Build branch main with version main (9f81386)

Build pipeline: viash-hub.biobox.main-tr92f

Source commit: 9f81386259

Source message: Fq subsample (#147)

CHANGELOG.md

@@ -142,6 +142,8 @@
     - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
                            intervals defined in a BED/GFF/VCF file (PR #59).
 
+*  `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
+
 ## MINOR CHANGES
 
 * Uniformize component metadata (PR #23).

src/fq_subsample/config.vsh.yaml

@@ -0,0 +1,68 @@
+name: fq_subsample
+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
+
+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
+  - path: test_data
+
+engines:  
+  - type: docker
+    image: rust:1.81-slim
+    setup:
+      - type: docker
+        run: |
+          apt-get update && apt-get install -y git procps && \
+          git clone --depth 1 --branch v0.12.0 https://github.com/stjude-rust-labs/fq.git && \
+          cd fq && \
+          cargo install --locked --path . && \
+          mv target/release/fq /usr/local/bin/ && \
+          cd / && rm -rf /fq
+
+runners:
+  - type: executable
+  - type: nextflow

src/fq_subsample/help.txt

@@ -0,0 +1,20 @@
+```
+fq subsample -h
+```
+
+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   

src/fq_subsample/script.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -eo pipefail
+
+
+required_args=("-p" "--probability" "-n" "--record_count")
+
+# 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 "FQ/SUBSAMPLE requires either --probability or --record_count to be specified"
+    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}
+

src/fq_subsample/test.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+echo ">>> Testing $meta_executable"
+
+echo ">>> Testing for paired-end reads"
+"$meta_executable" \
+    --input_1 $meta_resources_dir/test_data/a.3.fastq.gz \
+    --input_2 $meta_resources_dir/test_data/a.4.fastq.gz \
+    --record_count 3 \
+    --seed 1 \
+    --output_1  a.1.subsampled.fastq \
+    --output_2  a.2.subsampled.fastq 
+
+echo ">> Checking if the correct files are present"
+[ ! -f "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file for read 1 is missing!" && exit 1
+[ $(wc -l < a.1.subsampled.fastq) -ne 12 ] && echo "Subsampled FASTQ file for read 1 does not contain the expected number of records" && exit 1
+[ ! -f "a.2.subsampled.fastq" ] && echo "Subsampled FASTQ file for read 2 is missing" && exit 1
+[ $(wc -l < a.2.subsampled.fastq) -ne 12 ] && echo "Subsampled FASTQ file for read 2 does not contain the expected number of records" && exit 1
+
+rm a.1.subsampled.fastq a.2.subsampled.fastq
+
+echo ">>> Testing for single-end reads"
+"$meta_executable" \
+    --input_1 $meta_resources_dir/test_data/a.3.fastq.gz \
+    --record_count 3 \
+    --seed 1 \
+    --output_1  a.1.subsampled.fastq 
+
+    
+echo ">> Checking if the correct files are present"
+[ ! -f "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file is missing" && exit 1
+[ $(wc -l < a.1.subsampled.fastq) -ne 12 ] && echo "Subsampled FASTQ file does not contain the expected number of records" && exit 1
+
+echo ">>> Tests finished successfully"
+exit 0
+

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

@@ -235,7 +235,7 @@ build_info:
   output: "target/executable/agat/agat_convert_bed2gff"
   executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff

@@ -515,9 +515,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:30Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:16Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -225,7 +225,7 @@ build_info:
   output: "target/executable/agat/agat_convert_embl2gff"
   executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff

@@ -505,9 +505,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:29Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:16Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -228,7 +228,7 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gff2gtf"
   executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf

@@ -519,9 +519,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:30Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:16Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -188,7 +188,7 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gff2tsv"
   executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv

@@ -484,9 +484,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:29Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:15Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -195,7 +195,7 @@ build_info:
   output: "target/executable/agat/agat_convert_sp_gxf2gxf"
   executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf

@@ -493,9 +493,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:29Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:15Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -706,7 +706,7 @@ build_info:
   output: "target/executable/arriba"
   executable: "target/executable/arriba/arriba"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/arriba/arriba

@@ -754,9 +754,9 @@ RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' >
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:31Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:18Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-06T21:51:25Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:11Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -418,7 +418,7 @@ build_info:
   output: "target/executable/bcl_convert"
   executable: "target/executable/bcl_convert/bcl_convert"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bcl_convert/bcl_convert

@@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:31Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -270,7 +270,7 @@ build_info:
   output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference

@@ -549,9 +549,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:34Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:21Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -187,7 +187,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_bamtofastq"
   executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq

@@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:19Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:03Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-06T21:51:17Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:02Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam

@@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:19Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:04Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-06T21:51:17Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:02Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -232,7 +232,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_getfasta"
   executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_getfasta/bedtools_getfasta

@@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:18Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:02Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -273,7 +273,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_groupby"
   executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_groupby/bedtools_groupby

@@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:19Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:04Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -410,7 +410,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_intersect"
   executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_intersect/bedtools_intersect

@@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:18Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:03Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -210,7 +210,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_links"
   executable: "target/executable/bedtools/bedtools_links/bedtools_links"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_links/bedtools_links

@@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:18Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:03Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -279,7 +279,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_merge"
   executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_merge/bedtools_merge

@@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:17Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:01Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -222,7 +222,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_sort"
   executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/bedtools/bedtools_sort/bedtools_sort

@@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:19Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:04Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -158,7 +158,7 @@ build_info:
   output: "target/executable/busco/busco_download_datasets"
   executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/busco/busco_download_datasets/busco_download_datasets

@@ -475,9 +475,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:28Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:14Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -145,7 +145,7 @@ build_info:
   output: "target/executable/busco/busco_list_datasets"
   executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/busco/busco_list_datasets/busco_list_datasets

@@ -465,9 +465,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:28Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:14Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -423,7 +423,7 @@ build_info:
   output: "target/executable/busco/busco_run"
   executable: "target/executable/busco/busco_run/busco_run"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/busco/busco_run/busco_run

@@ -632,9 +632,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:28Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:14Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -740,7 +740,7 @@ build_info:
   output: "target/executable/cutadapt"
   executable: "target/executable/cutadapt/cutadapt"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/cutadapt/cutadapt

@@ -831,9 +831,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:33Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:19Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -317,7 +317,7 @@ build_info:
   output: "target/executable/falco"
   executable: "target/executable/falco/falco"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/falco/falco

@@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:33Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:20Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -1083,7 +1083,7 @@ build_info:
   output: "target/executable/fastp"
   executable: "target/executable/fastp/fastp"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/fastp/fastp

@@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:30Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:17Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

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="2024-09-06T21:51:24Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:09Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -645,7 +645,7 @@ build_info:
   output: "target/executable/featurecounts"
   executable: "target/executable/featurecounts/featurecounts"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/featurecounts/featurecounts

@@ -754,9 +754,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:26Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:12Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/fq_subsample/.config.vsh.yaml

@@ -0,0 +1,216 @@
+name: "fq_subsample"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input_1"
+    description: "First input fastq file to subsample. Accepts both raw and gzipped\
+      \ FASTQ inputs."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_2"
+    description: "Second input fastq files to subsample. Accepts both raw and gzipped\
+      \ FASTQ inputs."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_1"
+    description: "Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_2"
+    description: "Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "double"
+    name: "--probability"
+    description: "The probability a record is kept, as a percentage (0.0, 1.0). Cannot\
+      \ be used with `record-count`"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--record_count"
+    description: "The exact number of records to keep. Cannot be used with `probability`"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--seed"
+    description: "Seed to use for the random number generator"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "fq subsample outputs a subset of records from single or paired FASTQ\
+  \ files."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "fastq"
+- "subsample"
+- "subset"
+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: "rust:1.81-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "apt-get update && apt-get install -y git procps && \\\ngit clone --depth 1\
+      \ --branch v0.12.0 https://github.com/stjude-rust-labs/fq.git && \\\ncd fq &&\
+      \ \\\ncargo install --locked --path . && \\\nmv target/release/fq /usr/local/bin/\
+      \ && \\\ncd / && rm -rf /fq\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/fq_subsample/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/fq_subsample"
+  executable: "target/executable/fq_subsample/fq_subsample"
+  viash_version: "0.9.0-RC7"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
+  git_remote: "https://github.com/viash-hub/biobox"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0-RC7"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"

target/executable/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: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/gffread/gffread

@@ -807,9 +807,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:16Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:00Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -507,7 +507,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_call"
   executable: "target/executable/lofreq/lofreq_call/lofreq_call"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/lofreq/lofreq_call/lofreq_call

@@ -656,9 +656,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:25Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -215,7 +215,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_indelqual"
   executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/lofreq/lofreq_indelqual/lofreq_indelqual

@@ -501,9 +501,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:25Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -456,7 +456,7 @@ build_info:
   output: "target/executable/multiqc"
   executable: "target/executable/multiqc/multiqc"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/multiqc/multiqc

@@ -637,9 +637,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:33Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:20Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -398,7 +398,7 @@ build_info:
   output: "target/executable/pear"
   executable: "target/executable/pear/pear"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/pear/pear

@@ -597,9 +597,9 @@ echo "pear: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:20Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:05Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -264,7 +264,7 @@ build_info:
   output: "target/executable/qualimap/qualimap_rnaseq"
   executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq

@@ -527,9 +527,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:23Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:09Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -416,7 +416,7 @@ build_info:
   output: "target/executable/rsem/rsem_prepare_reference"
   executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference

@@ -656,9 +656,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:28Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:15Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -277,7 +277,7 @@ build_info:
   output: "target/executable/salmon/salmon_index"
   executable: "target/executable/salmon/salmon_index/salmon_index"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/salmon/salmon_index/salmon_index

@@ -546,9 +546,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:32Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:18Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -1173,7 +1173,7 @@ build_info:
   output: "target/executable/salmon/salmon_quant"
   executable: "target/executable/salmon/salmon_quant/salmon_quant"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/salmon/salmon_quant/salmon_quant

@@ -1168,9 +1168,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:32Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:19Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -264,7 +264,7 @@ build_info:
   output: "target/executable/samtools/samtools_collate"
   executable: "target/executable/samtools/samtools_collate/samtools_collate"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_collate/samtools_collate

@@ -519,9 +519,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:22Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:07Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -243,7 +243,7 @@ build_info:
   output: "target/executable/samtools/samtools_faidx"
   executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_faidx/samtools_faidx

@@ -512,9 +512,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:22Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:07Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -433,7 +433,7 @@ build_info:
   output: "target/executable/samtools/samtools_fasta"
   executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_fasta/samtools_fasta

@@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:22Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:08Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -433,7 +433,7 @@ build_info:
   output: "target/executable/samtools/samtools_fastq"
   executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_fastq/samtools_fastq

@@ -626,9 +626,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:21Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:07Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -173,7 +173,7 @@ build_info:
   output: "target/executable/samtools/samtools_flagstat"
   executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_flagstat/samtools_flagstat

@@ -474,9 +474,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:21Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:06Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -183,7 +183,7 @@ build_info:
   output: "target/executable/samtools/samtools_idxstats"
   executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_idxstats/samtools_idxstats

@@ -478,9 +478,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:20Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:05Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -189,7 +189,7 @@ build_info:
   output: "target/executable/samtools/samtools_index"
   executable: "target/executable/samtools/samtools_index/samtools_index"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_index/samtools_index

@@ -485,9 +485,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:20Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:05Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -332,7 +332,7 @@ build_info:
   output: "target/executable/samtools/samtools_sort"
   executable: "target/executable/samtools/samtools_sort/samtools_sort"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_sort/samtools_sort

@@ -556,9 +556,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:23Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:08Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -401,7 +401,7 @@ build_info:
   output: "target/executable/samtools/samtools_stats"
   executable: "target/executable/samtools/samtools_stats/samtools_stats"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/samtools/samtools_stats/samtools_stats

@@ -575,9 +575,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-09-06T21:51:23Z"
+LABEL org.opencontainers.image.created="2024-09-09T06:25:08Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d"
+LABEL org.opencontainers.image.revision="9f813862592fb10f8d15df59697bdaae82c7921a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -665,7 +665,7 @@ build_info:
   output: "target/executable/samtools/samtools_view"
   executable: "target/executable/samtools/samtools_view/samtools_view"
   viash_version: "0.9.0-RC7"
-  git_commit: "99dec5923bfb3da165601a3f13502d498395b14d"
+  git_commit: "9f813862592fb10f8d15df59697bdaae82c7921a"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"