Build branch main with version main (f3e87e5)

Build pipeline: viash-hub.biobox.main-7qmtp

Source commit: f3e87e58c9

Source message: Bedtools bed12tobed6 (#140)

* Initial commit

* Update test.sh

* help file + n option

* adding n_score option

* small changes

* Update CHANGELOG.md

* Update CHANGELOG.md

---------

Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>

CHANGELOG.md

@@ -33,6 +33,7 @@
   - `bedtools/bedtools_merge`: Merges overlapping BED/GFF/VCF entries into a single interval (PR #118).
   - `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101).
   - `bedtools/bedtools_bedtobam`: Converts genomic feature records (bed/gff/vcf) to BAM format (PR #111).
+  - `bedtools/bedtools_bed12tobed6`: Converts BED12 files to BED6 files (PR #140).
   - `bedtools/bedtools_links`: Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a (bed/gff/vcf) file (PR #137).
  
 * `qualimap/qualimap_rnaseq`: RNA-seq QC analysis using qualimap (PR #74). 

src/bedtools/bedtools_bed12tobed6/config.vsh.yaml

@@ -0,0 +1,67 @@
+name: bedtools_bed12tobed6
+namespace: bedtools
+description: | 
+  Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features.
+  For example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).
+keywords: [Converts, BED12, BED6]
+links:
+  documentation: https://bedtools.readthedocs.io/en/latest/content/tools/bed12tobed6.html
+  repository: https://github.com/arq5x/bedtools2
+  homepage: https://bedtools.readthedocs.io/en/latest/#
+  issue_tracker: https://github.com/arq5x/bedtools2/issues
+references:
+  doi: 10.1093/bioinformatics/btq033
+license: MIT
+requirements:
+  commands: [bedtools]
+authors:
+  - __merge__: /src/_authors/theodoro_gasperin.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+
+  - name: Inputs
+    arguments:
+      - name: --input
+        alternatives: -i
+        type: file
+        description: Input BED12 file.
+        required: true
+    
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: -o
+        type: file
+        direction: output
+        description: Output BED6 file to be written.
+
+  - name: Options
+    arguments:
+      - name: --n_score
+        alternatives: -n
+        type: boolean_true
+        description: | 
+          Force the score to be the (1-based) block number from the BED12.
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages: [bedtools, procps]
+      - type: docker
+        run: |
+          echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow

src/bedtools/bedtools_bed12tobed6/help.txt

@@ -0,0 +1,13 @@
+```
+bedtools bed12tobed6 -h
+```
+
+Tool:    bedtools bed12tobed6 (aka bed12ToBed6)
+Version: v2.30.0
+Summary: Splits BED12 features into discrete BED6 features.
+
+Usage:   bedtools bed12tobed6 [OPTIONS] -i <bed12>
+
+Options: 
+	-n	Force the score to be the (1-based) block number from the BED12.
+

src/bedtools/bedtools_bed12tobed6/script.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -eo pipefail
+
+# Unset parameters
+[[ "$par_n_score" == "false" ]] && unset par_n_score
+
+# Execute bedtools bed12tobed6 conversion 
+bedtools bed12tobed6 \
+    ${par_n_score:+-n} \
+    -i "$par_input" \
+    > "$par_output"

src/bedtools/bedtools_bed12tobed6/test.sh

@@ -0,0 +1,85 @@
+#!/bin/bash
+
+# exit on error
+set -eo pipefail
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_identical_content() {
+  diff -a "$2" "$1" \
+    || (echo "Files are not identical!" && exit 1)
+}
+#############################################
+
+# Create directories for tests
+echo "Creating Test Data..."
+TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Create example BED12 file
+cat <<EOF > "$TMPDIR/example.bed12"
+chr21	10079666	10120808	uc002yiv.1	0	-	10081686	1	0	1	2	0	6	0	8	0	4	528,91,101,215,	0,1930,39750,40927,
+chr21	10080031	10081687	uc002yiw.1	0	-	10080031	1	0	0	8	0	0	3	1	0	2	200,91,	0,1565,
+chr21	10081660	10120796	uc002yix.2	0	-	10081660	1	0	0	8	1	6	6	0	0	3	27,101,223,	0,37756,38913,
+EOF
+
+# Expected output bed6 file
+cat <<EOF > "$TMPDIR/expected.bed6"
+chr21	10079666	10120808	uc002yiv.1	0	-
+chr21	10080031	10081687	uc002yiw.1	0	-
+chr21	10081660	10120796	uc002yix.2	0	-
+EOF
+# Expected output bed6 file with -n option
+cat <<EOF > "$TMPDIR/expected_n.bed6"
+chr21	10079666	10120808	uc002yiv.1	1	-
+chr21	10080031	10081687	uc002yiw.1	1	-
+chr21	10081660	10120796	uc002yix.2	1	-
+EOF
+
+# Test 1: Default conversion BED12 to BED6
+mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
+
+echo "> Run bedtools_bed12tobed6 on BED12 file"
+"$meta_executable" \
+  --input "../example.bed12" \
+  --output "output.bed6"
+
+# checks
+assert_file_exists "output.bed6"
+assert_file_not_empty "output.bed6"
+assert_identical_content "output.bed6" "../expected.bed6"
+echo "- test1 succeeded -"
+
+popd > /dev/null
+
+# Test 2: Conversion BED12 to BED6 with -n option
+mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null
+
+echo "> Run bedtools_bed12tobed6 on BED12 file with -n option"
+"$meta_executable" \
+  --input "../example.bed12" \
+  --output "output.bed6" \
+  --n_score
+
+# checks
+assert_file_exists "output.bed6"
+assert_file_not_empty "output.bed6"
+assert_identical_content "output.bed6" "../expected_n.bed6"
+echo "- test2 succeeded -"
+
+popd > /dev/null
+
+echo "---- All tests succeeded! ----"
+exit 0

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

@@ -235,7 +235,7 @@ build_info:
   output: "target/executable/agat/agat_convert_bed2gff"
   executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:49Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:20Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml

@@ -225,7 +225,7 @@ build_info:
   output: "target/executable/agat/agat_convert_embl2gff"
   executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:49Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:20Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:50Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:20Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml

@@ -188,7 +188,7 @@ 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:49Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:19Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml

@@ -195,7 +195,7 @@ 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:48Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:19Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:51Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:21Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:50Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:21Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference

@@ -549,9 +549,9 @@ 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="2024-09-02T13:02:53Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:24Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -187,7 +187,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_bamtofastq"
   executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:39Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:09Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml

@@ -0,0 +1,202 @@
+name: "bedtools_bed12tobed6"
+namespace: "bedtools"
+version: "main"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "theodorogtc@gmail.com"
+      github: "tgaspe"
+      linkedin: "theodoro-gasperin-terra-camargo"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Input BED12 file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output BED6 file to be written."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--n_score"
+    alternatives:
+    - "-n"
+    description: "Force the score to be the (1-based) block number from the BED12.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Converts BED features in BED12 (a.k.a. “blocked” BED features such as\
+  \ genes) to discrete BED6 features.\nFor example, in the case of a gene with six\
+  \ exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each\
+  \ exon).\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Converts"
+- "BED12"
+- "BED6"
+license: "MIT"
+references:
+  doi:
+  - "10.1093/bioinformatics/btq033"
+links:
+  repository: "https://github.com/arq5x/bedtools2"
+  homepage: "https://bedtools.readthedocs.io/en/latest/#"
+  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/bed12tobed6.html"
+  issue_tracker: "https://github.com/arq5x/bedtools2/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: "debian:stable-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "bedtools"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\
+      \ > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bedtools/bedtools_bed12tobed6/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_bed12tobed6"
+  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
+  viash_version: "0.9.0-RC7"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
+  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-RC7"
+  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/bedtools/bedtools_bedtobam/.config.vsh.yaml

@@ -214,7 +214,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_bedtobam"
   executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:40Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:10Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:38Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:08Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -273,7 +273,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_groupby"
   executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:39Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:09Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:38Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:08Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -210,7 +210,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_links"
   executable: "target/executable/bedtools/bedtools_links/bedtools_links"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:38Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:09Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -279,7 +279,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_merge"
   executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:37Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:07Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:39Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:10Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:47Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:18Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:47Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:18Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:48Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:18Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:52Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:23Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:53Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:24Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:50Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:20Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:45Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:16Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:37Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:07Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:45Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:16Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:45Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:15Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:53Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:40Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:10Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml

@@ -264,7 +264,7 @@ build_info:
   output: "target/executable/qualimap/qualimap_rnaseq"
   executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:44Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:14Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -416,7 +416,7 @@ build_info:
   output: "target/executable/rsem/rsem_prepare_reference"
   executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
   viash_version: "0.9.0-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-02T13:02:48Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:19Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/salmon/salmon_index/salmon_index

@@ -546,9 +546,9 @@ 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="2024-09-02T13:02:51Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:22Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/salmon/salmon_quant/salmon_quant

@@ -1168,9 +1168,9 @@ 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="2024-09-02T13:02:52Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:22Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_collate/samtools_collate

@@ -519,9 +519,9 @@ 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="2024-09-02T13:02:42Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:13Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_faidx/samtools_faidx

@@ -512,9 +512,9 @@ 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="2024-09-02T13:02:42Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:12Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_fasta/samtools_fasta

@@ -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_fasta"
-LABEL org.opencontainers.image.created="2024-09-02T13:02:43Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:13Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_fastq/samtools_fastq

@@ -626,9 +626,9 @@ 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="2024-09-02T13:02:42Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:12Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_flagstat/samtools_flagstat

@@ -474,9 +474,9 @@ 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="2024-09-02T13:02:41Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:12Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_idxstats/samtools_idxstats

@@ -478,9 +478,9 @@ 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="2024-09-02T13:02:41Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:11Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_index/samtools_index

@@ -485,9 +485,9 @@ 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="2024-09-02T13:02:40Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:11Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_sort/samtools_sort

@@ -556,9 +556,9 @@ 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="2024-09-02T13:02:43Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:13Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_stats/samtools_stats

@@ -575,9 +575,9 @@ 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="2024-09-02T13:02:43Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:14Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_view/samtools_view

@@ -825,9 +825,9 @@ 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="2024-09-02T13:02:41Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:11Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/seqtk/seqtk_sample/seqtk_sample

@@ -481,9 +481,9 @@ 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="2024-09-02T13:02:54Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:24Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/seqtk/seqtk_subseq/seqtk_subseq

@@ -491,9 +491,9 @@ 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="2024-09-02T13:02:54Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:24Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/star/star_align_reads/star_align_reads

@@ -1920,9 +1920,9 @@ 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="2024-09-02T13:02:46Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:17Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/star/star_genome_generate/star_genome_generate

@@ -577,9 +577,9 @@ 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="2024-09-02T13:02:46Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:10:16Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
+LABEL org.opencontainers.image.revision="f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
 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-RC7"
-  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
+  git_commit: "f3e87e58c921a4ef59fe8946edcd066cdfc8de9c"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"