done
@@ -2295,12 +2297,9 @@ IFS="," read -ra samtools_idxstats <<< \$par_samtools_idxstats && for file in "\
 
 IFS="," read -ra markduplicates_multiqc <<< \$par_markduplicates_multiqc && for file in "\${markduplicates_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
 
-IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseudo_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
-
-
 IFS="," read -ra featurecounts_multiqc <<< \$par_featurecounts_multiqc && for file in "\${featurecounts_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
 
-IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc&& for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
+IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc && for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
 
 [ -e "\$par_aligner_pca_multiqc" ] && cp -r "\$par_aligner_pca_multiqc" "\$par_output/"
 

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:15Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:05Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:53Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:03Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml

@@ -60,15 +60,6 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
-  - type: "file"
-    name: "--versions"
-    info: null
-    must_exist: false
-    create_parent: true
-    required: false
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
 - name: "Output"
   arguments:
   - type: "file"
@@ -308,8 +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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression

@@ -201,9 +201,6 @@ function ViashHelp {
   echo "        type: string"
   echo "        Extra rsem-calculate-expression arguments in addition to the defaults."
   echo ""
-  echo "    --versions"
-  echo "        type: file"
-  echo ""
   echo "Output:"
   echo "    --counts_gene"
   echo "        type: file, output, file must exist"
@@ -545,9 +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="2024-09-14T08:49:17Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -759,17 +756,6 @@ while [[ $# -gt 0 ]]; do
             VIASH_PAR_EXTRA_ARGS=$(ViashRemoveFlags "$1")
             shift 1
             ;;
-        --versions)
-            [ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_VERSIONS="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --versions. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --versions=*)
-            [ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions=*\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_VERSIONS=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
         --counts_gene)
             [ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
             VIASH_PAR_COUNTS_GENE="$2"
@@ -1205,10 +1191,6 @@ if [ ! -z "$VIASH_PAR_INDEX" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX")" )
   VIASH_PAR_INDEX=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX")
 fi
-if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
-  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_VERSIONS")" )
-  VIASH_PAR_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_VERSIONS")
-fi
 if [ ! -z "$VIASH_PAR_COUNTS_GENE" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS_GENE")" )
   VIASH_PAR_COUNTS_GENE=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS_GENE")
@@ -1319,7 +1301,6 @@ $( if [ ! -z ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
 $( if [ ! -z ${VIASH_PAR_INDEX+x} ]; then echo "${VIASH_PAR_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_index='&'#" ; else echo "# par_index="; fi )
 $( if [ ! -z ${VIASH_PAR_EXTRA_ARGS+x} ]; then echo "${VIASH_PAR_EXTRA_ARGS}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_args='&'#" ; else echo "# par_extra_args="; fi )
-$( if [ ! -z ${VIASH_PAR_VERSIONS+x} ]; then echo "${VIASH_PAR_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_versions='&'#" ; else echo "# par_versions="; fi )
 $( if [ ! -z ${VIASH_PAR_COUNTS_GENE+x} ]; then echo "${VIASH_PAR_COUNTS_GENE}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_gene='&'#" ; else echo "# par_counts_gene="; fi )
 $( if [ ! -z ${VIASH_PAR_COUNTS_TRANSCRIPTS+x} ]; then echo "${VIASH_PAR_COUNTS_TRANSCRIPTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_transcripts='&'#" ; else echo "# par_counts_transcripts="; fi )
 $( if [ ! -z ${VIASH_PAR_STAT+x} ]; then echo "${VIASH_PAR_STAT}" | sed "s#'#'\"'\"'#g;s#.*#par_stat='&'#" ; else echo "# par_stat="; fi )
@@ -1368,10 +1349,10 @@ fi
 
 IFS="," read -ra input <<< \$par_input
 
-INDEX=\`find -L \$meta_resources_dir/ -name "*.grp" | sed 's/\\.grp\$//'\`
+INDEX=\`find -L \$par_index/ -name "*.grp" | sed 's/\\.grp\$//'\`
 
 rsem-calculate-expression \\
-    \${meta_cpus:+--num-theads \$meta_cpus} \\
+    \${meta_cpus:+--num-threads \$meta_cpus} \\
     \$strandedness \\
     \${par_paired:+--paired-end} \\
     \$par_extra_args \\
@@ -1379,6 +1360,13 @@ rsem-calculate-expression \\
     \$INDEX \\
     \$par_id
     
+[[ -e "\${par_id}.genes.results" ]] && mv "\${par_id}.genes.results" \$par_counts_gene
+[[ -e "\${par_id}id.isoforms.results" ]] && mv "\${par_id}id.isoforms.results" \$par_counts_transcripts
+[[ -e "\${par_id}.stat" ]] && mv -r "\${par_id}.stat" \$par_stat
+# [[ -e "\${par_id}.log" ]] && mv "\${par_id}.log" \$par_logs
+[[ -e "\${par_id}.STAR.genome.bam" ]] && mv "\${par_id}.STAR.genome.bam" \$par_bam_star
+[[ -e "\${par_id}.genome.bam" ]] && mv "\${par_id}.genome.bam" \$par_bam_genome
+[[ -e "\${par_id}.transcript.bam" ]] && mv "\${par_id}.transcript.bam" \$par_bam_transcript
 VIASHMAIN
 bash "\$tempscript" &
 wait "\$!"
@@ -1405,9 +1393,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
   if [ ! -z "$VIASH_PAR_INDEX" ]; then
     VIASH_PAR_INDEX=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX")
   fi
-  if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
-    VIASH_PAR_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_VERSIONS")
-  fi
   if [ ! -z "$VIASH_PAR_COUNTS_GENE" ]; then
     VIASH_PAR_COUNTS_GENE=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS_GENE")
   fi

target/executable/rsem/rsem_merge_counts/.config.vsh.yaml

@@ -24,15 +24,6 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
-  - type: "file"
-    name: "--versions"
-    info: null
-    must_exist: false
-    create_parent: true
-    required: false
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
 - name: "Output"
   arguments:
   - type: "file"
@@ -83,17 +74,6 @@ argument_groups:
     direction: "output"
     multiple: false
     multiple_sep: ";"
-  - type: "file"
-    name: "--updated_versions"
-    info: null
-    default:
-    - "versions.yml"
-    must_exist: true
-    create_parent: true
-    required: false
-    direction: "output"
-    multiple: false
-    multiple_sep: ";"
 resources:
 - type: "bash_script"
   path: "script.sh"
@@ -202,8 +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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/rsem/rsem_merge_counts/rsem_merge_counts

@@ -185,9 +185,6 @@ function ViashHelp {
   echo "        type: file, file must exist"
   echo "        Expression counts on transcript level (isoforms)"
   echo ""
-  echo "    --versions"
-  echo "        type: file"
-  echo ""
   echo "Output:"
   echo "    --merged_gene_counts"
   echo "        type: file, output, file must exist"
@@ -208,10 +205,6 @@ function ViashHelp {
   echo "        type: file, output, file must exist"
   echo "        default: rsem.merged.transcript_tpm.tsv"
   echo "        File containing transcript TPM across all samples."
-  echo ""
-  echo "    --updated_versions"
-  echo "        type: file, output, file must exist"
-  echo "        default: versions.yml"
 }
 
 # initialise variables
@@ -490,9 +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="2024-09-14T08:49:17Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -654,17 +647,6 @@ while [[ $# -gt 0 ]]; do
             VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashRemoveFlags "$1")
             shift 1
             ;;
-        --versions)
-            [ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_VERSIONS="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --versions. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --versions=*)
-            [ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions=*\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_VERSIONS=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
         --merged_gene_counts)
             [ -n "$VIASH_PAR_MERGED_GENE_COUNTS" ] && ViashError Bad arguments for option \'--merged_gene_counts\': \'$VIASH_PAR_MERGED_GENE_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
             VIASH_PAR_MERGED_GENE_COUNTS="$2"
@@ -709,17 +691,6 @@ while [[ $# -gt 0 ]]; do
             VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashRemoveFlags "$1")
             shift 1
             ;;
-        --updated_versions)
-            [ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_UPDATED_VERSIONS="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --updated_versions. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --updated_versions=*)
-            [ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions=*\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_UPDATED_VERSIONS=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
         ---engine)
             VIASH_ENGINE_ID="$2"
             shift 2
@@ -930,9 +901,6 @@ fi
 if [ -z ${VIASH_PAR_MERGED_TRANSCRIPT_TPM+x} ]; then
   VIASH_PAR_MERGED_TRANSCRIPT_TPM="rsem.merged.transcript_tpm.tsv"
 fi
-if [ -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then
-  VIASH_PAR_UPDATED_VERSIONS="versions.yml"
-fi
 
 # check whether required files exist
 if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE" ]; then
@@ -1031,9 +999,6 @@ fi
 if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ] && [ ! -d "$(dirname "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")" ]; then
   mkdir -p "$(dirname "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")"
 fi
-if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")" ]; then
-  mkdir -p "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")"
-fi
 
 if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
   if [ "$VIASH_MODE" == "run" ]; then
@@ -1055,10 +1020,6 @@ if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS_TRANSCRIPTS")" )
   VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS_TRANSCRIPTS")
 fi
-if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
-  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_VERSIONS")" )
-  VIASH_PAR_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_VERSIONS")
-fi
 if [ ! -z "$VIASH_PAR_MERGED_GENE_COUNTS" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MERGED_GENE_COUNTS")" )
   VIASH_PAR_MERGED_GENE_COUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_MERGED_GENE_COUNTS")
@@ -1079,11 +1040,6 @@ if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ]; then
   VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashDockerAutodetectMount "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")
   VIASH_CHOWN_VARS+=( "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" )
 fi
-if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
-  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_UPDATED_VERSIONS")" )
-  VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_UPDATED_VERSIONS")
-  VIASH_CHOWN_VARS+=( "$VIASH_PAR_UPDATED_VERSIONS" )
-fi
 if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
   VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
   VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1155,12 +1111,10 @@ cat > "\$tempscript" << 'VIASHMAIN'
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_COUNTS_GENE+x} ]; then echo "${VIASH_PAR_COUNTS_GENE}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_gene='&'#" ; else echo "# par_counts_gene="; fi )
 $( if [ ! -z ${VIASH_PAR_COUNTS_TRANSCRIPTS+x} ]; then echo "${VIASH_PAR_COUNTS_TRANSCRIPTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_transcripts='&'#" ; else echo "# par_counts_transcripts="; fi )
-$( if [ ! -z ${VIASH_PAR_VERSIONS+x} ]; then echo "${VIASH_PAR_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_versions='&'#" ; else echo "# par_versions="; fi )
 $( if [ ! -z ${VIASH_PAR_MERGED_GENE_COUNTS+x} ]; then echo "${VIASH_PAR_MERGED_GENE_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_gene_counts='&'#" ; else echo "# par_merged_gene_counts="; fi )
 $( if [ ! -z ${VIASH_PAR_MERGED_GENE_TPM+x} ]; then echo "${VIASH_PAR_MERGED_GENE_TPM}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_gene_tpm='&'#" ; else echo "# par_merged_gene_tpm="; fi )
 $( if [ ! -z ${VIASH_PAR_MERGED_TRANSCRIPT_COUNTS+x} ]; then echo "${VIASH_PAR_MERGED_TRANSCRIPT_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_transcript_counts='&'#" ; else echo "# par_merged_transcript_counts="; fi )
 $( if [ ! -z ${VIASH_PAR_MERGED_TRANSCRIPT_TPM+x} ]; then echo "${VIASH_PAR_MERGED_TRANSCRIPT_TPM}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_transcript_tpm='&'#" ; else echo "# par_merged_transcript_tpm="; fi )
-$( if [ ! -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then echo "${VIASH_PAR_UPDATED_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_updated_versions='&'#" ; else echo "# par_updated_versions="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
 $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -1225,9 +1179,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
   if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then
     VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS_TRANSCRIPTS")
   fi
-  if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
-    VIASH_PAR_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_VERSIONS")
-  fi
   if [ ! -z "$VIASH_PAR_MERGED_GENE_COUNTS" ]; then
     VIASH_PAR_MERGED_GENE_COUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_MERGED_GENE_COUNTS")
   fi
@@ -1240,9 +1191,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
   if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ]; then
     VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashDockerStripAutomount "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")
   fi
-  if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
-    VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_UPDATED_VERSIONS")
-  fi
   if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
     VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
   fi
@@ -1275,10 +1223,6 @@ if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ] && [ ! -e "$VIASH_PAR_MERGED_TRAN
   ViashError "Output file '$VIASH_PAR_MERGED_TRANSCRIPT_TPM' does not exist."
   exit 1
 fi
-if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -e "$VIASH_PAR_UPDATED_VERSIONS" ]; then
-  ViashError "Output file '$VIASH_PAR_UPDATED_VERSIONS' does not exist."
-  exit 1
-fi
 
 
 exit 0

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:15Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:13Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:14Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-09-14T08:49:14Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation

@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "RSeQC"
 
 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml

@@ -162,8 +162,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_readdistribution"
   executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
   viash_version: "0.9.0"
-  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution

@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "RSeQC"
 
 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml

@@ -211,8 +211,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_readduplication"
   executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
   viash_version: "0.9.0"
-  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/rseqc/rseqc_readduplication/rseqc_readduplication

@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "RSeQC"
 
 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:02Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_tin/.config.vsh.yaml

@@ -214,8 +214,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_tin"
   executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
   viash_version: "0.9.0"
-  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/rseqc/rseqc_tin/rseqc_tin

@@ -501,9 +501,9 @@ RUN apt-get update && \
 RUN pip3 install RSeQC
 
 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:02Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/sortmerna/.config.vsh.yaml

@@ -198,8 +198,8 @@ build_info:
   output: "target/executable/sortmerna"
   executable: "target/executable/sortmerna/sortmerna"
   viash_version: "0.9.0"
-  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/sortmerna/sortmerna

@@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down
 bash sortmerna-4.3.6-Linux.sh --skip-license
 
 LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:19Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/stringtie/.config.vsh.yaml

@@ -216,8 +216,8 @@ build_info:
   output: "target/executable/stringtie"
   executable: "target/executable/stringtie/stringtie"
   viash_version: "0.9.0"
-  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/stringtie/stringtie

@@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
 cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
 
 LABEL org.opencontainers.image.description="Companion container for running component stringtie"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/summarizedexperiment/.config.vsh.yaml

@@ -199,8 +199,8 @@ build_info:
   output: "target/executable/summarizedexperiment"
   executable: "target/executable/summarizedexperiment/summarizedexperiment"
   viash_version: "0.9.0"
-  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/summarizedexperiment/summarizedexperiment

@@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
   Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
 
 LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
-LABEL org.opencontainers.image.created="2024-09-14T08:49:20Z"
+LABEL org.opencontainers.image.created="2024-10-01T10:02:10Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
+LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/trimgalore/.config.vsh.yaml

@@ -540,7 +540,7 @@ argument_groups:
       \ files (paired-end) are specified, but not for longer lists."
     info: null
     example:
-    - "read_1.fastq"
+    - "read_1.fastq.gz"
     must_exist: true
     create_parent: true
     required: false
@@ -553,7 +553,7 @@ argument_groups:
       \ files (paired-end) are specified, but not for longer lists."
     info: null
     example:
-    - "read_2.fastq"
+    - "read_2.fastq.gz"
     must_exist: true
     create_parent: true
     required: false
@@ -788,8 +788,8 @@ build_info:
   output: "target/executable/trimgalore"
   executable: "target/executable/trimgalore/trimgalore"
   viash_version: "0.9.0"
-  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
-  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info: