Build branch add-labels with version add-labels (e244fcf)

Build pipeline: viash-hub.rnaseq.add-labels-n4fx6

Source commit: e244fcf554

Source message: Move inline TODO items to Github issue

src/workflows/genome_alignment_and_quant/main.nf

@@ -1,5 +1,3 @@
-// TODO: Improve logic of this wf, e.g. by splitting up in 2 subwfs
-// TODO: See if this can be aligned with the pseudo-alignment branch of the logic
 workflow run_wf {
   take:
     input_ch

src/workflows/prepare_genome/main.nf

@@ -204,7 +204,6 @@ workflow run_wf {
         directives: [ label: [ "lowmem", "midcpu" ] ]
       )
 
-      // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode 
       | star_genome_generate.run (
         runIf: {id, state -> !state.star_index && !state.skip_alignment}, 
         fromState: [ 

src/workflows/pseudo_alignment_and_quant/main.nf

@@ -1,4 +1,3 @@
-// TODO: See if the logic of this can be aligned with the STAR aligner logic
 workflow run_wf {
   take:
     input_ch

src/workflows/quality_control/main.nf

@@ -1,4 +1,3 @@
-// TODO: Split in /sample and integrated QC
 workflow run_wf {
 
   take: 
@@ -9,7 +8,6 @@ workflow run_wf {
     qc_ch = input_ch
 
       // temporary fix to force assignment when alignment is skipped
-      // TODO: Check this
       | map {it} 
 
       // Feature biotype QC using featureCounts
@@ -699,7 +697,6 @@ workflow run_wf {
       | map { list -> [list[0], list[1] + list[2]] }
 
       | map { id, state -> 
-        // TODO: Check this, necessary for setState
         def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
         [ id, mod_state ]
       }

src/workflows/rnaseq/config.vsh.yaml

@@ -895,6 +895,11 @@ resources:
     path: main.nf
     entrypoint: run_wf
 
+test_resources:
+  - type: nextflow_script
+    path: test.nf
+    entrypoint: test_wf
+
 dependencies: 
   - name: workflows/prepare_genome
   - name: cat_fastq

src/workflows/rnaseq/main.nf

@@ -92,7 +92,6 @@ workflow run_wf {
       )
 
       // Check if contigs in genome fasta file > 512 Mbp
-      // TODO: check where this is required and move if necessary
       | map { id, state -> 
         (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]]
       }
@@ -172,15 +171,13 @@ workflow run_wf {
       )
 
       // Infer strandedness from Salmon pseudo-alignment results
-      // TODO: Turn this into a workflow step and include as a dependency
       | map { id, state -> 
-      (state.strandedness == 'auto') ? 
-        [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : 
-        [id, state] 
+        (state.strandedness == 'auto') ? 
+          [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : 
+          [id, state] 
       }
 
       // Filter FastQ files based on minimum trimmed read count after adapter trimming
-      // TODO: Turn this into a workflow step and include as a dependency
       | map { id, state -> 
         def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
         def num_reads = (state.skip_trimming) ? 
@@ -249,7 +246,6 @@ workflow run_wf {
       )
 
       // Filter channels to get samples that passed STAR minimum mapping percentage
-      // TODO: Move to reporting or later step
       | map { id, state -> 
         def percent_mapped = (!state.skip_alignment && state.passed_trimmed_reads) ? getStarPercentMapped(state.star_multiqc) : 0.0
         def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false

target/executable/bedtools_genomecov/.config.vsh.yaml

@@ -183,8 +183,8 @@ build_info:
   output: "target/executable/bedtools_genomecov"
   executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:22Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/cat_additional_fasta/.config.vsh.yaml

@@ -187,8 +187,8 @@ build_info:
   output: "target/executable/cat_additional_fasta"
   executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -174,8 +174,8 @@ build_info:
   output: "target/executable/cat_fastq"
   executable: "target/executable/cat_fastq/cat_fastq"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/cat_fastq/cat_fastq

@@ -472,9 +472,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:20Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/deseq2_qc/.config.vsh.yaml

@@ -242,8 +242,8 @@ build_info:
   output: "target/executable/deseq2_qc"
   executable: "target/executable/deseq2_qc/deseq2_qc"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/deseq2_qc/deseq2_qc

@@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
   Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")'
 
 LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/dupradar/.config.vsh.yaml

@@ -271,8 +271,8 @@ build_info:
   output: "target/executable/dupradar"
   executable: "target/executable/dupradar/dupradar"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/getchromsizes/.config.vsh.yaml

@@ -172,8 +172,8 @@ build_info:
   output: "target/executable/getchromsizes"
   executable: "target/executable/getchromsizes/getchromsizes"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/gtf2bed/.config.vsh.yaml

@@ -150,8 +150,8 @@ build_info:
   output: "target/executable/gtf2bed"
   executable: "target/executable/gtf2bed/gtf2bed"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/gtf_filter/.config.vsh.yaml

@@ -160,8 +160,8 @@ build_info:
   output: "target/executable/gtf_filter"
   executable: "target/executable/gtf_filter/gtf_filter"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:22Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/gunzip/.config.vsh.yaml

@@ -149,8 +149,8 @@ build_info:
   output: "target/executable/gunzip"
   executable: "target/executable/gunzip/gunzip"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:14Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/multiqc_custom_biotype/multiqc_custom_biotype

@@ -476,9 +476,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/picard_markduplicates/.config.vsh.yaml

@@ -212,8 +212,8 @@ build_info:
   output: "target/executable/picard_markduplicates"
   executable: "target/executable/picard_markduplicates/picard_markduplicates"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:15Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/prepare_multiqc_input/.config.vsh.yaml

@@ -417,8 +417,8 @@ build_info:
   output: "target/executable/prepare_multiqc_input"
   executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/prepare_multiqc_input/prepare_multiqc_input

@@ -558,9 +558,9 @@ 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="2024-12-03T19:47:13Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:17Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/preprocess_transcripts_fasta/.config.vsh.yaml

@@ -143,8 +143,8 @@ build_info:
   output: "target/executable/preprocess_transcripts_fasta"
   executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:15Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/preseq_lcextrap/.config.vsh.yaml

@@ -196,8 +196,8 @@ build_info:
   output: "target/executable/preseq_lcextrap"
   executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:14Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -186,8 +186,8 @@ build_info:
   output: "target/executable/rsem_merge_counts"
   executable: "target/executable/rsem_merge_counts/rsem_merge_counts"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/rsem_merge_counts/rsem_merge_counts

@@ -483,9 +483,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component rsem_merge_counts"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:20Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -265,8 +265,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_junctionannotation"
   executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:20Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -254,8 +254,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_junctionsaturation"
   executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -167,8 +167,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_readdistribution"
   executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:20Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -216,8 +216,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_readduplication"
   executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:15Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -219,8 +219,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_tin"
   executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:20Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -197,8 +197,8 @@ build_info:
   output: "target/executable/sortmerna"
   executable: "target/executable/sortmerna/sortmerna"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/sortmerna/sortmerna

@@ -486,9 +486,9 @@ function ViashDockerfile {
 FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:20Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -221,8 +221,8 @@ build_info:
   output: "target/executable/stringtie"
   executable: "target/executable/stringtie/stringtie"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:20Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

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

@@ -204,8 +204,8 @@ build_info:
   output: "target/executable/summarizedexperiment"
   executable: "target/executable/summarizedexperiment/summarizedexperiment"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

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="2024-12-03T19:47:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/tx2gene/.config.vsh.yaml

@@ -190,8 +190,8 @@ build_info:
   output: "target/executable/tx2gene"
   executable: "target/executable/tx2gene/tx2gene"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/tx2gene/tx2gene

@@ -483,9 +483,9 @@ RUN apt-get update && \
 RUN pip install --upgrade pip
 
 LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:22Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/tximport/.config.vsh.yaml

@@ -256,8 +256,8 @@ build_info:
   output: "target/executable/tximport"
   executable: "target/executable/tximport/tximport"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/tximport/tximport

@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
   Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
 
 LABEL org.opencontainers.image.description="Companion container for running component tximport"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:22Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/ucsc/bedclip/.config.vsh.yaml

@@ -169,8 +169,8 @@ build_info:
   output: "target/executable/ucsc/bedclip"
   executable: "target/executable/ucsc/bedclip/bedclip"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/ucsc/bedclip/bedclip

@@ -473,9 +473,9 @@ RUN apt-get update && \
 RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
 
 LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml

@@ -169,8 +169,8 @@ build_info:
   output: "target/executable/ucsc/bedgraphtobigwig"
   executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig

@@ -473,9 +473,9 @@ RUN apt-get update && \
 RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
 
 LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
-LABEL org.opencontainers.image.created="2024-12-03T19:47:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="0b5aea9962d5e17eff2714df166b5f976f49a92e"
+LABEL org.opencontainers.image.created="2024-12-05T05:12:22Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="e244fcf554ffba49eafd8534e96f52004dcc5dee"
 LABEL org.opencontainers.image.version="add-labels"
 
 VIASHDOCKER

target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml

@@ -595,8 +595,8 @@ build_info:
   output: "target/executable/workflows/genome_alignment_and_quant"
   executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant

@@ -1314,8 +1314,6 @@ cat > "\$tempscript" << 'VIASHMAIN'
 // The following code has been auto-generated by Viash.
 
 //// VIASH END
-// TODO: Improve logic of this wf, e.g. by splitting up in 2 subwfs
-// TODO: See if this can be aligned with the pseudo-alignment branch of the logic
 workflow run_wf {
   take:
     input_ch

target/executable/workflows/merge_quant_results/.config.vsh.yaml

@@ -283,8 +283,8 @@ build_info:
   output: "target/executable/workflows/merge_quant_results"
   executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/tx2gene"
   - "target/nextflow/tximport"

target/executable/workflows/post_processing/.config.vsh.yaml

@@ -482,8 +482,8 @@ build_info:
   output: "target/executable/workflows/post_processing"
   executable: "target/executable/workflows/post_processing/post_processing"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/picard_markduplicates"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

target/executable/workflows/pre_processing/.config.vsh.yaml

@@ -637,8 +637,8 @@ build_info:
   output: "target/executable/workflows/pre_processing"
   executable: "target/executable/workflows/pre_processing/pre_processing"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract"

target/executable/workflows/prepare_genome/.config.vsh.yaml

@@ -507,8 +507,8 @@ build_info:
   output: "target/executable/workflows/prepare_genome"
   executable: "target/executable/workflows/prepare_genome/prepare_genome"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/gunzip"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"

target/executable/workflows/prepare_genome/prepare_genome

@@ -1375,7 +1375,6 @@ workflow run_wf {
         directives: [ label: [ "lowmem", "midcpu" ] ]
       )
 
-      // TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode 
       | star_genome_generate.run (
         runIf: {id, state -> !state.star_index && !state.skip_alignment}, 
         fromState: [ 

target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml

@@ -290,8 +290,8 @@ build_info:
   output: "target/executable/workflows/pseudo_alignment_and_quant"
   executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant"

target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant

@@ -800,7 +800,6 @@ cat > "\$tempscript" << 'VIASHMAIN'
 // The following code has been auto-generated by Viash.
 
 //// VIASH END
-// TODO: See if the logic of this can be aligned with the STAR aligner logic
 workflow run_wf {
   take:
     input_ch

target/executable/workflows/quality_control/.config.vsh.yaml

@@ -1561,8 +1561,8 @@ build_info:
   output: "target/executable/workflows/quality_control"
   executable: "target/executable/workflows/quality_control/quality_control"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment"

target/executable/workflows/quality_control/quality_control

@@ -3303,7 +3303,6 @@ cat > "\$tempscript" << 'VIASHMAIN'
 // The following code has been auto-generated by Viash.
 
 //// VIASH END
-// TODO: Split in /sample and integrated QC
 workflow run_wf {
 
   take: 
@@ -3314,7 +3313,6 @@ workflow run_wf {
     qc_ch = input_ch
 
       // temporary fix to force assignment when alignment is skipped
-      // TODO: Check this
       | map {it} 
 
       // Feature biotype QC using featureCounts
@@ -4004,7 +4002,6 @@ workflow run_wf {
       | map { list -> [list[0], list[1] + list[2]] }
 
       | map { id, state -> 
-        // TODO: Check this, necessary for setState
         def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
         [ id, mod_state ]
       }

target/executable/workflows/rnaseq/.config.vsh.yaml

@@ -1941,6 +1941,11 @@ resources:
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
 description: "A viash workflow for the nf-core/rnaseq pipeline.\n"
+test_resources:
+- type: "nextflow_script"
+  path: "test.nf"
+  is_executable: true
+  entrypoint: "test_wf"
 info: null
 status: "enabled"
 requirements:
@@ -2054,8 +2059,8 @@ build_info:
   output: "target/executable/workflows/rnaseq"
   executable: "target/executable/workflows/rnaseq/rnaseq"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/workflows/prepare_genome"
   - "target/nextflow/cat_fastq"

target/executable/workflows/rnaseq/rnaseq

@@ -4432,7 +4432,6 @@ workflow run_wf {
       )
 
       // Check if contigs in genome fasta file > 512 Mbp
-      // TODO: check where this is required and move if necessary
       | map { id, state -> 
         (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]]
       }
@@ -4512,15 +4511,13 @@ workflow run_wf {
       )
 
       // Infer strandedness from Salmon pseudo-alignment results
-      // TODO: Turn this into a workflow step and include as a dependency
       | map { id, state -> 
-      (state.strandedness == 'auto') ? 
-        [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : 
-        [id, state] 
+        (state.strandedness == 'auto') ? 
+          [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : 
+          [id, state] 
       }
 
       // Filter FastQ files based on minimum trimmed read count after adapter trimming
-      // TODO: Turn this into a workflow step and include as a dependency
       | map { id, state -> 
         def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
         def num_reads = (state.skip_trimming) ? 
@@ -4589,7 +4586,6 @@ workflow run_wf {
       )
 
       // Filter channels to get samples that passed STAR minimum mapping percentage
-      // TODO: Move to reporting or later step
       | map { id, state -> 
         def percent_mapped = (!state.skip_alignment && state.passed_trimmed_reads) ? getStarPercentMapped(state.star_multiqc) : 0.0
         def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false

target/nextflow/bedtools_genomecov/.config.vsh.yaml

@@ -183,8 +183,8 @@ build_info:
   output: "target/nextflow/bedtools_genomecov"
   executable: "target/nextflow/bedtools_genomecov/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/bedtools_genomecov/main.nf

@@ -3039,8 +3039,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/cat_additional_fasta/.config.vsh.yaml

@@ -187,8 +187,8 @@ build_info:
   output: "target/nextflow/cat_additional_fasta"
   executable: "target/nextflow/cat_additional_fasta/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/cat_additional_fasta/main.nf

@@ -3040,8 +3040,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/cat_fastq/.config.vsh.yaml

@@ -174,8 +174,8 @@ build_info:
   output: "target/nextflow/cat_fastq"
   executable: "target/nextflow/cat_fastq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/cat_fastq/main.nf

@@ -3031,8 +3031,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/cat_fastq",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/deseq2_qc/.config.vsh.yaml

@@ -242,8 +242,8 @@ build_info:
   output: "target/nextflow/deseq2_qc"
   executable: "target/nextflow/deseq2_qc/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/deseq2_qc/main.nf

@@ -3112,8 +3112,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/deseq2_qc",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/dupradar/.config.vsh.yaml

@@ -271,8 +271,8 @@ build_info:
   output: "target/nextflow/dupradar"
   executable: "target/nextflow/dupradar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/dupradar/main.nf

@@ -3144,8 +3144,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dupradar",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/getchromsizes/.config.vsh.yaml

@@ -172,8 +172,8 @@ build_info:
   output: "target/nextflow/getchromsizes"
   executable: "target/nextflow/getchromsizes/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/getchromsizes/main.nf

@@ -3021,8 +3021,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/getchromsizes",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/gtf2bed/.config.vsh.yaml

@@ -150,8 +150,8 @@ build_info:
   output: "target/nextflow/gtf2bed"
   executable: "target/nextflow/gtf2bed/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/gtf2bed/main.nf

@@ -3003,8 +3003,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gtf2bed",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/gtf_filter/.config.vsh.yaml

@@ -160,8 +160,8 @@ build_info:
   output: "target/nextflow/gtf_filter"
   executable: "target/nextflow/gtf_filter/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/gtf_filter/main.nf

@@ -3011,8 +3011,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gtf_filter",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/gunzip/.config.vsh.yaml

@@ -149,8 +149,8 @@ build_info:
   output: "target/nextflow/gunzip"
   executable: "target/nextflow/gunzip/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/gunzip/main.nf

@@ -3000,8 +3000,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gunzip",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/multiqc_custom_biotype/.config.vsh.yaml

@@ -170,8 +170,8 @@ build_info:
   output: "target/nextflow/multiqc_custom_biotype"
   executable: "target/nextflow/multiqc_custom_biotype/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/multiqc_custom_biotype/main.nf

@@ -3020,8 +3020,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/picard_markduplicates/.config.vsh.yaml

@@ -212,8 +212,8 @@ build_info:
   output: "target/nextflow/picard_markduplicates"
   executable: "target/nextflow/picard_markduplicates/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/picard_markduplicates/main.nf

@@ -3071,8 +3071,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/prepare_multiqc_input/.config.vsh.yaml

@@ -417,8 +417,8 @@ build_info:
   output: "target/nextflow/prepare_multiqc_input"
   executable: "target/nextflow/prepare_multiqc_input/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/prepare_multiqc_input/main.nf

@@ -3290,8 +3290,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml

@@ -143,8 +143,8 @@ build_info:
   output: "target/nextflow/preprocess_transcripts_fasta"
   executable: "target/nextflow/preprocess_transcripts_fasta/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"

target/nextflow/preprocess_transcripts_fasta/main.nf

@@ -2990,8 +2990,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta",
     "viash_version" : "0.9.0",
-    "git_commit" : "0b5aea9962d5e17eff2714df166b5f976f49a92e",
-    "git_remote" : "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+    "git_commit" : "e244fcf554ffba49eafd8534e96f52004dcc5dee",
+    "git_remote" : "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/preseq_lcextrap/.config.vsh.yaml

@@ -196,8 +196,8 @@ build_info:
   output: "target/nextflow/preseq_lcextrap"
   executable: "target/nextflow/preseq_lcextrap/main.nf"
   viash_version: "0.9.0"
-  git_commit: "0b5aea9962d5e17eff2714df166b5f976f49a92e"
-  git_remote: "https://x-access-token:ghs_K1l4tLngEkomUqIQmvtQnd1V942PTZ1leHqC@github.com/viash-hub/rnaseq"
+  git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
+  git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "add-labels"