Build branch main with version main (bc9cc0a)

Build pipeline: viash-hub.biobox.main-bd96b Source commit: bc9cc0a6ce Source message: Kallisto quant (#152) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2. * complete component * Update changelog * add help.txt * apply suggested changes (changelog, config)
2024-09-19 04:13:10 +00:00
parent bca90c9331
commit 6a8cd85cf3
269 changed files with 6899 additions and 699 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -65,6 +65,16 @@

 * `fastqc`: High throughput sequence quality control analysis tool (PR #92).

+* `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from
+  metatranscriptomic data (PR #146).
+
+* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
+
+* `kallisto`:
+    - `kallisto_index`: Create a kallisto index (PR #149).
+    - `kallisto_quant`: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads (PR #152).
+
+
 ## MINOR CHANGES

 * `busco` components: update BUSCO to `5.7.1` (PR #72).
@@ -161,13 +171,7 @@
    - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
                           intervals defined in a BED/GFF/VCF file (PR #59).

-* `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from metatranscriptomic 
-               data. (PR #146)

-* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
-
-* `kallisto`:
-    - `kallisto_index`: Create a kallisto index (PR #149).


 ## MINOR CHANGES
--- a/src/kallisto/kallisto_quant/config.vsh.yaml
+++ b/src/kallisto/kallisto_quant/config.vsh.yaml
@@ -0,0 +1,105 @@
+name: kallisto_quant
+namespace: kallisto
+description: |
+  Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
+keywords: [kallisto, quant, pseudoalignment]
+links:
+  homepage: https://pachterlab.github.io/kallisto/about
+  documentation: https://pachterlab.github.io/kallisto/manual
+  repository: https://github.com/pachterlab/kallisto
+  issue_tracker: https://github.com/pachterlab/kallisto/issues
+references: 
+  doi: 10.1038/nbt.3519
+license: BSD 2-Clause License
+
+argument_groups:
+- name: "Input"
+  arguments:
+  - name: "--input"
+    type: file
+    description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
+    direction: "input"
+    multiple: true
+    required: true
+  - name: "--index"
+    alternatives: ["-i"]
+    type: file
+    description: Kallisto genome index.
+    must_exist: true
+    required: true
+
+- name: "Output"
+  arguments:
+  - name: "--output_dir"
+    alternatives: ["-o"]
+    type: string
+    description: Directory to write output to.
+    required: true
+
+- name: "Options"
+  arguments:
+  - name: "--single"
+    type: boolean_true
+    description: Single end mode.
+  - name: "--single_overhang"
+    type: boolean_true
+    description: Include reads where unobserved rest of fragment is predicted to lie outside a transcript.
+  - name: "--fr_stranded"
+    type: boolean_true
+    description: Strand specific reads, first read forward.
+  - name: "--rf_stranded"
+    type: boolean_true
+    description: Strand specific reads, first read reverse.
+  - name: "--fragment_length"
+    alternatives: ["-l"]
+    type: double
+    description: The estimated average fragment length.
+  - name: "--sd"
+    alternatives: ["-s"]
+    type: double
+    description: |
+      The estimated standard deviation of the fragment length (default: -l, -s values are estimated 
+      from paired end data, but are required when using --single).
+  - name: "--plaintext"
+    type: boolean_true
+    description: Output plaintext instead of HDF5.
+  - name: "--bootstrap_samples"
+    alternatives: ["-b"]
+    type: integer
+    description: |
+      Number of bootstrap samples to draw. Default: '0'
+    example: 0
+  - name: "--seed"
+    type: integer
+    description: |
+      Random seed for bootstrap. Default: '42'
+    example: 42
+
+
+resources:
+- type: bash_script
+  path: script.sh
+
+test_resources:
+- type: bash_script
+  path: test.sh
+- type: file
+  path: test_data
+
+engines:
+  - type: docker
+    image: ubuntu:22.04
+    setup:
+      - type: docker
+        run: |
+          apt-get update && \
+          apt-get install -y --no-install-recommends wget && \
+          wget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz && \
+          tar -xzf kallisto_linux-v0.50.1.tar.gz && \
+          mv kallisto/kallisto /usr/local/bin/
+      - type: docker
+        run: |
+          echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow  
--- a/src/kallisto/kallisto_quant/help.txt
+++ b/src/kallisto/kallisto_quant/help.txt
@@ -0,0 +1,33 @@
+```
+kallisto quant
+```
+
+kallisto 0.50.1
+Computes equivalence classes for reads and quantifies abundances
+
+Usage: kallisto quant [arguments] FASTQ-files
+
+Required arguments:
+-i, --index=STRING            Filename for the kallisto index to be used for
+                              quantification
+-o, --output-dir=STRING       Directory to write output to
+
+Optional arguments:
+-b, --bootstrap-samples=INT   Number of bootstrap samples (default: 0)
+    --seed=INT                Seed for the bootstrap sampling (default: 42)
+    --plaintext               Output plaintext instead of HDF5
+    --single                  Quantify single-end reads
+    --single-overhang         Include reads where unobserved rest of fragment is
+                              predicted to lie outside a transcript
+    --fr-stranded             Strand specific reads, first read forward
+    --rf-stranded             Strand specific reads, first read reverse
+-l, --fragment-length=DOUBLE  Estimated average fragment length
+-s, --sd=DOUBLE               Estimated standard deviation of fragment length
+                              (default: -l, -s values are estimated from paired
+                               end data, but are required when using --single)
+-p, --priors                  Priors for the EM algorithm, either as raw counts or as
+                              probabilities. Pseudocounts are added to raw reads to
+                              prevent zero valued priors. Supplied in the same order
+                              as the transcripts in the transcriptome
+-t, --threads=INT             Number of threads to use (default: 1)
+    --verbose                 Print out progress information every 1M proccessed reads
--- a/src/kallisto/kallisto_quant/script.sh
+++ b/src/kallisto/kallisto_quant/script.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -eo pipefail
+
+unset_if_false=( par_single par_single_overhang par_rf_stranded par_fr_stranded par_plaintext )
+
+for var in "${unset_if_false[@]}"; do
+    temp_var="${!var}"
+    [[ "$temp_var" == "false" ]] && unset $var
+done
+
+IFS=";" read -ra input <<< $par_input
+
+# Check if par_single is not set and ensure even number of input files
+if [ -z "$par_single" ]; then
+    if [ $((${#input[@]} % 2)) -ne 0 ]; then
+        echo "Error: When running in paired-end mode, the number of input files must be even."
+        echo "Number of input files provided: ${#input[@]}"
+        exit 1
+    fi
+fi
+
+
+mkdir -p $par_output_dir
+
+
+kallisto quant \
+    ${meta_cpus:+--threads $meta_cpus} \
+    -i $par_index \
+    ${par_gtf:+--gtf "${par_gtf}"} \
+    ${par_single:+--single} \
+    ${par_single_overhang:+--single-overhang} \
+    ${par_fr_stranded:+--fr-stranded} \
+    ${par_rf_stranded:+--rf-stranded} \
+    ${par_plaintext:+--plaintext} \
+    ${par_bootstrap_samples:+--bootstrap-samples "${par_bootstrap_samples}"} \
+    ${par_fragment_length:+--fragment-length "${par_fragment_length}"} \
+    ${par_sd:+--sd "${par_sd}"} \
+    ${par_seed:+--seed "${par_seed}"} \
+    -o $par_output_dir \
+    ${input[*]}
+
+
--- a/src/kallisto/kallisto_quant/test.sh
+++ b/src/kallisto/kallisto_quant/test.sh
@@ -0,0 +1,53 @@
+#!/bin/bash
+
+echo ">>> Testing $meta_functionality_name"
+
+echo ">>> Test 1: Testing for paired-end reads"
+"$meta_executable" \
+  --index "$meta_resources_dir/test_data/index/transcriptome.idx" \
+  --rf_stranded \
+  --output_dir . \
+  --input "$meta_resources_dir/test_data/reads/A_R1.fastq;$meta_resources_dir/test_data/reads/A_R2.fastq"
+
+echo ">>> Checking whether output exists"
+[ ! -f "run_info.json" ] && echo "run_info.json does not exist!" && exit 1
+[ ! -s "run_info.json" ] && echo "run_info.json is empty!" && exit 1
+[ ! -f "abundance.tsv" ] && echo "abundance.tsv does not exist!" && exit 1
+[ ! -s "abundance.tsv" ] && echo "abundance.tsv is empty!" && exit 1
+[ ! -f "abundance.h5" ] && echo "abundance.h5 does not exist!" && exit 1
+[ ! -s "abundance.h5" ] && echo "abundance.h5 is empty!" && exit 1
+
+echo ">>> Checking if output is correct"
+diff "abundance.tsv" "$meta_resources_dir/test_data/abundance_1.tsv" || { echo "abundance.tsv is not correct"; exit 1; }
+
+rm -rf abundance.tsv abundance.h5 run_info.json
+
+################################################################################
+
+echo ">>> Test 2: Testing for single-end reads"
+"$meta_executable" \
+  --index "$meta_resources_dir/test_data/index/transcriptome.idx" \
+  --rf_stranded \
+  --output_dir . \
+  --single \
+  --input "$meta_resources_dir/test_data/reads/A_R1.fastq" \
+  --fragment_length 101 \
+  --sd 50
+
+echo ">>> Checking whether output exists"
+[ ! -f "run_info.json" ] && echo "run_info.json does not exist!" && exit 1
+[ ! -s "run_info.json" ] && echo "run_info.json is empty!" && exit 1
+[ ! -f "abundance.tsv" ] && echo "abundance.tsv does not exist!" && exit 1
+[ ! -s "abundance.tsv" ] && echo "abundance.tsv is empty!" && exit 1
+[ ! -f "abundance.h5" ] && echo "abundance.h5 does not exist!" && exit 1
+[ ! -s "abundance.h5" ] && echo "abundance.h5 is empty!" && exit 1
+
+echo ">>> Checking if output is correct"
+diff "abundance.tsv" "$meta_resources_dir/test_data/abundance_2.tsv" || { echo "abundance.tsv is not correct"; exit 1; }
+
+rm -rf abundance.tsv abundance.h5 run_info.json
+
+################################################################################
+
+echo "All tests succeeded!"
+exit 0
--- a/src/kallisto/kallisto_quant/test_data/abundance_1.tsv
+++ b/src/kallisto/kallisto_quant/test_data/abundance_1.tsv
@@ -0,0 +1,2 @@
+target_id	length	eff_length	est_counts	tpm
+Sheila	35	36	0	-nan
--- a/src/kallisto/kallisto_quant/test_data/abundance_2.tsv
+++ b/src/kallisto/kallisto_quant/test_data/abundance_2.tsv
@@ -0,0 +1,2 @@
+target_id	length	eff_length	est_counts	tpm
+Sheila	35	15.0373	0	-nan
--- a/src/kallisto/kallisto_quant/test_data/index/transcriptome.idx
+++ b/src/kallisto/kallisto_quant/test_data/index/transcriptome.idx
--- a/src/kallisto/kallisto_quant/test_data/reads/A_R1.fastq
+++ b/src/kallisto/kallisto_quant/test_data/reads/A_R1.fastq
@@ -0,0 +1,4 @@
+@1
+GCTAGCTCAGAAAAAAAAAATCGTCGCGTGCGCGT
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
--- a/src/kallisto/kallisto_quant/test_data/reads/A_R2.fastq
+++ b/src/kallisto/kallisto_quant/test_data/reads/A_R2.fastq
@@ -0,0 +1,4 @@
+@1
+GCTAGCTCAGAAAAAAAAAATCGTCGCGTGCGCGT
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
--- a/src/kallisto/kallisto_quant/test_data/script.sh
+++ b/src/kallisto/kallisto_quant/test_data/script.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+# copy test data
+cp -r /tmp/snakemake-wrappers/bio/kallisto/quant/test/* src/kallisto/kallisto_quant/test_data
+
+rm src/kallisto/kallisto_quant/test_data/Snakefile
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -235,9 +235,9 @@ build_info:
  output: "target/executable/agat/agat_convert_bed2gff"
  executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -515,9 +515,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:05Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:22Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,9 +225,9 @@ build_info:
  output: "target/executable/agat/agat_convert_embl2gff"
  executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -505,9 +505,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:05Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:22Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
@@ -230,9 +230,9 @@ build_info:
  output: "target/executable/agat/agat_convert_genscan2gff"
  executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
+++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
@@ -514,9 +514,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:06Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:23Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,9 +228,9 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gff2gtf"
  executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -519,9 +519,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:06Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:22Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,9 +188,9 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gff2tsv"
  executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -484,9 +484,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:05Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:21Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,9 +195,9 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gxf2gxf"
  executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -493,9 +493,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:04Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:21Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -706,9 +706,9 @@ build_info:
  output: "target/executable/arriba"
  executable: "target/executable/arriba/arriba"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -754,9 +754,9 @@ RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' >

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:08Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:24Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -469,9 +469,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_annotate"
  executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate
+++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
@@ -650,9 +650,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:58Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:15Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
@@ -335,9 +335,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_concat"
  executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_concat/bcftools_concat
+++ b/target/executable/bcftools/bcftools_concat/bcftools_concat
@@ -566,9 +566,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:58Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:15Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_norm"
  executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_norm/bcftools_norm
+++ b/target/executable/bcftools/bcftools_norm/bcftools_norm
@@ -589,9 +589,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:59Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:16Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
@@ -185,9 +185,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_sort"
  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_sort/bcftools_sort
+++ b/target/executable/bcftools/bcftools_sort/bcftools_sort
@@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:57Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:14Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
@@ -458,9 +458,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_stats"
  executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_stats/bcftools_stats
+++ b/target/executable/bcftools/bcftools_stats/bcftools_stats
@@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:59Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:15Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -418,9 +418,9 @@ build_info:
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/

 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:07Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -274,9 +274,9 @@ build_info:
  output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
  executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
@@ -554,9 +554,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:11Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:27Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
@@ -1115,9 +1115,9 @@ build_info:
  output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis"
  executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
@@ -954,9 +954,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:11Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:27Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,9 +187,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bamtofastq"
  executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:50Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:07Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -176,9 +176,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bed12tobed6"
  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
+++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
@@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:48Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:06Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,9 +214,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bedtobam"
  executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:51Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:08Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -337,9 +337,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_genomecov"
  executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
@@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:48Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:06Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,9 +232,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:49Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:06Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -273,9 +273,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_groupby"
  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby
+++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
@@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:50Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:08Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,9 +410,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_intersect"
  executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:49Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:07Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
@@ -210,9 +210,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_links"
  executable: "target/executable/bedtools/bedtools_links/bedtools_links"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_links/bedtools_links
+++ b/target/executable/bedtools/bedtools_links/bedtools_links
@@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:49Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:07Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
@@ -279,9 +279,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_merge"
  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_merge/bedtools_merge
+++ b/target/executable/bedtools/bedtools_merge/bedtools_merge
@@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:48Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:05Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_sort"
  executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:50Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:08Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,9 +158,9 @@ build_info:
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -475,9 +475,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:02Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:19Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,9 +145,9 @@ build_info:
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -465,9 +465,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:02Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:19Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -423,9 +423,9 @@ build_info:
  output: "target/executable/busco/busco_run"
  executable: "target/executable/busco/busco_run/busco_run"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -632,9 +632,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:03Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:19Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -740,9 +740,9 @@ build_info:
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -831,9 +831,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions

 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:09Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:25Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -317,9 +317,9 @@ build_info:
  output: "target/executable/falco"
  executable: "target/executable/falco/falco"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio

 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:10Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:26Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1083,9 +1083,9 @@ build_info:
  output: "target/executable/fastp"
  executable: "target/executable/fastp/fastp"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:06Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:23Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -340,9 +340,9 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -601,9 +601,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:56Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:13Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -645,9 +645,9 @@ build_info:
  output: "target/executable/featurecounts"
  executable: "target/executable/featurecounts/featurecounts"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -754,9 +754,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:00Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:17Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -190,9 +190,9 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -493,9 +493,9 @@ mv target/release/fq /usr/local/bin/ && \
 cd / && rm -rf /fq

 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:56Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:13Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -685,9 +685,9 @@ build_info:
  output: "target/executable/gffread"
  executable: "target/executable/gffread/gffread"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -807,9 +807,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:47Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:05Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -218,9 +218,9 @@ build_info:
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -506,9 +506,9 @@ 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="2024-09-18T13:53:04Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:21Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -0,0 +1,261 @@
+name: "kallisto_quant"
+namespace: "kallisto"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "List of input FastQ files of size 1 and 2 for single-end and paired-end\
+      \ data, respectively."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--index"
+    alternatives:
+    - "-i"
+    description: "Kallisto genome index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "string"
+    name: "--output_dir"
+    alternatives:
+    - "-o"
+    description: "Directory to write output to."
+    info: null
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--single"
+    description: "Single end mode."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--single_overhang"
+    description: "Include reads where unobserved rest of fragment is predicted to\
+      \ lie outside a transcript."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--fr_stranded"
+    description: "Strand specific reads, first read forward."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--rf_stranded"
+    description: "Strand specific reads, first read reverse."
+    info: null
+    direction: "input"
+  - type: "double"
+    name: "--fragment_length"
+    alternatives:
+    - "-l"
+    description: "The estimated average fragment length."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--sd"
+    alternatives:
+    - "-s"
+    description: "The estimated standard deviation of the fragment length (default:\
+      \ -l, -s values are estimated \nfrom paired end data, but are required when\
+      \ using --single).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--plaintext"
+    description: "Output plaintext instead of HDF5."
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--bootstrap_samples"
+    alternatives:
+    - "-b"
+    description: "Number of bootstrap samples to draw. Default: '0'\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--seed"
+    description: "Random seed for bootstrap. Default: '42'\n"
+    info: null
+    example:
+    - 42
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Quantifying abundances of transcripts from RNA-Seq data, or more generally\
+  \ of target sequences using high-throughput sequencing reads.\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:
+- "kallisto"
+- "quant"
+- "pseudoalignment"
+license: "BSD 2-Clause License"
+references:
+  doi:
+  - "10.1038/nbt.3519"
+links:
+  repository: "https://github.com/pachterlab/kallisto"
+  homepage: "https://pachterlab.github.io/kallisto/about"
+  documentation: "https://pachterlab.github.io/kallisto/manual"
+  issue_tracker: "https://github.com/pachterlab/kallisto/issues"
+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: "ubuntu:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "apt-get update && \\\napt-get install -y --no-install-recommends wget && \\\
+      \nwget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz\
+      \ && \\\ntar -xzf kallisto_linux-v0.50.1.tar.gz && \\\nmv kallisto/kallisto\
+      \ /usr/local/bin/\n"
+  - type: "docker"
+    run:
+    - "echo \"kallisto: $(kallisto version | sed 's/kallisto, version //')\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/kallisto/kallisto_quant/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/kallisto/kallisto_quant"
+  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
+  viash_version: "0.9.0"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
+package_config:
+  name: "biobox"
+  version: "main"
+  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 := 'main'"
+  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"
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -507,9 +507,9 @@ build_info:
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -656,9 +656,9 @@ echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:00Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:16Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
  output: "target/executable/lofreq/lofreq_indelqual"
  executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -501,9 +501,9 @@ echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:59Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:16Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -456,9 +456,9 @@ build_info:
  output: "target/executable/multiqc"
  executable: "target/executable/multiqc/multiqc"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -637,9 +637,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:10Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:26Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -398,9 +398,9 @@ build_info:
  output: "target/executable/pear"
  executable: "target/executable/pear/pear"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -597,9 +597,9 @@ echo "pear: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:51Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:09Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -264,9 +264,9 @@ build_info:
  output: "target/executable/qualimap/qualimap_rnaseq"
  executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -527,9 +527,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-09-18T13:52:55Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:12Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -852,9 +852,9 @@ 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: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -991,9 +991,9 @@ echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\
 echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:03Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:20Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
  output: "target/executable/rsem/rsem_prepare_reference"
  executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
+++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
@@ -656,9 +656,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
-LABEL org.opencontainers.image.created="2024-09-18T13:53:03Z"
+LABEL org.opencontainers.image.created="2024-09-19T03:54:20Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="619f1bbb6d040e650233d3b0380f5298e624ecef"
+LABEL org.opencontainers.image.revision="bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -277,9 +277,9 @@ build_info:
  output: "target/executable/salmon/salmon_index"
  executable: "target/executable/salmon/salmon_index/salmon_index"
  viash_version: "0.9.0"
-  git_commit: "619f1bbb6d040e650233d3b0380f5298e624ecef"
-  git_remote: "https://x-access-token:ghs_Vi76hXSsWXZ7Nqew1pu2fjagXguaxI2jku9D@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-4-g619f1bb"
+  git_commit: "bc9cc0a6ce4e0b87a4ce47561b4812b449e101ca"
+  git_remote: "https://x-access-token:ghs_lSKHBbqnO6mkOoPjjavM2ghphcCkFP1NX9Uo@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-5-gbc9cc0a"
 package_config:
  name: "biobox"
  version: "main"
--- a/Show More
+++ b/Show More