Build branch main with version main (219ba1d)

Build pipeline: viash-hub.biobox.main-w9wb7

Source commit: 219ba1d3d0

Source message: Add more fq components (#179)

* add fq_lint, move fq_subsample, improve unit tests

* update changelog

CHANGELOG.md

@@ -1,5 +1,15 @@
 # biobox 0.3.2
 
+## NEW FUNCTIONALITY
+
+* `fq`:
+  - `fq/fq_lint`: Validate FASTQ files for common issues (PR #179).
+  - `fq/fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #179).
+
+## MAJOR CHANGES
+
+* `fq_subsample`: This component has been deprecated in favour of `fq/fq_subsample`, and will be removed in biobox 0.4.0 (PR #179).
+
 ## MINOR CHANGES
 
 * Update README (PR #177).

src/fq/fq_lint/config.vsh.yaml

@@ -0,0 +1,72 @@
+name: fq_lint
+namespace: fq
+description: Validates a single or paired FASTQ file.
+keywords: [fastq, lint, validate, quality-control]
+links:
+  homepage: https://github.com/stjude-rust-labs/fq/blob/master/README.md
+  documentation: https://github.com/stjude-rust-labs/fq/blob/master/README.md
+  repository: https://github.com/stjude-rust-labs/fq
+license: MIT
+
+authors:
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/emma_rousseau.yaml
+    roles: [ author ]
+
+argument_groups:
+- name: "Input"
+  description: "Input FASTQ files to validate."
+  arguments:
+  - name: "--input_1"
+    type: file
+    required: true
+    description: "Read 1 source. Accepts both raw and gzipped FASTQ inputs."
+    example: "reads_1.fastq.gz"
+  - name: "--input_2"
+    type: file
+    required: false
+    description: "Read 2 source. Accepts both raw and gzipped FASTQ inputs."
+    example: "reads_2.fastq.gz"
+
+- name: "Options"
+  description: "Validation parameters."
+  arguments:
+  - name: "--lint_mode"
+    type: string
+    default: "panic"
+    choices: ["panic", "log"]
+    description: "Panic on first error or log all errors."
+  - name: "--single_read_validation_level"
+    type: string
+    default: "high"
+    choices: ["low", "medium", "high"]
+    description: "Only use single read validators up to a given level."
+  - name: "--paired_read_validation_level"
+    type: string
+    default: "high"
+    choices: ["low", "medium", "high"]
+    description: "Only use paired read validators up to a given level."
+  - name: "--disable_validator"
+    type: string
+    multiple: true
+    description: "Disable validators by code. Use multiple times to disable more than one."
+  - name: "--record_definition_separator"
+    type: string
+    description: "Define a record definition separator."
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: quay.io/biocontainers/fq:0.12.0--h9ee0642_0
+
+runners:
+  - type: executable
+  - type: nextflow

src/fq/fq_lint/help.txt

@@ -0,0 +1,27 @@
+```
+docker run --rm -it quay.io/biocontainers/fq:0.12.0--h9ee0642_0 fq lint -h >> src/fq/fq_lint/help.txt
+```
+
+Validates a FASTQ file pair
+
+Usage: fq lint [OPTIONS] <R1_SRC> [R2_SRC]
+
+Arguments:
+  <R1_SRC>  Read 1 source. Accepts both raw and gzipped FASTQ inputs
+  [R2_SRC]  Read 2 source. Accepts both raw and gzipped FASTQ inputs
+
+Options:
+      --lint-mode <LINT_MODE>
+          Panic on first error or log all errors [default: panic] [possible values: panic, log]
+      --single-read-validation-level <SINGLE_READ_VALIDATION_LEVEL>
+          Only use single read validators up to a given level [default: high] [possible values: low, medium, high]
+      --paired-read-validation-level <PAIRED_READ_VALIDATION_LEVEL>
+          Only use paired read validators up to a given level [default: high] [possible values: low, medium, high]
+      --disable-validator <DISABLE_VALIDATOR>
+          Disable validators by code. Use multiple times to disable more than one
+      --record-definition-separator <RECORD_DEFINITION_SEPARATOR>
+          Define a record definition separator
+  -h, --help
+          Print help (see more with '--help')
+  -V, --version
+          Print version

src/fq/fq_lint/script.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+## VIASH START
+# par_input_1="reads_1.fastq.gz"
+# par_input_2="reads_2.fastq.gz"
+# par_lint_mode="panic"
+# par_disable_validator="S001;P002"
+## VIASH END
+
+# Exit immediately if a command exits with a non-zero status.
+set -eo pipefail
+
+# split the disable_validator string into an array
+IFS=';' read -r -a par_disable_validator <<< "$par_disable_validator"
+
+# Construct and execute the fq lint command.
+fq lint \
+  ${par_lint_mode:+--lint-mode "$par_lint_mode"} \
+  ${par_single_read_validation_level:+--single-read-validation-level "$par_single_read_validation_level"} \
+  ${par_paired_read_validation_level:+--paired-read-validation-level "$par_paired_read_validation_level"} \
+  ${par_record_definition_separator:+--record-definition-separator "$par_record_definition_separator"} \
+  ${par_disable_validator[@]/#/--disable-validator } \
+  "$par_input_1" \
+  ${par_input_2:+"$par_input_2"}

src/fq/fq_lint/test.sh

@@ -0,0 +1,96 @@
+#!/bin/bash
+
+set -e
+
+TEMP_DIR="$meta_temp_dir"
+
+# --- Helper function to create FASTQ files ---
+create_fastq() {
+  file_path="$1"
+  header_prefix="$2"
+  num_records="$3"
+  mismatch_quality="$4" # 'true' or 'false'
+  
+  rm -f "$file_path"
+  for i in $(seq 1 "$num_records"); do
+    seq="AATTGGCC"
+    qual="FFFFFFFF"
+    if [[ "$mismatch_quality" == "true" && "$i" -eq 2 ]]; then
+      qual="FFFF" # Mismatched length for the second record
+    fi
+    echo "@${header_prefix}.${i} description" >> "$file_path"
+    echo "$seq" >> "$file_path"
+    echo "+" >> "$file_path"
+    echo "$qual" >> "$file_path"
+  done
+}
+
+# --- Test Case 1: Valid Paired-End FASTQ files ---
+echo ">>> Test 1: Running on valid paired-end FASTQ files. Expecting success."
+create_fastq "$TEMP_DIR/valid_r1.fastq" "PAIR" 10 "false"
+create_fastq "$TEMP_DIR/valid_r2.fastq" "PAIR" 10 "false"
+
+"$meta_executable" \
+  --input_1 "$TEMP_DIR/valid_r1.fastq" \
+  --input_2 "$TEMP_DIR/valid_r2.fastq"
+echo ">> OK: fq lint succeeded on valid paired-end files."
+
+
+# --- Test Case 2: Valid Single-End FASTQ file ---
+echo ">>> Test 2: Running on a valid single-end FASTQ file. Expecting success."
+"$meta_executable" \
+  --input_1 "$TEMP_DIR/valid_r1.fastq"
+echo ">> OK: fq lint succeeded on a valid single-end file."
+
+
+# --- Test Case 3: Invalid Paired-End FASTQ (mismatched headers) ---
+echo ">>> Test 3: Running on paired-end files with mismatched headers. Expecting failure."
+create_fastq "$TEMP_DIR/mismatch_r1.fastq" "PAIR_A" 10 "false"
+create_fastq "$TEMP_DIR/mismatch_r2.fastq" "PAIR_B" 10 "false"
+
+# Disable exit on error temporarily to catch the expected failure
+set +e
+"$meta_executable" \
+  --input_1 "$TEMP_DIR/mismatch_r1.fastq" \
+  --input_2 "$TEMP_DIR/mismatch_r2.fastq"
+exit_code=$?
+set -e
+
+if [ $exit_code -eq 0 ]; then
+  echo ">> FAIL: fq lint should have failed on mismatched headers but succeeded."
+  exit 1
+else
+  echo ">> OK: fq lint correctly failed on mismatched headers (Exit code: $exit_code)."
+fi
+
+
+# --- Test Case 4: Invalid Single-End FASTQ (sequence/quality length mismatch) ---
+echo ">>> Test 4: Running on a single-end file with seq/qual length mismatch. Expecting failure."
+create_fastq "$TEMP_DIR/bad_qual.fastq" "BAD" 5 "true"
+
+set +e
+"$meta_executable" \
+  --input_1 "$TEMP_DIR/bad_qual.fastq"
+exit_code=$?
+set -e
+
+if [ $exit_code -eq 0 ]; then
+  echo ">> FAIL: fq lint should have failed on bad quality scores but succeeded."
+  exit 1
+else
+  echo ">> OK: fq lint correctly failed on bad quality scores (Exit code: $exit_code)."
+fi
+
+# --- Test Case 5: Using --disable-validator to ignore mismatched headers ---
+echo ">>> Test 5: Running on mismatched paired-end files but disabling validator P001. Expecting success."
+# The validator for mismatched read names is P001 in `fq`.
+"$meta_executable" \
+  --input_1 "$TEMP_DIR/mismatch_r1.fastq" \
+  --input_2 "$TEMP_DIR/mismatch_r2.fastq" \
+  --disable_validator "P001"
+echo ">> OK: fq lint succeeded when header mismatch validator was disabled."
+
+
+echo ""
+echo ">>> All tests finished successfully"
+exit 0

src/fq/fq_subsample/config.vsh.yaml

@@ -0,0 +1,66 @@
+name: fq_subsample
+namespace: fq
+description: fq subsample outputs a subset of records from single or paired FASTQ files.
+keywords: [fastq, subsample, subset]
+links:
+  homepage: https://github.com/stjude-rust-labs/fq/blob/master/README.md
+  documentation: https://github.com/stjude-rust-labs/fq/blob/master/README.md
+  repository: https://github.com/stjude-rust-labs/fq
+license: MIT
+
+authors:
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/emma_rousseau.yaml
+    roles: [ author ]
+
+argument_groups: 
+- name: "Input"
+  arguments: 
+  - name: "--input_1"
+
+    type: file
+    required: true
+    description: First input fastq file to subsample. Accepts both raw and gzipped FASTQ inputs.
+  - name: "--input_2"
+    type: file
+    description: Second input fastq files to subsample. Accepts both raw and gzipped FASTQ inputs.
+
+- name: "Output"
+  arguments: 
+  - name: "--output_1"
+    type: file
+    direction: output
+    description: Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`.
+  - name: "--output_2"
+    type: file
+    direction: output
+    description: Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`.
+
+- name: "Options"
+  arguments: 
+  - name: "--probability"
+    type: double
+    description: The probability a record is kept, as a percentage (0.0, 1.0). Cannot be used with `record-count`
+  - name: "--record_count"
+    type: integer
+    description: The exact number of records to keep. Cannot be used with `probability`
+  - name: "--seed"
+    type: integer
+    description: Seed to use for the random number generator
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:  
+  - type: docker
+    image: quay.io/biocontainers/fq:0.12.0--h9ee0642_0
+
+runners:
+  - type: executable
+  - type: nextflow

src/fq/fq_subsample/help.txt

@@ -0,0 +1,20 @@
+```
+docker run --rm -it quay.io/biocontainers/fq:0.12.0--h9ee0642_0 fq subsample -h >> src/fq/fq_subsample/help.txt
+```
+
+Outputs a subset of records
+
+Usage: fq subsample [OPTIONS] --r1-dst <R1_DST> <--probability <PROBABILITY>|--record-count <RECORD_COUNT>> <R1_SRC> [R2_SRC]
+
+Arguments:
+  <R1_SRC>  Read 1 source. Accepts both raw and gzipped FASTQ inputs
+  [R2_SRC]  Read 2 source. Accepts both raw and gzipped FASTQ inputs
+
+Options:
+  -p, --probability <PROBABILITY>    The probability a record is kept, as a percentage (0.0, 1.0). Cannot be used with `record-count`
+  -n, --record-count <RECORD_COUNT>  The exact number of records to keep. Cannot be used with `probability`
+  -s, --seed <SEED>                  Seed to use for the random number generator
+      --r1-dst <R1_DST>              Read 1 destination. Output will be gzipped if ends in `.gz`
+      --r2-dst <R2_DST>              Read 2 destination. Output will be gzipped if ends in `.gz`
+  -h, --help                         Print help
+  -V, --version                      Print version

src/fq/fq_subsample/script.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -eo pipefail
+
+# exclusive OR for required arguments $par_probability and $par_record_count
+if { [ -n "$par_probability" ] && [ -n "$par_record_count" ]; } || \
+   { [ -z "$par_probability" ] && [ -z "$par_record_count" ]; }; then
+  echo "Error: Please specify either --probability or --record_count, but not both." >&2
+  exit 1
+fi
+
+fq subsample \
+    ${par_output_1:+--r1-dst "${par_output_1}"} \
+    ${par_output_2:+--r2-dst "${par_output_2}"} \
+    ${par_probability:+--probability "${par_probability}"} \
+    ${par_record_count:+--record-count "${par_record_count}"} \
+    ${par_seed:+--seed "${par_seed}"} \
+    ${par_input_1} \
+    ${par_input_2:+"$par_input_2"}

src/fq/fq_subsample/test.sh

@@ -0,0 +1,98 @@
+#!/bin/bash
+
+set -e
+
+TEMP_DIR="$meta_temp_dir"
+
+# --- Helper function to create a FASTQ file ---
+create_fastq() {
+  file_path="$1"
+  num_records="$2"
+  
+  rm -f "$file_path"
+  for i in $(seq 1 "$num_records"); do
+    echo "@READ.${i} description" >> "$file_path"
+    echo "GATTACA" >> "$file_path"
+    echo "+" >> "$file_path"
+    echo "FFFFFFF" >> "$file_path"
+  done
+}
+
+# --- Test Case 1: Paired-End Subsampling with --record_count ---
+echo ">>> Test 1: Paired-end subsampling with --record_count"
+create_fastq "$TEMP_DIR/r1.fastq" 100
+create_fastq "$TEMP_DIR/r2.fastq" 100
+
+"$meta_executable" \
+  --input_1 "$TEMP_DIR/r1.fastq" \
+  --input_2 "$TEMP_DIR/r2.fastq" \
+  --record_count 15 \
+  --seed 42 \
+  --output_1 "$TEMP_DIR/sub1.r1.fastq" \
+  --output_2 "$TEMP_DIR/sub1.r2.fastq"
+
+echo ">> Checking output files..."
+if [ ! -f "$TEMP_DIR/sub1.r1.fastq" ]; then
+  echo "FAIL: Subsampled R1 file was not created." && exit 1
+fi
+if [ ! -f "$TEMP_DIR/sub1.r2.fastq" ]; then
+  echo "FAIL: Subsampled R2 file was not created." && exit 1
+fi
+
+# Each FASTQ record is 4 lines. 15 records * 4 lines/record = 60 lines.
+line_count_r1=$(wc -l < "$TEMP_DIR/sub1.r1.fastq")
+line_count_r2=$(wc -l < "$TEMP_DIR/sub1.r2.fastq")
+
+if [ "$line_count_r1" -ne 60 ]; then
+  echo "FAIL: R1 output has incorrect number of lines. Expected 60, got $line_count_r1." && exit 1
+fi
+if [ "$line_count_r2" -ne 60 ]; then
+  echo "FAIL: R2 output has incorrect number of lines. Expected 60, got $line_count_r2." && exit 1
+fi
+echo ">> OK: Paired-end test with --record_count passed."
+
+# --- Test Case 2: Single-End Subsampling with --probability and Gzipped Output ---
+echo ">>> Test 2: Single-end subsampling with --probability and gzipped output"
+create_fastq "$TEMP_DIR/r1.fastq" 500
+
+"$meta_executable" \
+  --input_1 "$TEMP_DIR/r1.fastq" \
+  --probability 0.1 \
+  --seed 42 \
+  --output_1 "$TEMP_DIR/sub2.r1.fastq.gz"
+
+echo ">> Checking gzipped output file..."
+if [ ! -f "$TEMP_DIR/sub2.r1.fastq.gz" ]; then
+  echo "FAIL: Gzipped subsampled file was not created." && exit 1
+fi
+
+# With a fixed seed, the number of records should be deterministic.
+# NOTE: For fq v0.12.0, seed 42 and p=0.1 on 500 records yields 53 records. 53 * 4 = 212 lines.
+gzipped_lines=$(gunzip -c "$TEMP_DIR/sub2.r1.fastq.gz" | wc -l)
+if [ "$gzipped_lines" -ne 212 ]; then
+  echo "FAIL: Gzipped output has incorrect number of lines. Expected 212, got $gzipped_lines." && exit 1
+fi
+echo ">> OK: Single-end test with --probability passed."
+
+
+# --- Test Case 3: Mutually Exclusive Argument Check ---
+echo ">>> Test 3: Expecting failure when both --record_count and --probability are provided"
+set +e # Disable exit on error to catch the failure
+"$meta_executable" \
+  --input_1 "$TEMP_DIR/r1.fastq" \
+  --record_count 10 \
+  --probability 0.1 \
+  --output_1 "$TEMP_DIR/sub3.r1.fastq"
+exit_code=$?
+set -e # Re-enable exit on error
+
+if [ $exit_code -eq 0 ]; then
+  echo "FAIL: Script should have failed when providing both count and probability."
+  exit 1
+else
+  echo ">> OK: Script correctly failed as expected."
+fi
+
+echo ""
+echo ">>> All tests finished successfully"
+exit 0

src/fq_subsample/config.vsh.yaml

@@ -1,5 +1,10 @@
 name: fq_subsample
-description: fq subsample outputs a subset of records from single or paired FASTQ files.
+# will be removed in biobox 0.4.0
+status: deprecated
+description: |
+  fq subsample outputs a subset of records from single or paired FASTQ files.
+
+  Note: This component is deprecated and will be removed in biobox 0.4.0. Please use `fq/fq_subsample` instead.
 keywords: [fastq, subsample, subset]
 links:
   homepage: https://github.com/stjude-rust-labs/fq/blob/master/README.md

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

@@ -233,9 +233,9 @@ build_info:
   output: "target/executable/agat/agat_convert_bed2gff"
   executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:19Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:25Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -223,9 +223,9 @@ build_info:
   output: "target/executable/agat/agat_convert_embl2gff"
   executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:20Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:34Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml

@@ -228,9 +228,9 @@ build_info:
   output: "target/executable/agat/agat_convert_genscan2gff"
   executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:25Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml

@@ -184,9 +184,9 @@ build_info:
   output: "target/executable/agat/agat_convert_mfannot2gff"
   executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff

@@ -452,9 +452,9 @@ 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_mfannot2gff"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:19Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:24Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -226,9 +226,9 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gff2gtf"
   executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:22Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:24Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -186,9 +186,9 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gff2tsv"
   executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:19Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:35Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -193,9 +193,9 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gxf2gxf"
   executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:19Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:34Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -184,9 +184,9 @@ build_info:
   output: "target/executable/agat/agat_sp_add_introns"
   executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_sp_add_introns/agat_sp_add_introns

@@ -452,9 +452,9 @@ 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_sp_add_introns"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:34Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -234,9 +234,9 @@ build_info:
   output: "target/executable/agat/agat_sp_filter_feature_from_kill_list"
   executable: "target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list

@@ -452,9 +452,9 @@ 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_sp_filter_feature_from_kill_list"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:23Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -182,9 +182,9 @@ build_info:
   output: "target/executable/agat/agat_sp_merge_annotations"
   executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations

@@ -452,9 +452,9 @@ 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_sp_merge_annotations"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:25Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -229,9 +229,9 @@ build_info:
   output: "target/executable/agat/agat_sp_statistics"
   executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_sp_statistics/agat_sp_statistics

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/softwa
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_statistics"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:25Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -225,9 +225,9 @@ build_info:
   output: "target/executable/agat/agat_sq_stat_basic"
   executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic

@@ -452,9 +452,9 @@ 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_sq_stat_basic"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:24Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -709,9 +709,9 @@ build_info:
   output: "target/executable/arriba"
   executable: "target/executable/arriba/arriba"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/arriba/arriba

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:25Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:29Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bases2fastq/.config.vsh.yaml

@@ -397,9 +397,9 @@ build_info:
   output: "target/executable/bases2fastq"
   executable: "target/executable/bases2fastq/bases2fastq"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bases2fastq/bases2fastq

@@ -456,9 +456,9 @@ RUN echo "bases2fastq: $(bases2fastq --version | cut -d' ' -f3)" > /var/software
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bases2fastq"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:29Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml

@@ -371,9 +371,9 @@ build_info:
   output: "target/executable/bbmap/bbmap_bbsplit"
   executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit

@@ -454,9 +454,9 @@ cp -r bbmap/* /usr/local/bin
 RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:30Z"
 LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bcftools/bcftools_annotate/.config.vsh.yaml

@@ -468,9 +468,9 @@ build_info:
   output: "target/executable/bcftools/bcftools_annotate"
   executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bcftools/bcftools_annotate/bcftools_annotate

@@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:33Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bcftools/bcftools_concat/.config.vsh.yaml

@@ -334,9 +334,9 @@ build_info:
   output: "target/executable/bcftools/bcftools_concat"
   executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bcftools/bcftools_concat/bcftools_concat

@@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:33Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bcftools/bcftools_norm/.config.vsh.yaml

@@ -415,9 +415,9 @@ build_info:
   output: "target/executable/bcftools/bcftools_norm"
   executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bcftools/bcftools_norm/bcftools_norm

@@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:33Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bcftools/bcftools_sort/.config.vsh.yaml

@@ -184,9 +184,9 @@ build_info:
   output: "target/executable/bcftools/bcftools_sort"
   executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bcftools/bcftools_sort/bcftools_sort

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:27Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:33Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bcftools/bcftools_stats/.config.vsh.yaml

@@ -457,9 +457,9 @@ build_info:
   output: "target/executable/bcftools/bcftools_stats"
   executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bcftools/bcftools_stats/bcftools_stats

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:27Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:32Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -431,9 +431,9 @@ build_info:
   output: "target/executable/bcl_convert"
   executable: "target/executable/bcl_convert/bcl_convert"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bcl_convert/bcl_convert

@@ -462,9 +462,9 @@ 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="2025-06-16T10:11:29Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -279,9 +279,9 @@ build_info:
   output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference

@@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:26Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -1120,9 +1120,9 @@ build_info:
   output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis"
   executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis

@@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:26Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -234,9 +234,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_bamtobed"
   executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed

@@ -456,9 +456,9 @@ 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_bamtobed"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:27Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -186,9 +186,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_bamtofastq"
   executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:28Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:26Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -175,9 +175,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_bed12tobed6"
   executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:26Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:28Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -213,9 +213,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_bedtobam"
   executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:26Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:28Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -336,9 +336,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_genomecov"
   executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_genomecov/bedtools_genomecov

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:28Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:26Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -235,9 +235,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_getfasta"
   executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_getfasta/bedtools_getfasta

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:27Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:27Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -272,9 +272,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_groupby"
   executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_groupby/bedtools_groupby

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:26Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:28Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -409,9 +409,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_intersect"
   executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_intersect/bedtools_intersect

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:27Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:26Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -209,9 +209,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_links"
   executable: "target/executable/bedtools/bedtools_links/bedtools_links"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_links/bedtools_links

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:26Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:25Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -278,9 +278,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_merge"
   executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_merge/bedtools_merge

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:27Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:27Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -221,9 +221,9 @@ build_info:
   output: "target/executable/bedtools/bedtools_sort"
   executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/bedtools/bedtools_sort/bedtools_sort

@@ -456,9 +456,9 @@ 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="2025-06-16T10:11:28Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:26Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -161,9 +161,9 @@ build_info:
   output: "target/executable/busco/busco_download_datasets"
   executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/busco/busco_download_datasets/busco_download_datasets

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:23Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:28Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -148,9 +148,9 @@ build_info:
   output: "target/executable/busco/busco_list_datasets"
   executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/busco/busco_list_datasets/busco_list_datasets

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:22Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:28Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -426,9 +426,9 @@ build_info:
   output: "target/executable/busco/busco_run"
   executable: "target/executable/busco/busco_run/busco_run"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/busco/busco_run/busco_run

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:22Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:29Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/cellranger/cellranger_count/.config.vsh.yaml

@@ -373,9 +373,9 @@ build_info:
   output: "target/executable/cellranger/cellranger_count"
   executable: "target/executable/cellranger/cellranger_count/cellranger_count"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/cellranger/cellranger_count/cellranger_count

@@ -456,9 +456,9 @@ RUN cellranger --version | sed 's/ cellranger-/: /' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_count"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:25Z"
 LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/bin/sc_rna/count"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/cellranger/cellranger_mkref/.config.vsh.yaml

@@ -193,9 +193,9 @@ build_info:
   output: "target/executable/cellranger/cellranger_mkref"
   executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/cellranger/cellranger_mkref/cellranger_mkref

@@ -454,9 +454,9 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_mkref"
-LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:24Z"
 LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -743,9 +743,9 @@ build_info:
   output: "target/executable/cutadapt"
   executable: "target/executable/cutadapt/cutadapt"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/cutadapt/cutadapt

@@ -455,9 +455,9 @@ 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="2025-06-16T10:11:18Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:34Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -320,9 +320,9 @@ build_info:
   output: "target/executable/falco"
   executable: "target/executable/falco/falco"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/falco/falco

@@ -464,9 +464,9 @@ 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="2025-06-16T10:11:25Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:30Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -1086,9 +1086,9 @@ build_info:
   output: "target/executable/fastp"
   executable: "target/executable/fastp/fastp"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/fastp/fastp

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:18Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:31Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/fastqc/.config.vsh.yaml

@@ -339,9 +339,9 @@ build_info:
   output: "target/executable/fastqc"
   executable: "target/executable/fastqc/fastqc"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/fastqc/fastqc

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:28Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:32Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -643,9 +643,9 @@ build_info:
   output: "target/executable/featurecounts"
   executable: "target/executable/featurecounts/featurecounts"
   viash_version: "0.9.4"
-  git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-36-gad89f43"
+  git_tag: "v0.2.0-37-g219ba1d"
 package_config:
   name: "biobox"
   version: "main"

target/executable/featurecounts/featurecounts

@@ -452,9 +452,9 @@ 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="2025-06-16T10:11:19Z"
+LABEL org.opencontainers.image.created="2025-06-23T06:29:35Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca"
+LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/fq/fq_lint/.config.vsh.yaml

@@ -0,0 +1,391 @@
+name: "fq_lint"
+namespace: "fq"
+version: "main"
+authors:
+- name: "Robrecht Cannoodt"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  info:
+    links:
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+argument_groups:
+- name: "Input"
+  description: "Input FASTQ files to validate."
+  arguments:
+  - type: "file"
+    name: "--input_1"
+    description: "Read 1 source. Accepts both raw and gzipped FASTQ inputs."
+    info: null
+    example:
+    - "reads_1.fastq.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_2"
+    description: "Read 2 source. Accepts both raw and gzipped FASTQ inputs."
+    info: null
+    example:
+    - "reads_2.fastq.gz"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  description: "Validation parameters."
+  arguments:
+  - type: "string"
+    name: "--lint_mode"
+    description: "Panic on first error or log all errors."
+    info: null
+    default:
+    - "panic"
+    required: false
+    choices:
+    - "panic"
+    - "log"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--single_read_validation_level"
+    description: "Only use single read validators up to a given level."
+    info: null
+    default:
+    - "high"
+    required: false
+    choices:
+    - "low"
+    - "medium"
+    - "high"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--paired_read_validation_level"
+    description: "Only use paired read validators up to a given level."
+    info: null
+    default:
+    - "high"
+    required: false
+    choices:
+    - "low"
+    - "medium"
+    - "high"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--disable_validator"
+    description: "Disable validators by code. Use multiple times to disable more than\
+      \ one."
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--record_definition_separator"
+    description: "Define a record definition separator."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Validates a single or paired FASTQ file."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "fastq"
+- "lint"
+- "validate"
+- "quality-control"
+license: "MIT"
+links:
+  repository: "https://github.com/stjude-rust-labs/fq"
+  homepage: "https://github.com/stjude-rust-labs/fq/blob/master/README.md"
+  documentation: "https://github.com/stjude-rust-labs/fq/blob/master/README.md"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/fq:0.12.0--h9ee0642_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/fq/fq_lint/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/fq/fq_lint"
+  executable: "target/executable/fq/fq_lint/fq_lint"
+  viash_version: "0.9.4"
+  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-37-g219ba1d"
+package_config:
+  name: "biobox"
+  version: "main"
+  summary: "A curated collection of high-quality, standalone bioinformatics components\
+    \ built with [Viash](https://viash.io).\n"
+  description: "`biobox` offers a suite of reliable bioinformatics components, similar\
+    \ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
+    \ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
+    \ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
+    \ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
+    \ Run components directly via the command line or seamlessly integrate them into\
+    \ Nextflow workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation\
+    \ for components and parameters.\n    * Full exposure of underlying tool arguments.\n\
+    \    * Containerized (Docker) for dependency management and reproducibility.\n\
+    \    * Unit tested for verified functionality.\n"
+  info: null
+  viash_version: "0.9.4"
+  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'"
+  authors:
+  - name: "Robrecht Cannoodt"
+    roles:
+    - "author"
+    - "maintainer"
+    info:
+      links:
+        email: "robrecht@data-intuitive.com"
+        github: "rcannood"
+        orcid: "0000-0003-3641-729X"
+        linkedin: "robrechtcannoodt"
+      organizations:
+      - name: "Data Intuitive"
+        href: "https://www.data-intuitive.com"
+        role: "Data Science Engineer"
+      - name: "Open Problems"
+        href: "https://openproblems.bio"
+        role: "Core Member"
+  - name: "Angela Oliveira Pisco"
+    roles:
+    - "author"
+    info:
+      role: "Contributor"
+      links:
+        github: "aopisco"
+        orcid: "0000-0003-0142-2355"
+        linkedin: "aopisco"
+      organizations:
+      - name: "Insitro"
+        href: "https://insitro.com"
+        role: "Director of Computational Biology"
+      - name: "Open Problems"
+        href: "https://openproblems.bio"
+        role: "Core Member"
+  - name: "Dorien Roosen"
+    roles:
+    - "author"
+    info:
+      links:
+        email: "dorien@data-intuitive.com"
+        github: "dorien-er"
+        linkedin: "dorien-roosen"
+      organizations:
+      - name: "Data Intuitive"
+        href: "https://www.data-intuitive.com"
+        role: "Data Scientist"
+  - name: "Dries Schaumont"
+    roles:
+    - "author"
+    info:
+      links:
+        email: "dries@data-intuitive.com"
+        github: "DriesSchaumont"
+        orcid: "0000-0002-4389-0440"
+        linkedin: "dries-schaumont"
+      organizations:
+      - name: "Data Intuitive"
+        href: "https://www.data-intuitive.com"
+        role: "Data Scientist"
+  - name: "Emma Rousseau"
+    roles:
+    - "author"
+    info:
+      links:
+        github: "emmarousseau"
+        linkedin: "emmarousseau1"
+  - name: "Jakub Majercik"
+    roles:
+    - "author"
+    info:
+      links:
+        email: "jakub@data-intuitive.com"
+        github: "jakubmajercik"
+        linkedin: "jakubmajercik"
+      organizations:
+      - name: "Data Intuitive"
+        href: "https://www.data-intuitive.com"
+        role: "Bioinformatics Engineer"
+  - name: "Kai Waldrant"
+    roles:
+    - "author"
+    info:
+      links:
+        github: "KaiWaldrant"
+        orcid: "0009-0003-8555-1361"
+        linkedin: "kaiwaldrant"
+  - name: "Leïla Paquay"
+    roles:
+    - "author"
+    info:
+      links:
+        github: "Leila011"
+        linkedin: "leilapaquay"
+  - name: "Sai Nirmayi Yasa"
+    roles:
+    - "author"
+    info:
+      links:
+        github: "sainirmayi"
+        linkedin: "sai-nirmayi-yasa"
+  - name: "Theodoro Gasperin Terra Camargo"
+    roles:
+    - "author"
+    info:
+      links:
+        email: "theodorogtc@gmail.com"
+        github: "tgaspe"
+        linkedin: "theodoro-gasperin-terra-camargo"
+  - name: "Toni Verbeiren"
+    roles:
+    - "author"
+    info:
+      links:
+        github: "tverbeiren"
+        linkedin: "verbeiren"
+      organizations:
+      - name: "Data Intuitive"
+        href: "https://www.data-intuitive.com"
+        role: "Data Scientist and CEO"
+  - name: "Weiwei Schultz"
+    roles:
+    - "author"
+    info:
+      links:
+        linkedin: "weiwei-schultz"
+      organizations:
+      - name: "Janssen R&D US"
+        role: "Associate Director Data Sciences"
+  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"