Build branch main with version main (c3ba4a7)

Build pipeline: viash-hub.biobox.main-n2mwd Source commit: c3ba4a7849 Source message: Bcftools annotate (#143) * Initial commit * Update config.vsh.yaml * changes in config file * Update script.sh * Help File * Update script.sh * Update test.sh * bug fixing and adding tests * Update test.sh * Update test.sh * adding 3rd test * More tests * Moreee tests * Update test.sh * small changes * Update CHANGELOG.md * Update config.vsh.yaml * bug fixing on config * Requested changes --------- Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
2024-09-10 14:11:21 +00:00
parent 0075a8df93
commit db2f4203b8
231 changed files with 8225 additions and 276 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,12 +42,12 @@
 * `rsem/rsem_prepare_reference`: Prepare transcript references for RSEM (PR #89).

 * `bcftools`:
+  - `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).

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

-
 ## MINOR CHANGES

 * `busco` components: update BUSCO to `5.7.1` (PR #72).
--- a/src/bcftools/bcftools_annotate/config.vsh.yaml
+++ b/src/bcftools/bcftools_annotate/config.vsh.yaml
@@ -0,0 +1,250 @@
+name: bcftools_annotate
+namespace: bcftools
+description: | 
+  Add or remove annotations from a VCF/BCF file.
+keywords: [Annotate, VCF, BCF]
+links:
+  homepage: https://samtools.github.io/bcftools/
+  documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
+  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
+        multiple: true
+        description: Input VCF/BCF file.
+        required: true
+    
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: -o
+        direction: output
+        type: file
+        description: Output annotated file.
+        required: true
+         
+  - name: Options
+    description: | 
+      For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.
+      For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.
+    arguments:
+      
+      - name: --annotations
+        alternatives: --a
+        type: file
+        description: | 
+          VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+ . 
+
+      - name: --columns
+        alternatives: --c
+        type: string
+        description: | 
+          List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. 
+          See man page for details.
+
+      - name: --columns_file
+        alternatives: --C
+        type: file
+        description: | 
+          Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE].
+
+      - name: --exclude
+        alternatives: --e
+        type: string
+        description: | 
+          Exclude sites for which the expression is true.
+          See https://samtools.github.io/bcftools/bcftools.html#expressions for details.
+        example: 'QUAL >= 30 && DP >= 10'
+
+      - name: --force
+        type: boolean_true
+        description: | 
+          continue even when parsing errors, such as undefined tags, are encountered. 
+          Note this can be an unsafe operation and can result in corrupted BCF files. 
+          If this option is used, make sure to sanity check the result thoroughly.
+
+      - name: --header_line
+        alternatives: --H
+        type: string
+        description: | 
+          Header line which should be appended to the VCF header, can be given multiple times.
+
+      - name: --header_lines
+        alternatives: --h
+        type: file
+        description: | 
+          File with header lines to append to the VCF header.
+          For example:
+            ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
+            ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
+
+      - name: --set_id
+        alternatives: --I
+        type: string
+        description: | 
+          Set ID column using a `bcftools query`-like expression, see man page for details.
+
+      - name: --include
+        type: string
+        description: | 
+          Select sites for which the expression is true.
+          See https://samtools.github.io/bcftools/bcftools.html#expressions for details.
+        example: 'QUAL >= 30 && DP >= 10'
+      
+      - name: --keep_sites
+        alternatives: --k
+        type: boolean_true
+        description: | 
+          Leave --include/--exclude sites unchanged instead of discarding them.
+
+      - name: --merge_logic
+        alternatives: --l
+        type: string
+        choices: 
+        description: | 
+          When multiple regions overlap a single record, this option defines how to treat multiple annotation values.
+          See man page for more details.
+
+      - name: --mark_sites
+        alternatives: --m
+        type: string
+        description: | 
+          Annotate sites which are present ("+") or absent ("-") in the -a file with a new INFO/TAG flag.
+
+      - name: --min_overlap
+        type: string
+        description: | 
+          Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), 
+          in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). 
+          By default overlaps of arbitrary length are sufficient. 
+          The option can be used only with the tab-delimited annotation -a file and with BEG and END columns present.
+
+      - name: --no_version
+        type: boolean_true
+        description: | 
+          Do not append version and command line information to the output VCF header.
+
+      - 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: --pair_logic
+        type: string
+        choices: ['snps', 'indels', 'both', 'all', 'some', 'exact']
+        description: | 
+          Controls how to match records from the annotation file to the target VCF. 
+          Effective only when -a is a VCF or BCF file. 
+          The option replaces the former uninuitive --collapse. 
+          See Common Options for more.
+      
+      - 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: --rename_annotations 
+        type: file
+        description: | 
+          Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT.
+
+      - name: --rename_chromosomes
+        type: file
+        description: | 
+          Rename chromosomes according to the map in file, with "old_name new_name\n" pairs 
+          separated by whitespaces, each on a separate line.
+
+      - name: --samples
+        type: string
+        description: | 
+          Subset of samples to annotate.
+          See also https://samtools.github.io/bcftools/bcftools.html#common_options.
+
+      - name: --samples_file
+        type: file
+        description: | 
+          Subset of samples to annotate in file format.
+          See also https://samtools.github.io/bcftools/bcftools.html#common_options.
+
+      - name: --single_overlaps
+        type: boolean_true
+        description: | 
+          Use this option to keep memory requirements low with very large annotation files. 
+          Note, however, that this comes at a cost, only single overlapping intervals are considered in this mode. 
+          This was the default mode until the commit af6f0c9 (Feb 24 2019).
+
+      - name: --remove
+        alternatives: --x
+        type: string
+        description: | 
+          List of annotations to remove. 
+          Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. 
+          Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. 
+          To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). 
+          "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
+
+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_annotate/help.txt
+++ b/src/bcftools/bcftools_annotate/help.txt
@@ -0,0 +1,41 @@
+```
+bcftools annotate -h
+```
+
+annotate: option requires an argument -- 'h'
+
+About:   Annotate and edit VCF/BCF files.
+Usage:   bcftools annotate [options] VCF
+
+Options:
+   -a, --annotations FILE          VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+
+   -c, --columns LIST              List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details
+   -C, --columns-file FILE         Read -c columns from FILE, one name per row, with optional --merge-logic TYPE: NAME[ TYPE]
+   -e, --exclude EXPR              Exclude sites for which the expression is true (see man page for details)
+       --force                     Continue despite parsing error (at your own risk!)
+   -H, --header-line STR           Header line which should be appended to the VCF header, can be given multiple times
+   -h, --header-lines FILE         Lines which should be appended to the VCF header
+   -I, --set-id [+]FORMAT          Set ID column using a `bcftools query`-like expression, see man page for details
+   -i, --include EXPR              Select sites for which the expression is true (see man page for details)
+   -k, --keep-sites                Leave -i/-e sites unchanged instead of discarding them
+   -l, --merge-logic TAG:TYPE      Merge logic for multiple overlapping regions (see man page for details), EXPERIMENTAL
+   -m, --mark-sites [+-]TAG        Add INFO/TAG flag to sites which are ("+") or are not ("-") listed in the -a file
+       --min-overlap ANN:VCF       Required overlap as a fraction of variant in the -a file (ANN), the VCF (:VCF), or reciprocal (ANN:VCF)
+       --no-version                Do not append version and command line to the header
+   -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]
+       --pair-logic STR            Matching records by <snps|indels|both|all|some|exact>, see man page for details [some]
+   -r, --regions REGION            Restrict to comma-separated list of regions
+   -R, --regions-file FILE         Restrict to regions listed in FILE
+       --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]
+       --rename-annots FILE        Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT
+       --rename-chrs FILE          Rename sequences according to the mapping: old\tnew
+   -s, --samples [^]LIST           Comma separated list of samples to annotate (or exclude with "^" prefix)
+   -S, --samples-file [^]FILE      File of samples to annotate (or exclude with "^" prefix)
+       --single-overlaps           Keep memory low by avoiding complexities arising from handling multiple overlapping intervals
+   -x, --remove LIST               List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with "^" prefix). See man page for details
+       --threads INT               Number of extra output compression threads [0]
+
+Examples:
+   http://samtools.github.io/bcftools/howtos/annotate.html
+
--- a/src/bcftools/bcftools_annotate/script.sh
+++ b/src/bcftools/bcftools_annotate/script.sh
@@ -0,0 +1,54 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+# Unset parameters
+unset_if_false=(
+    par_force
+    par_keep_sites
+    par_no_version
+    par_single_overlaps
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+# Execute bcftools annotate with the provided arguments
+bcftools annotate \
+    ${par_annotations:+-a "$par_annotations"} \
+    ${par_columns:+-c "$par_columns"} \
+    ${par_columns_file:+-C "$par_columns_file"} \
+    ${par_exclude:+-e "$par_exclude"} \
+    ${par_force:+--force} \
+    ${par_header_line:+-H "$par_header_line"} \
+    ${par_header_lines:+-h "$par_header_lines"} \
+    ${par_set_id:+-I "$par_set_id"} \
+    ${par_include:+-i "$par_include"} \
+    ${par_keep_sites:+-k} \
+    ${par_merge_logic:+-l "$par_merge_logic"} \
+    ${par_mark_sites:+-m "$par_mark_sites"} \
+    ${par_min_overlap:+--min-overlap "$par_min_overlap"} \
+    ${par_no_version:+--no-version} \
+    ${par_samples_file:+-S "$par_samples_file"} \
+    ${par_output_type:+-O "$par_output_type"} \
+    ${par_pair_logic:+--pair-logic "$par_pair_logic"} \
+    ${par_regions:+-r "$par_regions"} \
+    ${par_regions_file:+-R "$par_regions_file"} \
+    ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \
+    ${par_rename_annotations:+--rename-annots "$par_rename_annotations"} \
+    ${par_rename_chromosomes:+--rename-chrs "$par_rename_chromosomes"} \
+    ${par_samples:+-s "$par_samples"} \
+    ${par_single_overlaps:+--single-overlaps} \
+    ${par_threads:+--threads "$par_threads"} \
+    ${par_remove:+-x "$par_remove"} \
+    -o $par_output \
+    $par_input
+    
+
+    
--- a/src/bcftools/bcftools_annotate/test.sh
+++ b/src/bcftools/bcftools_annotate/test.sh
@@ -0,0 +1,305 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+#test_data="$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	A	C	.	.	.	.	.
+1	752722	.	G	A	.	.	.	.	.
+EOF
+
+bgzip -c $TMPDIR/example.vcf > $TMPDIR/example.vcf.gz
+tabix -p vcf $TMPDIR/example.vcf.gz
+
+cat <<EOF > "$TMPDIR/annots.tsv"
+1	752567	752567	FooValue1	12345
+1	752722	752722	FooValue2	67890
+EOF
+
+cat <<EOF > "$TMPDIR/rename.tsv"
+INFO/.	Luigi
+EOF
+
+bgzip $TMPDIR/annots.tsv
+tabix -s1 -b2 -e3 $TMPDIR/annots.tsv.gz
+
+cat <<EOF > "$TMPDIR/header.hdr"
+##FORMAT=<ID=FOO,Number=1,Type=String,Description="Some description">
+##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">
+EOF
+
+cat <<EOF > "$TMPDIR/rename_chrm.tsv"
+1	chr1
+2	chr2
+EOF
+
+# Test 1: Remove ID annotations
+mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
+
+echo "> Run bcftools_annotate remove annotations"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --remove "ID" \
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "1	752567	.	A	C"
+echo "- test1 succeeded -"
+
+popd > /dev/null
+
+# Test 2: Annotate with -a, -c and -h options
+mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null
+
+echo "> Run bcftools_annotate with -a, -c and -h options"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --annotations "../annots.tsv.gz" \
+  --header_lines "../header.hdr" \
+  --columns "CHROM,FROM,TO,FMT/FOO,BAR" \
+  --mark_sites "BAR" \
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" $(echo -e "1\t752567\tllama\tA\tC\t.\t.\tBAR=12345\tFOO\tFooValue1")
+echo "- test2 succeeded -"
+
+popd > /dev/null
+
+# Test 3: 
+mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null
+
+echo "> Run bcftools_annotate with --set_id option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --set_id "+'%CHROM\_%POS\_%REF\_%FIRST_ALT'" \
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "'1_752722_G_A'"
+echo "- test3 succeeded -"
+
+popd > /dev/null
+
+# Test 4:
+mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null
+
+echo "> Run bcftools_annotate with --rename-annotations option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --rename_annotations "../rename.tsv"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate --rename-annots ../rename.tsv -o annotated.vcf"
+echo "- test4 succeeded -"
+
+popd > /dev/null
+
+# Test 5: Rename chromosomes
+mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null
+
+echo "> Run bcftools_annotate with --rename-chromosomes option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --rename_chromosomes "../rename_chrm.tsv"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "chr1"
+echo "- test5 succeeded -"
+
+popd > /dev/null
+
+# Test 6: Sample option
+mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null
+
+echo "> Run bcftools_annotate with -s option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --samples "SAMPLE1"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate -s SAMPLE1 -o annotated.vcf ../example.vcf"
+echo "- test6 succeeded -"
+
+popd > /dev/null
+
+# Test 7: Single overlaps
+mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null
+
+echo "> Run bcftools_annotate with --single-overlaps option"	
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --single_overlaps \
+  --keep_sites \
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "annotate -k --single-overlaps -o annotated.vcf ../example.vcf"
+echo "- test7 succeeded -"
+
+popd > /dev/null
+
+# Test 8: Min overlap
+mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null
+
+echo "> Run bcftools_annotate with --min-overlap option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --annotations "../annots.tsv.gz" \
+  --columns "CHROM,FROM,TO,FMT/FOO,BAR" \
+  --header_lines "../header.hdr" \
+  --min_overlap "1"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "annotate -a ../annots.tsv.gz -c CHROM,FROM,TO,FMT/FOO,BAR -h ../header.hdr --min-overlap 1 -o annotated.vcf ../example.vcf"
+echo "- test8 succeeded -"
+
+popd > /dev/null
+
+# Test 9: Regions
+mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null
+
+echo "> Run bcftools_annotate with -r option"
+"$meta_executable" \
+  --input "../example.vcf.gz" \
+  --output "annotated.vcf" \
+  --regions "1:752567-752722"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "annotate -r 1:752567-752722 -o annotated.vcf ../example.vcf.gz"
+echo "- test9 succeeded -"
+
+popd > /dev/null
+
+# Test 10: pair-logic
+mkdir "$TMPDIR/test10" && pushd "$TMPDIR/test10" > /dev/null
+
+echo "> Run bcftools_annotate with --pair-logic option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --pair_logic "all"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "annotate --pair-logic all -o annotated.vcf ../example.vcf"
+echo "- test10 succeeded -"
+
+popd > /dev/null
+
+# Test 11: regions-overlap
+mkdir "$TMPDIR/test11" && pushd "$TMPDIR/test11" > /dev/null
+
+echo "> Run bcftools_annotate with --regions-overlap option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --regions_overlap "1"
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "annotate --regions-overlap 1 -o annotated.vcf ../example.vcf"
+echo "- test11 succeeded -"
+
+popd > /dev/null
+
+# Test 12: include 
+mkdir "$TMPDIR/test12" && pushd "$TMPDIR/test12" > /dev/null
+
+echo "> Run bcftools_annotate with -i option"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --include "FILTER='PASS'" \
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "annotate -i FILTER='PASS' -o annotated.vcf ../example.vcf"
+echo "- test12 succeeded -"
+
+popd > /dev/null
+
+# Test 13: exclude
+mkdir "$TMPDIR/test13" && pushd "$TMPDIR/test13" > /dev/null
+
+echo "> Run bcftools_annotate with -e option"
+"$meta_executable" \
+  --annotations "../annots.tsv.gz" \
+  --input "../example.vcf" \
+  --output "annotated.vcf" \
+  --exclude "FILTER='PASS'" \
+  --header_lines "../header.hdr" \
+  --columns "CHROM,FROM,TO,FMT/FOO,BAR" \
+  --merge_logic "FOO:first" \
+
+# checks
+assert_file_exists "annotated.vcf"
+assert_file_not_empty "annotated.vcf"
+assert_file_contains "annotated.vcf" "annotate -a ../annots.tsv.gz -c CHROM,FROM,TO,FMT/FOO,BAR -e FILTER='PASS' -h ../header.hdr -l FOO:first -o annotated.vcf ../example.vcf"
+echo "- test13 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:49Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:49Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:50Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:49Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:48Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:51Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:11Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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
@@ -0,0 +1,495 @@
+name: "bcftools_annotate"
+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: true
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output annotated file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  description: "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\n\
+    For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n"
+  arguments:
+  - type: "file"
+    name: "--annotations"
+    alternatives:
+    - "--a"
+    description: "VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\
+      \ . \n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--columns"
+    alternatives:
+    - "--c"
+    description: "List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG.\
+      \ \nSee man page for details.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--columns_file"
+    alternatives:
+    - "--C"
+    description: "Read -c columns from FILE, one name per row, with optional --merge_logic\
+      \ TYPE: NAME[ TYPE].\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--exclude"
+    alternatives:
+    - "--e"
+    description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
+      \ for details.\n"
+    info: null
+    example:
+    - "QUAL >= 30 && DP >= 10"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--force"
+    description: "continue even when parsing errors, such as undefined tags, are encountered.\
+      \ \nNote this can be an unsafe operation and can result in corrupted BCF files.\
+      \ \nIf this option is used, make sure to sanity check the result thoroughly.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--header_line"
+    alternatives:
+    - "--H"
+    description: "Header line which should be appended to the VCF header, can be given\
+      \ multiple times.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--header_lines"
+    alternatives:
+    - "--h"
+    description: "File with header lines to append to the VCF header.\nFor example:\n\
+      \  ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example header\
+      \ line\">\n  ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description=\"Yet another\
+      \ header line\">\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--set_id"
+    alternatives:
+    - "--I"
+    description: "Set ID column using a `bcftools query`-like expression, see man\
+      \ page for details.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--include"
+    description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
+      \ for details.\n"
+    info: null
+    example:
+    - "QUAL >= 30 && DP >= 10"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--keep_sites"
+    alternatives:
+    - "--k"
+    description: "Leave --include/--exclude sites unchanged instead of discarding\
+      \ them.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--merge_logic"
+    alternatives:
+    - "--l"
+    description: "When multiple regions overlap a single record, this option defines\
+      \ how to treat multiple annotation values.\nSee man page for more details.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--mark_sites"
+    alternatives:
+    - "--m"
+    description: "Annotate sites which are present (\"+\") or absent (\"-\") in the\
+      \ -a file with a new INFO/TAG flag.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--min_overlap"
+    description: "Minimum overlap required as a fraction of the variant in the annotation\
+      \ -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap\
+      \ (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe\
+      \ option can be used only with the tab-delimited annotation -a file and with\
+      \ BEG and END columns present.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_version"
+    description: "Do not append version and command line information to the output\
+      \ VCF header.\n"
+    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: "--pair_logic"
+    description: "Controls how to match records from the annotation file to the target\
+      \ VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces\
+      \ the former uninuitive --collapse. \nSee Common Options for more.\n"
+    info: null
+    required: false
+    choices:
+    - "snps"
+    - "indels"
+    - "both"
+    - "all"
+    - "some"
+    - "exact"
+    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: "file"
+    name: "--rename_annotations"
+    description: "Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--rename_chromosomes"
+    description: "Rename chromosomes according to the map in file, with \"old_name\
+      \ new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--samples"
+    description: "Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--samples_file"
+    description: "Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--single_overlaps"
+    description: "Use this option to keep memory requirements low with very large\
+      \ annotation files. \nNote, however, that this comes at a cost, only single\
+      \ overlapping intervals are considered in this mode. \nThis was the default\
+      \ mode until the commit af6f0c9 (Feb 24 2019).\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--remove"
+    alternatives:
+    - "--x"
+    description: "List of annotations to remove. \nUse \"FILTER\" to remove all filters\
+      \ or \"FILTER/SomeFilter\" to remove a specific filter. \nSimilarly, \"INFO\"\
+      \ can be used to remove all INFO tags and \"FORMAT\" to remove all FORMAT tags\
+      \ except GT. \nTo remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\"\
+      \ (and similarly for FORMAT and FILTER). \n\"INFO\" can be abbreviated to \"\
+      INF\" and \"FORMAT\" to \"FMT\".\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Add or remove annotations from a VCF/BCF file.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Annotate"
+- "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#annotate"
+  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_annotate/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bcftools/bcftools_annotate"
+  executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
+  viash_version: "0.9.0-RC7"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
+  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_annotate/bcftools_annotate
+++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
--- 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:44Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:03Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:44Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:04Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:50Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:54Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:13Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:37Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:36Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:38Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:36Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:36Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:38Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:37Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:37Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:35Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:38Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:47Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:47Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:48Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:53Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:12Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:53Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:13Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:50Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:10Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:43Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:45Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:05Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:43Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:35Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:54Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:45Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:45Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:04Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:53Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:13Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:39Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:42Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:48Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:52Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:11Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:52Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:12Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:41Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:41Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:41Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:01Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:40Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:40Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:59Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:39Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:59Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  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="2024-09-10T13:55:39Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 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: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -556,9 +556,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-09-10T13:55:42Z"
+LABEL org.opencontainers.image.created="2024-09-10T13:57:01Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -401,7 +401,7 @@ build_info:
  output: "target/executable/samtools/samtools_stats"
  executable: "target/executable/samtools/samtools_stats/samtools_stats"
  viash_version: "0.9.0-RC7"
-  git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
+  git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/Show More
+++ b/Show More