Build branch main with version main (4aa0a89)

Build pipeline: viash-hub.biobox.main-rgg5q

Source commit: 4aa0a893d2

Source message: Add agat convert bed2gff (#97)

* add config

* add help

* add script

* add test data and expected output file

* add script to get test data

* add tests

* update changelog

* fix path to test data

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

CHANGELOG.md

@@ -19,11 +19,14 @@
   - `seqtk/seqtk_subseq`: Extract the sequences (complete or subsequence) from the FASTA/FASTQ files
                 based on a provided sequence IDs or region coordinates file (PR #85).
 
-* `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+* `agat`:
+  - `agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+  - `/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
 
 * `bedtools`:
-    - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
+  - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
-    - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
+  - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
+
 
 ## MINOR CHANGES
 

src/agat/agat_convert_bed2gff/config.vsh.yaml

@@ -0,0 +1,86 @@
+name: agat_convert_bed2gff
+namespace: agat
+description: |
+  The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).
+keywords: [gene annotations, GFF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_bed2gff.html
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --bed
+        description: Input bed file that will be converted.
+        type: file
+        required: true
+        direction: input
+        example: input.bed
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile, --gff]
+        description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --source
+        description: |
+          The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
+        type: string
+        required: false
+        example: Stringtie
+      - name: --primary_tag
+        description: |
+          The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
+        type: string
+        required: false
+        example: gene
+      - name: --inflate_off
+        description: |
+          By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.
+        type: boolean_false
+      - name: --inflate_type
+        description: |
+          Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
+        type: string
+        required: false
+        example: exon
+      - name: --verbose
+        description: add verbosity
+        type: boolean_true
+      - name: --config
+        alternatives: [-c]
+        description: |
+          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+        type: file
+        required: false
+        example: custom_agat_config.yaml
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow

src/agat/agat_convert_bed2gff/help.txt

@@ -0,0 +1,89 @@
+```sh
+agat_convert_bed2gff.pl --help
+```
+ ------------------------------------------------------------------------------
+|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+|   https://github.com/NBISweden/AGAT                                          |
+|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+ ------------------------------------------------------------------------------
+
+
+Name:
+    agat_convert_bed2gff.pl
+
+Description:
+    The script takes a bed file as input, and will translate it in gff
+    format. The BED format is described here:
+    https://genome.ucsc.edu/FAQ/FAQformat.html#format1 The script converts
+    0-based, half-open [start-1, end) bed file to 1-based, closed [start,
+    end] General Feature Format v3 (GFF3).
+
+Usage:
+        agat_convert_bed2gff.pl --bed infile.bed [ -o outfile ]
+        agat_convert_bed2gff.pl -h
+
+Options:
+    --bed   Input bed file that will be converted.
+
+    --source
+            The source informs about the tool used to produce the data and
+            is stored in 2nd field of a gff file. Example:
+            Stringtie,Maker,Augustus,etc. [default: data]
+
+    --primary_tag
+            The primary_tag corresponds to the data type and is stored in
+            3rd field of a gff file. Example: gene,mRNA,CDS,etc. [default:
+            gene]
+
+    --inflate_off
+            By default we inflate the block fields (blockCount, blockSizes,
+            blockStarts) to create subfeatures of the main feature
+            (primary_tag). The type of subfeature created is based on the
+            inflate_type parameter. If you do not want this inflating
+            behaviour you can deactivate it by using the --inflate_off
+            option.
+
+    --inflate_type
+            Feature type (3rd column in gff) created when inflate parameter
+            activated [default: exon].
+
+    --verbose
+            add verbosity
+
+    -o , --output , --out , --outfile or --gff
+            Output GFF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -c or --config
+            String - Input agat config file. By default AGAT takes as input
+            agat_config.yaml file from the working directory if any,
+            otherwise it takes the orignal agat_config.yaml shipped with
+            AGAT. To get the agat_config.yaml locally type: "agat config
+            --expose". The --config option gives you the possibility to use
+            your own AGAT config file (located elsewhere or named
+            differently).
+
+    -h or --help
+            Display this helpful text.
+
+Feedback:
+  Did you find a bug?:
+    Do not hesitate to report bugs to help us keep track of the bugs and
+    their resolution. Please use the GitHub issue tracking system available
+    at this address:
+
+                https://github.com/NBISweden/AGAT/issues
+
+     Ensure that the bug was not already reported by searching under Issues.
+     If you're unable to find an (open) issue addressing the problem, open a new one.
+     Try as much as possible to include in the issue when relevant:
+     - a clear description,
+     - as much relevant information as possible,
+     - the command used,
+     - a data sample,
+     - an explanation of the expected behaviour that is not occurring.
+
+  Do you want to contribute?:
+    You are very welcome, visit this address for the Contributing
+    guidelines:
+    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md

src/agat/agat_convert_bed2gff/script.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# run agat_convert_sp_bed2gff.pl
+agat_convert_bed2gff.pl \
+  --bed "$par_bed" \
+  -o "$par_output" \
+  ${par_source:+--source "${par_source}"} \
+  ${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
+  ${par_inflate_off:+--inflate_off} \
+  ${par_inflate_type:+--inflate_type "${par_inflate_type}"} \
+  ${par_verbose:+--verbose}
+  ${par_config:+--config "${par_config}"} \

src/agat/agat_convert_bed2gff/test.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/out_data"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --bed "$test_dir/test.bed" \
+  --output "$out_dir/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$out_dir/output.gff" "$test_dir/agat_convert_bed2gff_1.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"

src/agat/agat_convert_bed2gff/test_data/agat_convert_bed2gff_1.gff

@@ -0,0 +1,12 @@
+##gff-version 3
+scaffold625	data	gene	337818	343277	.	+	.	ID=1;Name=CLUHART00000008717;blockCount=4;blockSizes=154%2C109%2C111%2C1314;blockStarts=0%2C2915%2C3700%2C4146;itemRgb=255%2C0%2C0;thickEnd=343033;thickStart=337914
+scaffold625	data	exon	337818	337971	.	+	.	ID=exon1;Parent=1
+scaffold625	data	exon	340733	340841	.	+	.	ID=exon2;Parent=1
+scaffold625	data	exon	341518	341628	.	+	.	ID=exon3;Parent=1
+scaffold625	data	exon	341964	343277	.	+	.	ID=exon4;Parent=1
+scaffold625	data	CDS	337915	337971	.	+	0	ID=CDS1;Parent=1
+scaffold625	data	CDS	340733	340841	.	+	0	ID=CDS2;Parent=1
+scaffold625	data	CDS	341518	341628	.	+	2	ID=CDS3;Parent=1
+scaffold625	data	CDS	341964	343033	.	+	2	ID=CDS4;Parent=1
+scaffold625	data	five_prime_UTR	337818	337914	.	+	.	ID=five_prime_UTR1;Parent=1
+scaffold625	data	three_prime_UTR	343034	343277	.	+	.	ID=three_prime_UTR1;Parent=1

src/agat/agat_convert_bed2gff/test_data/script.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/agat_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
+fi
+
+# copy test data
+cp -r /tmp/agat_source/t/scripts_output/in/test.bed src/agat/agat_convert_bed2gff/test_data/test.bed
+cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_bed2gff_1.gff src/agat/agat_convert_bed2gff/test_data/agat_convert_bed2gff_1.gff

src/agat/agat_convert_bed2gff/test_data/test.bed

@@ -0,0 +1 @@
+scaffold625	337817	343277	CLUHART00000008717	0	+	337914	343033	255,0,0	4	154,109,111,1314	0,2915,3700,4146

target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml

@@ -0,0 +1,261 @@
+name: "agat_convert_bed2gff"
+namespace: "agat"
+version: "main"
+authors:
+- name: "Leïla Paquay"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "leila@data-intuitive.com"
+      github: "Leila011"
+      linkedin: "leilapaquay"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Software Developer"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--bed"
+    description: "Input bed file that will be converted."
+    info: null
+    example:
+    - "input.bed"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    - "--outfile"
+    - "--gff"
+    description: "Output GFF file. If no output file is specified, the output will\
+      \ be written to STDOUT."
+    info: null
+    example:
+    - "output.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--source"
+    description: "The source informs about the tool used to produce the data and is\
+      \ stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc.\
+      \ [default: data]\n"
+    info: null
+    example:
+    - "Stringtie"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--primary_tag"
+    description: "The primary_tag corresponds to the data type and is stored in 3rd\
+      \ field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
+    info: null
+    example:
+    - "gene"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_false"
+    name: "--inflate_off"
+    description: "By default we inflate the block fields (blockCount, blockSizes,\
+      \ blockStarts) to create subfeatures of the main feature (primary_tag). The\
+      \ type of subfeature created is based on the inflate_type parameter. If you\
+      \ do not want this inflating behaviour you can deactivate it by using the --inflate_off\
+      \ option.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--inflate_type"
+    description: "Feature type (3rd column in gff) created when inflate parameter\
+      \ activated [default: exon].\n"
+    info: null
+    example:
+    - "exon"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "add verbosity"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "Input agat config file. By default AGAT takes as input agat_config.yaml\
+      \ file from the working directory if any, otherwise it takes the orignal agat_config.yaml\
+      \ shipped with AGAT. To get the agat_config.yaml locally type: \"agat config\
+      \ --expose\". The --config option gives you the possibility to use your own\
+      \ AGAT config file (located elsewhere or named differently).\n"
+    info: null
+    example:
+    - "custom_agat_config.yaml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "The script takes a bed file as input, and will translate it in gff format.\
+  \ The BED format is described here The script converts 0-based, half-open [start-1,\
+  \ end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\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:
+- "gene annotations"
+- "GFF conversion"
+license: "GPL-3.0"
+references:
+  doi:
+  - "10.5281/zenodo.3552717"
+links:
+  repository: "https://github.com/NBISweden/AGAT"
+  homepage: "https://github.com/NBISweden/AGAT"
+  documentation: "https://agat.readthedocs.io/en/latest/tools/agat_convert_bed2gff.html"
+  issue_tracker: "https://github.com/NBISweden/AGAT/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: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "agat --version | sed 's/AGAT\\s\\(.*\\)/agat: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/agat/agat_convert_bed2gff/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_bed2gff"
+  executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
+  viash_version: "0.9.0-RC6"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
+  git_remote: "https://github.com/viash-hub/biobox"
+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-RC6"
+  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"

target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml

@@ -228,7 +228,7 @@ 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-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf

@@ -518,9 +518,9 @@ 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="2024-07-31T19:24:26Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:40Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/arriba/.config.vsh.yaml

@@ -706,7 +706,7 @@ build_info:
   output: "target/executable/arriba"
   executable: "target/executable/arriba/arriba"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/arriba/arriba

@@ -753,9 +753,9 @@ 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="2024-07-31T19:24:15Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:32Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bcl_convert/.config.vsh.yaml

@@ -418,7 +418,7 @@ build_info:
   output: "target/executable/bcl_convert"
   executable: "target/executable/bcl_convert/bcl_convert"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bcl_convert/bcl_convert

@@ -598,9 +598,9 @@ 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="2024-07-31T19:24:16Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml

@@ -270,7 +270,7 @@ 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-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference

@@ -548,9 +548,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /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="2024-07-31T19:24:26Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:40Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml

@@ -232,7 +232,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_getfasta"
   executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_getfasta/bedtools_getfasta

@@ -525,9 +525,9 @@ 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="2024-07-31T19:24:18Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:35Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bedtools/bedtools_intersect/.config.vsh.yaml

@@ -410,7 +410,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_intersect"
   executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_intersect/bedtools_intersect

@@ -632,9 +632,9 @@ 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="2024-07-31T19:24:18Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:35Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bedtools/bedtools_sort/.config.vsh.yaml

@@ -222,7 +222,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_sort"
   executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_sort/bedtools_sort

@@ -508,9 +508,9 @@ 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="2024-07-31T19:24:18Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:35Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/busco/busco_download_datasets/.config.vsh.yaml

@@ -158,7 +158,7 @@ build_info:
   output: "target/executable/busco/busco_download_datasets"
   executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/busco/busco_download_datasets/busco_download_datasets

@@ -474,9 +474,9 @@ 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="2024-07-31T19:24:13Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:31Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/busco/busco_list_datasets/.config.vsh.yaml

@@ -145,7 +145,7 @@ build_info:
   output: "target/executable/busco/busco_list_datasets"
   executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/busco/busco_list_datasets/busco_list_datasets

@@ -464,9 +464,9 @@ 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="2024-07-31T19:24:13Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:31Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/busco/busco_run/.config.vsh.yaml

@@ -423,7 +423,7 @@ build_info:
   output: "target/executable/busco/busco_run"
   executable: "target/executable/busco/busco_run/busco_run"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/busco/busco_run/busco_run

@@ -631,9 +631,9 @@ 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="2024-07-31T19:24:13Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:31Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/cutadapt/.config.vsh.yaml

@@ -740,7 +740,7 @@ build_info:
   output: "target/executable/cutadapt"
   executable: "target/executable/cutadapt/cutadapt"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/cutadapt/cutadapt

@@ -830,9 +830,9 @@ 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="2024-07-31T19:24:10Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:29Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/falco/.config.vsh.yaml

@@ -317,7 +317,7 @@ build_info:
   output: "target/executable/falco"
   executable: "target/executable/falco/falco"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/falco/falco

@@ -588,9 +588,9 @@ 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="2024-07-31T19:24:11Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:30Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/fastp/.config.vsh.yaml

@@ -1083,7 +1083,7 @@ build_info:
   output: "target/executable/fastp"
   executable: "target/executable/fastp/fastp"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/fastp/fastp

@@ -1027,9 +1027,9 @@ 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="2024-07-31T19:24:19Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:36Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/featurecounts/.config.vsh.yaml

@@ -645,7 +645,7 @@ build_info:
   output: "target/executable/featurecounts"
   executable: "target/executable/featurecounts/featurecounts"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/featurecounts/featurecounts

@@ -753,9 +753,9 @@ 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="2024-07-31T19:24:14Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:32Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/gffread/.config.vsh.yaml

@@ -685,7 +685,7 @@ build_info:
   output: "target/executable/gffread"
   executable: "target/executable/gffread/gffread"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/gffread/gffread

@@ -806,9 +806,9 @@ 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="2024-07-31T19:24:12Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:30Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/lofreq/lofreq_call/.config.vsh.yaml

@@ -507,7 +507,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_call"
   executable: "target/executable/lofreq/lofreq_call/lofreq_call"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/lofreq/lofreq_call/lofreq_call

@@ -655,9 +655,9 @@ 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="2024-07-31T19:24:25Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml

@@ -215,7 +215,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_indelqual"
   executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/lofreq/lofreq_indelqual/lofreq_indelqual

@@ -500,9 +500,9 @@ 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="2024-07-31T19:24:25Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/multiqc/.config.vsh.yaml

@@ -456,7 +456,7 @@ build_info:
   output: "target/executable/multiqc"
   executable: "target/executable/multiqc/multiqc"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/multiqc/multiqc

@@ -636,9 +636,9 @@ 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="2024-07-31T19:24:15Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:33Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/pear/.config.vsh.yaml

@@ -398,7 +398,7 @@ build_info:
   output: "target/executable/pear"
   executable: "target/executable/pear/pear"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/pear/pear

@@ -596,9 +596,9 @@ 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="2024-07-31T19:24:24Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:39Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/salmon/salmon_index/.config.vsh.yaml

@@ -277,7 +277,7 @@ build_info:
   output: "target/executable/salmon/salmon_index"
   executable: "target/executable/salmon/salmon_index/salmon_index"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/salmon/salmon_index/salmon_index

@@ -545,9 +545,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:16Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:34Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/salmon/salmon_quant/.config.vsh.yaml

@@ -1173,7 +1173,7 @@ build_info:
   output: "target/executable/salmon/salmon_quant"
   executable: "target/executable/salmon/salmon_quant/salmon_quant"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/salmon/salmon_quant/salmon_quant

@@ -1167,9 +1167,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:17Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:34Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_collate/.config.vsh.yaml

@@ -264,7 +264,7 @@ build_info:
   output: "target/executable/samtools/samtools_collate"
   executable: "target/executable/samtools/samtools_collate/samtools_collate"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_collate/samtools_collate

@@ -518,9 +518,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:30Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:43Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_faidx/.config.vsh.yaml

@@ -243,7 +243,7 @@ build_info:
   output: "target/executable/samtools/samtools_faidx"
   executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_faidx/samtools_faidx

@@ -511,9 +511,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:31Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:44Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_fasta/.config.vsh.yaml

@@ -433,7 +433,7 @@ build_info:
   output: "target/executable/samtools/samtools_fasta"
   executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_fasta/samtools_fasta

@@ -624,9 +624,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:28Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:41Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_fastq/.config.vsh.yaml

@@ -433,7 +433,7 @@ build_info:
   output: "target/executable/samtools/samtools_fastq"
   executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_fastq/samtools_fastq

@@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:32Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:44Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_flagstat/.config.vsh.yaml

@@ -173,7 +173,7 @@ build_info:
   output: "target/executable/samtools/samtools_flagstat"
   executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_flagstat/samtools_flagstat

@@ -473,9 +473,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:28Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:42Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_idxstats/.config.vsh.yaml

@@ -183,7 +183,7 @@ build_info:
   output: "target/executable/samtools/samtools_idxstats"
   executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_idxstats/samtools_idxstats

@@ -477,9 +477,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:29Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:42Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_index/.config.vsh.yaml

@@ -189,7 +189,7 @@ build_info:
   output: "target/executable/samtools/samtools_index"
   executable: "target/executable/samtools/samtools_index/samtools_index"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_index/samtools_index

@@ -484,9 +484,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:30Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:43Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_sort/.config.vsh.yaml

@@ -332,7 +332,7 @@ build_info:
   output: "target/executable/samtools/samtools_sort"
   executable: "target/executable/samtools/samtools_sort/samtools_sort"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_sort/samtools_sort

@@ -555,9 +555,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:31Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:43Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_stats/.config.vsh.yaml

@@ -401,7 +401,7 @@ build_info:
   output: "target/executable/samtools/samtools_stats"
   executable: "target/executable/samtools/samtools_stats/samtools_stats"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_stats/samtools_stats

@@ -574,9 +574,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:29Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:42Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/samtools/samtools_view/.config.vsh.yaml

@@ -665,7 +665,7 @@ build_info:
   output: "target/executable/samtools/samtools_view"
   executable: "target/executable/samtools/samtools_view/samtools_view"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_view/samtools_view

@@ -824,9 +824,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:27Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:41Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/seqtk/seqtk_sample/.config.vsh.yaml

@@ -173,7 +173,7 @@ build_info:
   output: "target/executable/seqtk/seqtk_sample"
   executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/seqtk/seqtk_sample/seqtk_sample

@@ -480,9 +480,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:21Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:37Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/seqtk/seqtk_subseq/.config.vsh.yaml

@@ -196,7 +196,7 @@ build_info:
   output: "target/executable/seqtk/seqtk_subseq"
   executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/seqtk/seqtk_subseq/seqtk_subseq

@@ -490,9 +490,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:21Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:36Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/star/star_align_reads/.config.vsh.yaml

@@ -2663,7 +2663,7 @@ build_info:
   output: "target/executable/star/star_align_reads"
   executable: "target/executable/star/star_align_reads/star_align_reads"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/star/star_align_reads/star_align_reads

@@ -1919,9 +1919,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:22Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:38Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/star/star_genome_generate/.config.vsh.yaml

@@ -333,7 +333,7 @@ build_info:
   output: "target/executable/star/star_genome_generate"
   executable: "target/executable/star/star_genome_generate/star_genome_generate"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/star/star_genome_generate/star_genome_generate

@@ -576,9 +576,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:21Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:37Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml

@@ -611,7 +611,7 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_dedup"
   executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup

@@ -769,9 +769,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:33Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:44Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml

@@ -449,7 +449,7 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_extract"
   executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/umi_tools/umi_tools_extract/umi_tools_extract

@@ -636,9 +636,9 @@ ENTRYPOINT []
 RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract"
-LABEL org.opencontainers.image.created="2024-07-31T19:24:33Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:27:45Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
+LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml

@@ -0,0 +1,261 @@
+name: "agat_convert_bed2gff"
+namespace: "agat"
+version: "main"
+authors:
+- name: "Leïla Paquay"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "leila@data-intuitive.com"
+      github: "Leila011"
+      linkedin: "leilapaquay"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Software Developer"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--bed"
+    description: "Input bed file that will be converted."
+    info: null
+    example:
+    - "input.bed"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    - "--outfile"
+    - "--gff"
+    description: "Output GFF file. If no output file is specified, the output will\
+      \ be written to STDOUT."
+    info: null
+    example:
+    - "output.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--source"
+    description: "The source informs about the tool used to produce the data and is\
+      \ stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc.\
+      \ [default: data]\n"
+    info: null
+    example:
+    - "Stringtie"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--primary_tag"
+    description: "The primary_tag corresponds to the data type and is stored in 3rd\
+      \ field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
+    info: null
+    example:
+    - "gene"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_false"
+    name: "--inflate_off"
+    description: "By default we inflate the block fields (blockCount, blockSizes,\
+      \ blockStarts) to create subfeatures of the main feature (primary_tag). The\
+      \ type of subfeature created is based on the inflate_type parameter. If you\
+      \ do not want this inflating behaviour you can deactivate it by using the --inflate_off\
+      \ option.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--inflate_type"
+    description: "Feature type (3rd column in gff) created when inflate parameter\
+      \ activated [default: exon].\n"
+    info: null
+    example:
+    - "exon"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "add verbosity"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "Input agat config file. By default AGAT takes as input agat_config.yaml\
+      \ file from the working directory if any, otherwise it takes the orignal agat_config.yaml\
+      \ shipped with AGAT. To get the agat_config.yaml locally type: \"agat config\
+      \ --expose\". The --config option gives you the possibility to use your own\
+      \ AGAT config file (located elsewhere or named differently).\n"
+    info: null
+    example:
+    - "custom_agat_config.yaml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "The script takes a bed file as input, and will translate it in gff format.\
+  \ The BED format is described here The script converts 0-based, half-open [start-1,\
+  \ end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\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:
+- "gene annotations"
+- "GFF conversion"
+license: "GPL-3.0"
+references:
+  doi:
+  - "10.5281/zenodo.3552717"
+links:
+  repository: "https://github.com/NBISweden/AGAT"
+  homepage: "https://github.com/NBISweden/AGAT"
+  documentation: "https://agat.readthedocs.io/en/latest/tools/agat_convert_bed2gff.html"
+  issue_tracker: "https://github.com/NBISweden/AGAT/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: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "agat --version | sed 's/AGAT\\s\\(.*\\)/agat: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/agat/agat_convert_bed2gff/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/agat/agat_convert_bed2gff"
+  executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
+  git_remote: "https://github.com/viash-hub/biobox"
+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-RC6"
+  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"

target/nextflow/agat/agat_convert_bed2gff/nextflow.config

@@ -0,0 +1,126 @@
+manifest {
+  name = 'agat/agat_convert_bed2gff'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'main'
+  description = 'The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n'
+  author = 'Leïla Paquay'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json

@@ -1,7 +1,7 @@
 {
 "$schema": "http://json-schema.org/draft-07/schema",
-"title": "samtools_faidx",
+"title": "agat_convert_bed2gff",
-"description": "Indexes FASTA files to enable random access to fasta and fastq files.",
+"description": "The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n",
 "type": "object",
 "definitions": {
 
@@ -14,32 +14,11 @@
     "properties": {
     
         
-                "input": {
+                "bed": {
                 "type":
                 "string",
-                "description": "Type: `file`. FASTA input file",
+                "description": "Type: `file`, required, example: `input.bed`. Input bed file that will be converted",
-                "help_text": "Type: `file`. FASTA input file.\n"
+                "help_text": "Type: `file`, required, example: `input.bed`. Input bed file that will be converted."
-            
-            }
-    
-
-        ,
-                "length": {
-                "type":
-                "integer",
-                "description": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping",
-                "help_text": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping. If zero, this means do not\nline wrap. Defaults to the line length in the input file.\n"
-            ,
-                "default": "60"
-            }
-    
-
-        ,
-                "region_file": {
-                "type":
-                "string",
-                "description": "Type: `file`. File of regions",
-                "help_text": "Type: `file`. File of regions. Format is chr:from-to. One per line.\nMust be used with --output to avoid sending output to stdout.\n"
             
             }
     
@@ -58,54 +37,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file",
+                "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file.\n"
+                "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file. If no output file is specified, the output will be written to STDOUT."
             ,
-                "default": "$id.$key.output.fasta"
+                "default": "$id.$key.output.gff"
-            }
-    
-
-        ,
-                "mark_strand": {
-                "type":
-                "string",
-                "description": "Type: `string`, default: `rc`. Add strand indicator to sequence name",
-                "help_text": "Type: `string`, default: `rc`. Add strand indicator to sequence name. Options are:\n[ rc, no, sign, custom,\u003cpos\u003e,\u003cneg\u003e ]\n"
-            ,
-                "default": "rc"
-            }
-    
-
-        ,
-                "fai_idx": {
-                "type":
-                "string",
-                "description": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file",
-                "help_text": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file.fa.fai).\n"
-            ,
-                "default": "$id.$key.fai_idx.fai"
-            }
-    
-
-        ,
-                "gzi_idx": {
-                "type":
-                "string",
-                "description": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with ",
-                "help_text": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with .gz files, default file.fa.gz.gzi).\n"
-            ,
-                "default": "$id.$key.gzi_idx.gzi"
-            }
-    
-
-        ,
-                "fastq": {
-                "type":
-                "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format",
-                "help_text": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format. Same as using samtools fqidx.\n"
-            ,
-                "default": "False"
             }
     
 
@@ -113,31 +48,71 @@
 },
     
     
-    "options" : {
+    "arguments" : {
-    "title": "Options",
+    "title": "Arguments",
     "type": "object",
     "description": "No description",
     "properties": {
     
         
-                "continue": {
+                "source": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file",
+                "help_text": "Type: `string`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]\n"
+            
+            }
+    
+
+        ,
+                "primary_tag": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file",
+                "help_text": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
+            
+            }
+    
+
+        ,
+                "inflate_off": {
                 "type":
                 "boolean",
-                "description": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested",
+                "description": "Type: `boolean_false`, default: `true`. By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag)",
-                "help_text": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested.\n"
+                "help_text": "Type: `boolean_false`, default: `true`. By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.\n"
+            ,
+                "default": "True"
+            }
+    
+
+        ,
+                "inflate_type": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon]",
+                "help_text": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n"
+            
+            }
+    
+
+        ,
+                "verbose": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. add verbosity",
+                "help_text": "Type: `boolean_true`, default: `false`. add verbosity"
             ,
                 "default": "False"
             }
     
 
         ,
-                "reverse_complement": {
+                "config": {
                 "type":
-                "boolean",
+                "string",
-                "description": "Type: `boolean_true`, default: `false`. Reverse complement sequences",
+                "description": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file",
-                "help_text": "Type: `boolean_true`, default: `false`. Reverse complement sequences.\n"
+                "help_text": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n"
-            ,
+            
-                "default": "False"
             }
     
 
@@ -186,7 +161,7 @@
     },
 
     {
-    "$ref": "#/definitions/options"
+    "$ref": "#/definitions/arguments"
     },
 
     {

target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml

@@ -228,7 +228,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gff2gtf"
   executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf

@@ -3042,7 +3042,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "de8b4248b64e0d2e04a6f20c35212403c57a1058",
+    "git_commit" : "4aa0a893d2f8be5f0d03797afc15a04c53664367",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {

target/nextflow/arriba/.config.vsh.yaml

@@ -706,7 +706,7 @@ build_info:
   output: "target/nextflow/arriba"
   executable: "target/nextflow/arriba/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/nextflow/arriba/main.nf

@@ -3566,7 +3566,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/arriba",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "de8b4248b64e0d2e04a6f20c35212403c57a1058",
+    "git_commit" : "4aa0a893d2f8be5f0d03797afc15a04c53664367",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {

target/nextflow/bcl_convert/.config.vsh.yaml

@@ -418,7 +418,7 @@ build_info:
   output: "target/nextflow/bcl_convert"
   executable: "target/nextflow/bcl_convert/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/nextflow/bcl_convert/main.nf

@@ -3303,7 +3303,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcl_convert",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "de8b4248b64e0d2e04a6f20c35212403c57a1058",
+    "git_commit" : "4aa0a893d2f8be5f0d03797afc15a04c53664367",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {

target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml

@@ -270,7 +270,7 @@ build_info:
   output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf

@@ -3116,7 +3116,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "de8b4248b64e0d2e04a6f20c35212403c57a1058",
+    "git_commit" : "4aa0a893d2f8be5f0d03797afc15a04c53664367",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {

target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml

@@ -232,7 +232,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_getfasta"
   executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/nextflow/bedtools/bedtools_getfasta/main.nf

@@ -3060,7 +3060,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_getfasta",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "de8b4248b64e0d2e04a6f20c35212403c57a1058",
+    "git_commit" : "4aa0a893d2f8be5f0d03797afc15a04c53664367",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {

target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml

@@ -410,7 +410,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_intersect"
   executable: "target/nextflow/bedtools/bedtools_intersect/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
+  git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/nextflow/bedtools/bedtools_intersect/main.nf

@@ -3256,7 +3256,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_intersect",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "de8b4248b64e0d2e04a6f20c35212403c57a1058",
+    "git_commit" : "4aa0a893d2f8be5f0d03797afc15a04c53664367",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {