Build branch main with version main (dc7b33d)

Build pipeline: viash-hub.biobox.main-62lvg Source commit: dc7b33d51f Source message: Bcftools Norm (#144) * Initial Commit * config and help.txt * script.sh * test template * More tests and debugging * test 5 and 6 * test 7, 8, 9 * Update test.sh * fixing bug on config * Changelog * Update config.vsh.yaml * Requested changes * Bug fixing --------- Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
2024-09-10 14:36:08 +00:00
parent db2f4203b8
commit 2a330fe450
235 changed files with 7748 additions and 280 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,6 +42,7 @@
 * `rsem/rsem_prepare_reference`: Prepare transcript references for RSEM (PR #89).

 * `bcftools`:
+  - `bcftools_norm`: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows (PR #144).
  - `bcftools_annotate`: Add or remove annotations from a VCF/BCF file (PR #143).
  - `bcftools/bcftools_stats`: Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats (PR #142).
  - `bcftools/bcftools_sort`: Sorts BCF/VCF files by position and other criteria (PR #141).
--- a/src/bcftools/bcftools_norm/config.vsh.yaml
+++ b/src/bcftools/bcftools_norm/config.vsh.yaml
@@ -0,0 +1,194 @@
+name: bcftools_norm
+namespace: bcftools
+description: | 
+  Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; 
+  recover multiallelics from multiple rows. 
+keywords: [Normalize, VCF, BCF]
+links:
+  homepage: https://samtools.github.io/bcftools/
+  documentation: https://samtools.github.io/bcftools/bcftools.html#norm
+  repository: https://github.com/samtools/bcftools
+  issue_tracker: https://github.com/samtools/bcftools/issues
+references:
+  doi: https://doi.org/10.1093/gigascience/giab008
+license: MIT/Expat, GNU
+requirements:
+  commands: [bcftools]
+authors:
+  - __merge__: /src/_authors/theodoro_gasperin.yaml
+    roles: [author]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        alternatives: -i
+        type: file
+        description: Input VCF/BCF file.
+        required: true
+    
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: -o
+        direction: output
+        type: file
+        description: Output normalized VCF/BCF file.
+        required: true
+         
+  - name: Options
+    arguments:
+      
+      - name: --atomize
+        alternatives: -a
+        type: boolean_true
+        description: |
+          Decompose complex variants (e.g., MNVs become consecutive SNVs).
+
+      - name: --atom_overlaps
+        type: string
+        choices: [".", "*"]
+        description: | 
+          Use the star allele (*) for overlapping alleles or set to missing (.).
+
+      - name: --check_ref
+        alternatives: -c
+        type: string
+        choices: ['e', 'w', 'x', 's']
+        description: | 
+          Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites.
+
+      - name: --remove_duplicates
+        alternatives: -d
+        type: string
+        choices: ['snps', 'indels', 'both', 'all', 'exact', 'none']
+        description: Remove duplicate snps, indels, both, all, exact matches, or none (old -D option).
+
+      - name: --fasta_ref
+        alternatives: -f
+        type: file
+        description: Reference fasta sequence file.
+
+      - name: --force
+        type: boolean_true
+        description: | 
+          Try to proceed even if malformed tags are encountered. 
+          Experimental, use at your own risk.
+
+      - name: --keep_sum
+        type: string
+        description: | 
+          Keep vector sum constant when splitting multiallelics (see github issue #360).
+
+      - name: --multiallelics
+        alternatives: -m
+        type: string
+        choices: ['+snps', '+indels', '+both', '+any', '-snps', '-indels', '-both', '-any']
+        description: | 
+          Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both].
+
+      - name: --no_version
+        type: boolean_true
+        description: Do not append version and command line information to the header.
+
+      - name: --do_not_normalize
+        alternatives: -N
+        type: boolean_true
+        description: Do not normalize indels (with -m or -c s).
+      
+      - name: --output_type
+        alternatives: --O
+        type: string
+        choices: ['u', 'z', 'b', 'v']
+        description: | 
+          Output type:
+            u: uncompressed BCF
+            z: compressed VCF
+            b: compressed BCF
+            v: uncompressed VCF
+      
+      - name: --old_rec_tag
+        type: string
+        description: Annotate modified records with INFO/STR indicating the original variant.
+
+      - name: --regions
+        alternatives: --r
+        type: string
+        description: | 
+          Restrict to comma-separated list of regions. 
+          Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…].
+        example: '20:1000000-2000000'
+
+      - name: --regions_file
+        alternatives: --R
+        type: file
+        description: | 
+          Restrict to regions listed in a file. 
+          Regions can be specified either on a VCF, BED, or tab-delimited file (the default). 
+          For more information check manual.
+
+      - name: --regions_overlap
+        type: string
+        choices: ['pos', 'record', 'variant', '0', '1', '2']
+        description: | 
+          This option controls how overlapping records are determined: 
+          set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); 
+          set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, 
+          and includes indels with POS at the end of a region, which are technically outside the region); 
+          or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-").
+
+      - name: --site_win
+        alternatives: -w
+        type: integer
+        description: | 
+          Buffer for sorting lines that changed position during realignment.
+
+      - name: --strict_filter
+        alternatives: -s
+        type: boolean_true
+        description: When merging (-m+), merged site is PASS only if all sites being merged PASS.
+
+      - name: --targets
+        alternatives: -t
+        type: string
+        description: Similar to --regions but streams rather than index-jumps.
+        example: '20:1000000-2000000'
+
+      - name: --targets_file
+        alternatives: -T
+        type: file
+        description: Similar to --regions_file but streams rather than index-jumps.
+
+      - name: --targets_overlap
+        type: string
+        choices: ['pos', 'record', 'variant', '0', '1', '2']
+        description: | 
+          Include if POS in the region (0), record overlaps (1), variant overlaps (2).
+          Similar to --regions_overlap.
+
+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: [bcftools, procps]
+      - type: docker
+        run: |
+          echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt
+    test_setup:  
+      - type: apt  
+        packages: [tabix]
+
+runners:
+  - type: executable
+  - type: nextflow
+
+
--- a/src/bcftools/bcftools_norm/help.txt
+++ b/src/bcftools/bcftools_norm/help.txt
@@ -0,0 +1,41 @@
+```
+bcftools norm -h
+```
+
+About:   Left-align and normalize indels; check if REF alleles match the reference;
+         split multiallelic sites into multiple rows; recover multiallelics from
+         multiple rows.
+Usage:   bcftools norm [options] <in.vcf.gz>
+
+Options:
+    -a, --atomize                   Decompose complex variants (e.g. MNVs become consecutive SNVs)
+        --atom-overlaps '*'|.       Use the star allele (*) for overlapping alleles or set to missing (.) [*]
+    -c, --check-ref e|w|x|s         Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]
+    -D, --remove-duplicates         Remove duplicate lines of the same type.
+    -d, --rm-dup TYPE               Remove duplicate snps|indels|both|all|exact
+    -f, --fasta-ref FILE            Reference sequence
+        --force                     Try to proceed even if malformed tags are encountered. Experimental, use at your own risk
+        --keep-sum TAG,..           Keep vector sum constant when splitting multiallelics (see github issue #360)
+    -m, --multiallelics -|+TYPE     Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]
+        --no-version                Do not append version and command line to the header
+    -N, --do-not-normalize          Do not normalize indels (with -m or -c s)
+        --old-rec-tag STR           Annotate modified records with INFO/STR indicating the original variant
+    -o, --output FILE               Write output to a file [standard output]
+    -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]
+    -r, --regions REGION            Restrict to comma-separated list of regions
+    -R, --regions-file FILE         Restrict to regions listed in a file
+        --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]
+    -s, --strict-filter             When merging (-m+), merged site is PASS only if all sites being merged PASS
+    -t, --targets REGION            Similar to -r but streams rather than index-jumps
+    -T, --targets-file FILE         Similar to -R but streams rather than index-jumps
+        --targets-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]
+        --threads INT               Use multithreading with <int> worker threads [0]
+    -w, --site-win INT              Buffer for sorting lines which changed position during realignment [1000]
+
+Examples:
+   # normalize and left-align indels
+   bcftools norm -f ref.fa in.vcf
+
+   # split multi-allelic sites
+   bcftools norm -m- in.vcf
+
--- a/src/bcftools/bcftools_norm/script.sh
+++ b/src/bcftools/bcftools_norm/script.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+# Unset parameters
+unset_if_false=(
+    par_atomize
+    par_remove_duplicates
+    par_force
+    par_no_version
+    par_do_not_normalize
+    par_strict_filter
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+# Execute bcftools norm with the provided arguments
+bcftools norm \
+    ${par_atomize:+--atomize} \
+    ${par_atom_overlaps:+--atom-overlaps "$par_atom_overlaps"} \
+    ${par_check_ref:+-c "$par_check_ref"} \
+    ${par_remove_duplicates:+-d "$par_remove_duplicates"} \
+    ${par_fasta_ref:+-f "$par_fasta_ref"} \
+    ${par_force:+--force} \
+    ${par_keep_sum:+--keep-sum "$par_keep_sum"} \
+    ${par_multiallelics:+-m "$par_multiallelics"} \
+    ${par_no_version:+--no-version} \
+    ${par_do_not_normalize:+-N} \
+    ${par_old_rec_tag:+--old-rec-tag "$par_old_rec_tag"} \
+    ${par_regions:+-r "$par_regions"} \
+    ${par_regions_file:+-R "$par_regions_file"} \
+    ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \
+    ${par_site_win:+-w "$par_site_win"} \
+    ${par_strict_filter:+-s} \
+    ${par_targets:+-t "$par_targets"} \
+    ${par_targets_file:+-T "$par_targets_file"} \
+    ${par_targets_overlap:+--targets-overlap "$par_targets_overlap"} \
+    ${meta_cpus:+--threads "$meta_cpus"} \
+    ${par_output_type:+-O "$par_output_type"} \
+    -o $par_output \
+    $par_input
+    
--- a/src/bcftools/bcftools_norm/test.sh
+++ b/src/bcftools/bcftools_norm/test.sh
@@ -0,0 +1,231 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+#test_data="$meta_resources_dir/test_data"
+
+#############################################
+# 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 "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Create test data
+cat <<EOF > "$TMPDIR/example.vcf"
+##fileformat=VCFv4.1
+##contig=<ID=1,length=249250621,assembly=b37>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE1
+1	752567	llama	G	C,A	.	.	.	.	1/2
+1	752722	.	G	A,AAA	.	.	.	.	./.
+EOF
+
+bgzip -c $TMPDIR/example.vcf > $TMPDIR/example.vcf.gz
+tabix -p vcf $TMPDIR/example.vcf.gz
+
+cat <<EOF > "$TMPDIR/reference.fa"
+>1
+ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG
+>2
+CGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT
+EOF
+
+# Test 1: Remove ID annotations
+mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
+
+echo "> Run bcftools_norm"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --atomize \
+  --atom_overlaps "." \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "bcftools_normCommand=norm --atomize --atom-overlaps . -o normalized.vcf ../example.vcf"
+echo "- test1 succeeded -"
+
+popd > /dev/null
+
+# Test 2: Check reference
+mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null
+
+echo "> Run bcftools_norm with remove duplicates"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --atomize \
+  --remove_duplicates 'all' \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "norm --atomize -d all -o normalized.vcf ../example.vcf"
+echo "- test2 succeeded -"
+
+popd > /dev/null
+
+# Test 3: Check reference and fasta reference
+mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null
+
+echo "> Run bcftools_norm with check reference and fasta reference"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --atomize \
+  --fasta_ref "../reference.fa" \
+  --check_ref "e" \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "norm --atomize -c e -f ../reference.fa -o normalized.vcf ../example.vcf"
+echo "- test3 succeeded -"
+
+popd > /dev/null
+
+# Test 4: Multiallelics
+mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null
+
+echo "> Run bcftools_norm with multiallelics"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --multiallelics "-any" \
+  --old_rec_tag "wazzaaa" \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "norm -m -any --old-rec-tag wazzaaa -o normalized.vcf ../example.vcf"
+echo "- test4 succeeded -"
+
+popd > /dev/null
+
+# Test 5: Regions
+mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null
+
+echo "> Run bcftools_norm with regions"
+"$meta_executable" \
+  --input "../example.vcf.gz" \
+  --output "normalized.vcf" \
+  --atomize \
+  --regions "1:752567-752722" \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "norm --atomize -r 1:752567-752722 -o normalized.vcf ../example.vcf.gz"
+echo "- test5 succeeded -"
+
+popd > /dev/null
+
+# Test 6: Targets
+mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null
+
+echo "> Run bcftools_norm with targets"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --atomize \
+  --targets "1:752567-752722" \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "norm --atomize -t 1:752567-752722 -o normalized.vcf ../example.vcf"
+echo "- test6 succeeded -"
+
+popd > /dev/null
+
+# Test 7: Regions overlap
+mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null
+
+echo "> Run bcftools_norm with regions overlap"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --atomize \
+  --regions_overlap "pos" \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "norm --atomize --regions-overlap pos -o normalized.vcf ../example.vcf"
+echo "- test7 succeeded -"
+
+popd > /dev/null
+
+# Test 8: Strict filter and targets overlap
+mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null
+
+echo "> Run bcftools_norm with strict filter and targets overlap"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --atomize \
+  --strict_filter \
+  --targets_overlap "1" \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "norm --atomize -s --targets-overlap 1 -o normalized.vcf ../example.vcf"
+echo "- test8 succeeded -"
+
+popd > /dev/null
+
+# Test 9: Do not normalize
+mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null
+
+echo "> Run bcftools_norm with do not normalize"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --do_not_normalize \
+  --atomize \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "norm --atomize -N -o normalized.vcf ../example.vcf"
+echo "- test9 succeeded -"
+
+popd > /dev/null
+
+echo "---- All tests succeeded! ----"
+exit 0
+
+
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -515,9 +515,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:00Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -505,9 +505,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:00Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -519,9 +519,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:00Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -484,9 +484,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:00Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -493,9 +493,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:59Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -754,9 +754,9 @@ RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' >

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:11Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:02Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -469,7 +469,7 @@ build_info:
  output: "target/executable/bcftools/bcftools_annotate"
  executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
  viash_version: "0.9.0-RC7"
-  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate
+++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
@@ -650,9 +650,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:04Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:54Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
@@ -0,0 +1,442 @@
+name: "bcftools_norm"
+namespace: "bcftools"
+version: "main"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  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 VCF/BCF 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 normalized VCF/BCF file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--atomize"
+    alternatives:
+    - "-a"
+    description: "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--atom_overlaps"
+    description: "Use the star allele (*) for overlapping alleles or set to missing\
+      \ (.).\n"
+    info: null
+    required: false
+    choices:
+    - "."
+    - "*"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--check_ref"
+    alternatives:
+    - "-c"
+    description: "Check REF alleles and exit (e), warn (w), exclude (x), or set (s)\
+      \ bad sites.\n"
+    info: null
+    required: false
+    choices:
+    - "e"
+    - "w"
+    - "x"
+    - "s"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--remove_duplicates"
+    alternatives:
+    - "-d"
+    description: "Remove duplicate snps, indels, both, all, exact matches, or none\
+      \ (old -D option)."
+    info: null
+    required: false
+    choices:
+    - "snps"
+    - "indels"
+    - "both"
+    - "all"
+    - "exact"
+    - "none"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fasta_ref"
+    alternatives:
+    - "-f"
+    description: "Reference fasta sequence file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--force"
+    description: "Try to proceed even if malformed tags are encountered. \nExperimental,\
+      \ use at your own risk.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--keep_sum"
+    description: "Keep vector sum constant when splitting multiallelics (see github\
+      \ issue #360).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--multiallelics"
+    alternatives:
+    - "-m"
+    description: "Split multiallelics (-) or join biallelics (+), type: snps, indels,\
+      \ both, any [default: both].\n"
+    info: null
+    required: false
+    choices:
+    - "+snps"
+    - "+indels"
+    - "+both"
+    - "+any"
+    - "-snps"
+    - "-indels"
+    - "-both"
+    - "-any"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_version"
+    description: "Do not append version and command line information to the header."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--do_not_normalize"
+    alternatives:
+    - "-N"
+    description: "Do not normalize indels (with -m or -c s)."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--output_type"
+    alternatives:
+    - "--O"
+    description: "Output type:\n  u: uncompressed BCF\n  z: compressed VCF\n  b: compressed\
+      \ BCF\n  v: uncompressed VCF\n"
+    info: null
+    required: false
+    choices:
+    - "u"
+    - "z"
+    - "b"
+    - "v"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--old_rec_tag"
+    description: "Annotate modified records with INFO/STR indicating the original\
+      \ variant."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions"
+    alternatives:
+    - "--r"
+    description: "Restrict to comma-separated list of regions. \nFollowing formats\
+      \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…].\n"
+    info: null
+    example:
+    - "20:1000000-2000000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--regions_file"
+    alternatives:
+    - "--R"
+    description: "Restrict to regions listed in a file. \nRegions can be specified\
+      \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
+      \ check manual.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions_overlap"
+    description: "This option controls how overlapping records are determined: \n\
+      set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
+      \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
+      \ also overlapping records with POS outside a region should be included (this\
+      \ is the default behavior of -r/-R, \nand includes indels with POS at the end\
+      \ of a region, which are technically outside the region); \nor set to 'variant'\
+      \ or '2' to include only true overlapping variation (compare the full VCF representation\
+      \ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
+    info: null
+    required: false
+    choices:
+    - "pos"
+    - "record"
+    - "variant"
+    - "0"
+    - "1"
+    - "2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--site_win"
+    alternatives:
+    - "-w"
+    description: "Buffer for sorting lines that changed position during realignment.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--strict_filter"
+    alternatives:
+    - "-s"
+    description: "When merging (-m+), merged site is PASS only if all sites being\
+      \ merged PASS."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--targets"
+    alternatives:
+    - "-t"
+    description: "Similar to --regions but streams rather than index-jumps."
+    info: null
+    example:
+    - "20:1000000-2000000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--targets_file"
+    alternatives:
+    - "-T"
+    description: "Similar to --regions_file but streams rather than index-jumps."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--targets_overlap"
+    description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
+      \ (2).\nSimilar to --regions_overlap.\n"
+    info: null
+    required: false
+    choices:
+    - "pos"
+    - "record"
+    - "variant"
+    - "0"
+    - "1"
+    - "2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Left-align and normalize indels, check if REF alleles match the reference,\
+  \ split multiallelic sites into multiple rows; \nrecover multiallelics from multiple\
+  \ rows. \n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Normalize"
+- "VCF"
+- "BCF"
+license: "MIT/Expat, GNU"
+references:
+  doi:
+  - "https://doi.org/10.1093/gigascience/giab008"
+links:
+  repository: "https://github.com/samtools/bcftools"
+  homepage: "https://samtools.github.io/bcftools/"
+  documentation: "https://samtools.github.io/bcftools/bcftools.html#norm"
+  issue_tracker: "https://github.com/samtools/bcftools/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:
+    - "bcftools"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
+      \ //p')\\\"\" > /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "tabix"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bcftools/bcftools_norm/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bcftools/bcftools_norm"
+  executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
+  viash_version: "0.9.0-RC7"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
+  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"
--- a/target/executable/bcftools/bcftools_norm/bcftools_norm
+++ b/target/executable/bcftools/bcftools_norm/bcftools_norm
--- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
  output: "target/executable/bcftools/bcftools_sort"
  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
  viash_version: "0.9.0-RC7"
-  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcftools/bcftools_sort/bcftools_sort
+++ b/target/executable/bcftools/bcftools_sort/bcftools_sort
@@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:03Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:54Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
@@ -458,7 +458,7 @@ build_info:
  output: "target/executable/bcftools/bcftools_stats"
  executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
  viash_version: "0.9.0-RC7"
-  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcftools/bcftools_stats/bcftools_stats
+++ b/target/executable/bcftools/bcftools_stats/bcftools_stats
@@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:04Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:55Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/

 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:10Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
@@ -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="2024-09-10T13:57:13Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:05Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:47Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -176,7 +176,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_bed12tobed6"
  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
  viash_version: "0.9.0-RC7"
-  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
+++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
@@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:46Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:48Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -337,7 +337,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_genomecov"
  executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0-RC7"
-  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
@@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:46Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:46Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -273,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby
+++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
@@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:48Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:47Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
@@ -210,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_links/bedtools_links
+++ b/target/executable/bedtools/bedtools_links/bedtools_links
@@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:47Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
@@ -279,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_merge/bedtools_merge
+++ b/target/executable/bedtools/bedtools_merge/bedtools_merge
@@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:46Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:48Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -475,9 +475,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:58Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -465,9 +465,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:58Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -423,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -632,9 +632,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:59Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -831,9 +831,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions

 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:12Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:03Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/falco/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio

 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:13Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:04Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:10Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:01Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -340,7 +340,7 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0-RC7"
-  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -601,9 +601,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:53Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -754,9 +754,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:05Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:56Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -190,7 +190,7 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0-RC7"
-  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -493,9 +493,9 @@ mv target/release/fq /usr/local/bin/ && \
 cd / && rm -rf /fq

 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:53Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -807,9 +807,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:54Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:45Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -656,9 +656,9 @@ echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:05Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -501,9 +501,9 @@ echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:04Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -637,9 +637,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:13Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:04Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/pear/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -597,9 +597,9 @@ echo "pear: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:49Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -264,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -527,9 +527,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:52Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
+++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
@@ -656,9 +656,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
-LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:59Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -277,7 +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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/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="2024-09-10T13:57:11Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:02Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/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="2024-09-10T13:57:12Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:20:03Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/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="2024-09-10T13:57:00Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:51Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/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="2024-09-10T13:57:00Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:51Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_fasta/samtools_fasta
+++ b/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="2024-09-10T13:57:01Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:51Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/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="2024-09-10T13:57:00Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:50Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/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="2024-09-10T13:56:59Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:50Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/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="2024-09-10T13:56:59Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:49Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/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="2024-09-10T13:56:58Z"
+LABEL org.opencontainers.image.created="2024-09-10T14:19:49Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+LABEL org.opencontainers.image.revision="dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/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: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  git_commit: "dc7b33d51f274cb156b1f1b0fbdc6fed0b757720"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/Show More
+++ b/Show More