Build branch main with version main (e6627ec)

Build pipeline: viash-hub.biobox.main-v4lxs Source commit: e6627ec728 Source message: FastQC (#92) * Starting Component * Creating Files * update on config file * Update on test.sh * Update on config * Update script.sh * Update on script.sh * trying to figure multiple: true * Update on script.sh * Update on script * Adding some tests * More tests * Update on script.sh * Added more tests * Small Changes * Update test.sh * Update on Script and Test - change the --zip and --html to take wild card '*' * Added one more test * Removed test_data dir * More description * Update CHANGELOG.md * Update on config and script - meta_cpus - meta_tmp_dir * Bug Fixed * unset_if_false * Updating Tests * Update script.sh * debugging * Minor changes * Update config.vsh.yaml * Update config.vsh.yaml * Required Changes - large changes on script.sh * Update config.vsh.yaml * Adding extra links * tmpdir bug * Updating tests * minor changes * Adding extra output options --summary --data * minor change * Update script.sh * small change in config
2024-09-03 09:13:58 +00:00
parent f066ef0ffa
commit ddad38b4a3
211 changed files with 7517 additions and 250 deletions
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -235,7 +235,7 @@ build_info:
  output: "target/executable/agat/agat_convert_bed2gff"
  executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -515,9 +515,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:20Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,7 +225,7 @@ build_info:
  output: "target/executable/agat/agat_convert_embl2gff"
  executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -505,9 +505,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:19Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gff2gtf"
  executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -519,9 +519,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:20Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,7 +188,7 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gff2tsv"
  executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -484,9 +484,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:19Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,7 +195,7 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gxf2gxf"
  executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -493,9 +493,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:19Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:44Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -706,7 +706,7 @@ build_info:
  output: "target/executable/arriba"
  executable: "target/executable/arriba/arriba"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -754,9 +754,9 @@ RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' >

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:21Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:47Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
  output: "target/executable/bcftools/bcftools_sort"
  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcftools/bcftools_sort/bcftools_sort
+++ b/target/executable/bcftools/bcftools_sort/bcftools_sort
@@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:15Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -418,7 +418,7 @@ build_info:
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/

 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:21Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -270,7 +270,7 @@ build_info:
  output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
  executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
@@ -549,9 +549,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:24Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:49Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_bamtofastq"
  executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:09Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:33Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -176,7 +176,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_bed12tobed6"
  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
+++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
@@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:07Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:32Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,7 +214,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_bedtobam"
  executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:10Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:34Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,7 +232,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:08Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:32Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -273,7 +273,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_groupby"
  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby
+++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
@@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:09Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:34Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,7 +410,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_intersect"
  executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:08Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:33Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
@@ -210,7 +210,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_links"
  executable: "target/executable/bedtools/bedtools_links/bedtools_links"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_links/bedtools_links
+++ b/target/executable/bedtools/bedtools_links/bedtools_links
@@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:08Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:33Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_merge"
  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_merge/bedtools_merge
+++ b/target/executable/bedtools/bedtools_merge/bedtools_merge
@@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:07Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:32Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_sort"
  executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:09Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:34Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -475,9 +475,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:17Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:43Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,7 +145,7 @@ build_info:
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -465,9 +465,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:18Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:43Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -423,7 +423,7 @@ build_info:
  output: "target/executable/busco/busco_run"
  executable: "target/executable/busco/busco_run/busco_run"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -632,9 +632,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:18Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:43Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -740,7 +740,7 @@ build_info:
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -831,9 +831,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions

 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:22Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:48Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -317,7 +317,7 @@ build_info:
  output: "target/executable/falco"
  executable: "target/executable/falco/falco"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio

 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:23Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:49Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1083,7 +1083,7 @@ build_info:
  output: "target/executable/fastp"
  executable: "target/executable/fastp/fastp"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:20Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:46Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -0,0 +1,366 @@
+name: "fastqc"
+version: "main"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "theodorogtc@gmail.com"
+      github: "tgaspe"
+      linkedin: "theodoro-gasperin-terra-camargo"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "FASTQ file(s) to be analyzed.\n"
+    info: null
+    example:
+    - "input.fq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  description: "At least one of the output options (--html, --zip, --summary, --data)\
+    \ must be used.\n"
+  arguments:
+  - type: "file"
+    name: "--html"
+    description: "Create the HTML report of the results. \n'*' wild card must be provided\
+      \ in the output file name. \nWild card will be replaced by the input file basename.\n\
+      e.g. \n  --input \"sample_1.fq\"\n  --html \"*.html\"\n  would create an output\
+      \ html file named sample_1.html\n"
+    info: null
+    example:
+    - "*.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--zip"
+    description: "Create the zip file(s) containing: html report, data, images, icons,\
+      \ summary, etc.\n'*' wild card must be provided in the output file name.\nWild\
+      \ card will be replaced by the input basename.\ne.g. \n  --input \"sample_1.fq\"\
+      \n  --html \"*.zip\"\n  would create an output zip file named sample_1.zip\n"
+    info: null
+    example:
+    - "*.zip"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--summary"
+    description: "Create the summary file(s).\n'*' wild card must be provided in the\
+      \ output file name.\nWild card will be replaced by the input basename.\ne.g.\
+      \ \n  --input \"sample_1.fq\"\n  --summary \"*_summary.txt\"\n  would create\
+      \ an output summary.txt file named sample_1_summary.txt\n"
+    info: null
+    example:
+    - "*_summary.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--data"
+    description: "Create the data file(s).\n'*' wild card must be provided in the\
+      \ output file name.\nWild card will be replaced by the input basename.\ne.g.\
+      \ \n  --input \"sample_1.fq\"\n  --summary \"*_data.txt\"\n  would create an\
+      \ output data.txt file named sample_1_data.txt\n"
+    info: null
+    example:
+    - "*_data.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--casava"
+    description: "Files come from raw casava output. Files in the same sample\ngroup\
+      \ (differing only by the group number) will be analysed\nas a set rather than\
+      \ individually. Sequences with the filter\nflag set in the header will be excluded\
+      \ from the analysis.\nFiles must have the same names given to them by casava\n\
+      (including being gzipped and ending with .gz) otherwise they\nwon't be grouped\
+      \ together correctly.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nano"
+    description: "Files come from nanopore sequences and are in fast5 format. In\n\
+      this mode you can pass in directories to process and the program\nwill take\
+      \ in all fast5 files within those directories and produce\na single output file\
+      \ from the sequences found in all files.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nofilter"
+    description: "If running with --casava then don't remove read flagged by\ncasava\
+      \ as poor quality when performing the QC analysis.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nogroup"
+    description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
+      \ data for every base in the read. \nWARNING: Using this option will cause fastqc\
+      \ to crash \nand burn if you use it on really long reads, and your \nplots may\
+      \ end up a ridiculous size. You have been warned!\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--min_length"
+    description: "Sets an artificial lower limit on the length of the \nsequence to\
+      \ be shown in the report. As long as you \nset this to a value greater or equal\
+      \ to your longest \nread length then this will be the sequence length used \n\
+      to create your read groups. This can be useful for making\ndirectly comparable\
+      \ statistics from datasets with somewhat \nvariable read lengths.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--format"
+    alternatives:
+    - "-f"
+    description: "Bypasses the normal sequence file format detection and \nforces\
+      \ the program to use the specified format. \nValid formats are bam, sam, bam_mapped,\
+      \ sam_mapped, and fastq.\n"
+    info: null
+    example:
+    - "bam"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--contaminants"
+    alternatives:
+    - "-c"
+    description: "Specifies a non-default file which contains the list \nof contaminants\
+      \ to screen overrepresented sequences against. \nThe file must contain sets\
+      \ of named contaminants in the form\nname[tab]sequence. Lines prefixed with\
+      \ a hash will be ignored.\n"
+    info: null
+    example:
+    - "contaminants.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--adapters"
+    alternatives:
+    - "-a"
+    description: "Specifies a non-default file which contains the list of \nadapter\
+      \ sequences which will be explicitly searched against \nthe library. The file\
+      \ must contain sets of named adapters \nin the form name[tab]sequence. Lines\
+      \ prefixed with a hash will be ignored.\n"
+    info: null
+    example:
+    - "adapters.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--limits"
+    alternatives:
+    - "-l"
+    description: "Specifies a non-default file which contains \na set of criteria\
+      \ which will be used to determine \nthe warn/error limits for the various modules.\
+      \ \nThis file can also be used to selectively remove \nsome modules from the\
+      \ output altogether. The format \nneeds to mirror the default limits.txt file\
+      \ found in \nthe Configuration folder.\n"
+    info: null
+    example:
+    - "limits.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--kmers"
+    alternatives:
+    - "-k"
+    description: "Specifies the length of Kmer to look for in the Kmer \ncontent module.\
+      \ Specified Kmer length must be between \n2 and 10. Default length is 7 if not\
+      \ specified.\n"
+    info: null
+    example:
+    - 7
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--quiet"
+    alternatives:
+    - "-q"
+    description: "Suppress all progress messages on stdout and only report errors.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "FastQC - A high throughput sequence QC analysis tool."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Quality control"
+- "BAM"
+- "SAM"
+- "FASTQ"
+license: "GPL-3.0, Apache-2.0"
+links:
+  repository: "https://github.com/s-andrews/FastQC"
+  homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+  documentation: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/"
+  issue_tracker: "https://github.com/s-andrews/FastQC/issues"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "biocontainers/fastqc:v0.11.9_cv8"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "echo \"fastqc: $(fastqc --version | sed -n 's/^FastQC //p')\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/fastqc/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/fastqc"
+  executable: "target/executable/fastqc/fastqc"
+  viash_version: "0.9.0-RC7"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
+  git_remote: "https://github.com/viash-hub/biobox"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0-RC7"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -645,7 +645,7 @@ build_info:
  output: "target/executable/featurecounts"
  executable: "target/executable/featurecounts/featurecounts"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -754,9 +754,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:16Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:41Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -685,7 +685,7 @@ build_info:
  output: "target/executable/gffread"
  executable: "target/executable/gffread/gffread"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -807,9 +807,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:07Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:31Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -507,7 +507,7 @@ build_info:
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -656,9 +656,9 @@ echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:15Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,7 +215,7 @@ build_info:
  output: "target/executable/lofreq/lofreq_indelqual"
  executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -501,9 +501,9 @@ echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:15Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -456,7 +456,7 @@ build_info:
  output: "target/executable/multiqc"
  executable: "target/executable/multiqc/multiqc"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -637,9 +637,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:23Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:49Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -398,7 +398,7 @@ build_info:
  output: "target/executable/pear"
  executable: "target/executable/pear/pear"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -597,9 +597,9 @@ echo "pear: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:10Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:34Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -264,7 +264,7 @@ build_info:
  output: "target/executable/qualimap/qualimap_rnaseq"
  executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -527,9 +527,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:14Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:38Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,7 +416,7 @@ build_info:
  output: "target/executable/rsem/rsem_prepare_reference"
  executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
+++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
@@ -656,9 +656,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:18Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:44Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -277,7 +277,7 @@ build_info:
  output: "target/executable/salmon/salmon_index"
  executable: "target/executable/salmon/salmon_index/salmon_index"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -546,9 +546,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:21Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:47Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,7 +1173,7 @@ build_info:
  output: "target/executable/salmon/salmon_quant"
  executable: "target/executable/salmon/salmon_quant/salmon_quant"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -1168,9 +1168,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:22Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:48Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -264,7 +264,7 @@ build_info:
  output: "target/executable/samtools/samtools_collate"
  executable: "target/executable/samtools/samtools_collate/samtools_collate"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -519,9 +519,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:12Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:37Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -243,7 +243,7 @@ build_info:
  output: "target/executable/samtools/samtools_faidx"
  executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -512,9 +512,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:12Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:37Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
  output: "target/executable/samtools/samtools_fasta"
  executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_fasta/samtools_fasta
+++ b/target/executable/samtools/samtools_fasta/samtools_fasta
@@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:13Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:37Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
  output: "target/executable/samtools/samtools_fastq"
  executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -626,9 +626,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:12Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:36Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
  output: "target/executable/samtools/samtools_flagstat"
  executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -474,9 +474,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:11Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:36Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
  output: "target/executable/samtools/samtools_idxstats"
  executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -478,9 +478,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:11Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -189,7 +189,7 @@ build_info:
  output: "target/executable/samtools/samtools_index"
  executable: "target/executable/samtools/samtools_index/samtools_index"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -485,9 +485,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:10Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -332,7 +332,7 @@ build_info:
  output: "target/executable/samtools/samtools_sort"
  executable: "target/executable/samtools/samtools_sort/samtools_sort"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -556,9 +556,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:13Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -401,7 +401,7 @@ build_info:
  output: "target/executable/samtools/samtools_stats"
  executable: "target/executable/samtools/samtools_stats/samtools_stats"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -575,9 +575,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:13Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/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: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -825,9 +825,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:11Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
  output: "target/executable/seqtk/seqtk_sample"
  executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/seqtk/seqtk_sample/seqtk_sample
+++ b/target/executable/seqtk/seqtk_sample/seqtk_sample
@@ -481,9 +481,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:24Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:50Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -196,7 +196,7 @@ build_info:
  output: "target/executable/seqtk/seqtk_subseq"
  executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq
+++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
@@ -491,9 +491,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:24Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:50Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/star/star_align_reads/.config.vsh.yaml
+++ b/target/executable/star/star_align_reads/.config.vsh.yaml
@@ -2663,7 +2663,7 @@ build_info:
  output: "target/executable/star/star_align_reads"
  executable: "target/executable/star/star_align_reads/star_align_reads"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/star/star_align_reads/star_align_reads
+++ b/target/executable/star/star_align_reads/star_align_reads
@@ -1920,9 +1920,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:17Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:42Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/star/star_genome_generate/.config.vsh.yaml
+++ b/target/executable/star/star_genome_generate/.config.vsh.yaml
@@ -333,7 +333,7 @@ build_info:
  output: "target/executable/star/star_genome_generate"
  executable: "target/executable/star/star_genome_generate/star_genome_generate"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/star/star_genome_generate/star_genome_generate
+++ b/target/executable/star/star_genome_generate/star_genome_generate
@@ -577,9 +577,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:16Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:42Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -611,7 +611,7 @@ build_info:
  output: "target/executable/umi_tools/umi_tools_dedup"
  executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
+++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
@@ -770,9 +770,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:14Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:40Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/Show More
+++ b/Show More