diff --git a/_viash.yaml b/_viash.yaml index a898ff17..18a798a3 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: biobox -version: 0.2.0 +version: v0.2.0 description: | A collection of bioinformatics tools for working with sequence data. license: MIT diff --git a/nextflow.config b/nextflow.config index bdd66d18..4260a534 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ manifest { name = "biobox" - version = "0.2.0" + version = "v0.2.0" defaultBranch = "main" nextflowVersion = "!>=20.12.1-edge" } diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index b0c219e6..1650c19d 100644 --- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_bed2gff" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -218,7 +218,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -235,11 +235,11 @@ build_info: output: "target/executable/agat/agat_convert_bed2gff" executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -249,7 +249,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index c97d038f..9bb7e9b0 100755 --- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff +++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# agat_convert_bed2gff 0.2.0 +# agat_convert_bed2gff v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_bed2gff 0.2.0" + echo "agat_convert_bed2gff v0.2.0" echo "" echo "The script takes a bed file as input, and will translate it in gff format. The" echo "BED format is described here The script converts 0-based, half-open [start-1," @@ -515,10 +515,10 @@ 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="2024-09-12T13:23:23Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:18Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_bed2gff 0.2.0" + echo "agat_convert_bed2gff v0.2.0" exit ;; --bed) @@ -851,7 +851,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_bed2gff:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_bed2gff:v0.2.0' fi # print dockerfile diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml index 90be12ee..0c1dab24 100644 --- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_embl2gff" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -208,7 +208,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -225,11 +225,11 @@ build_info: output: "target/executable/agat/agat_convert_embl2gff" executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -239,7 +239,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index ddaa98df..36c02eb5 100755 --- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff +++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# agat_convert_embl2gff 0.2.0 +# agat_convert_embl2gff v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_embl2gff 0.2.0" + echo "agat_convert_embl2gff v0.2.0" echo "" echo "The script takes an EMBL file as input, and will translate it in gff format." echo "" @@ -505,10 +505,10 @@ 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="2024-09-12T13:23:23Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:18Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_embl2gff 0.2.0" + echo "agat_convert_embl2gff v0.2.0" exit ;; --embl) @@ -858,7 +858,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_embl2gff:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_embl2gff:v0.2.0' fi # print dockerfile diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 65fdedef..32f95329 100644 --- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gff2gtf" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -211,7 +211,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -228,11 +228,11 @@ 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" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -242,7 +242,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf index e863af61..b211f915 100755 --- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf +++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# agat_convert_sp_gff2gtf 0.2.0 +# agat_convert_sp_gff2gtf v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_sp_gff2gtf 0.2.0" + echo "agat_convert_sp_gff2gtf v0.2.0" echo "" echo "The script aims to convert any GTF/GFF file into a proper GTF file. Full" echo "information about the format can be found here:" @@ -519,10 +519,10 @@ 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="2024-09-12T13:23:23Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:19Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_sp_gff2gtf 0.2.0" + echo "agat_convert_sp_gff2gtf v0.2.0" exit ;; --gff) @@ -829,7 +829,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gff2gtf:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gff2gtf:v0.2.0' fi # print dockerfile diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index 97f88a49..0201fad8 100644 --- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gff2tsv" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -171,7 +171,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -188,11 +188,11 @@ 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" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -202,7 +202,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv index 75c82b06..65950b8c 100755 --- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv +++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# agat_convert_sp_gff2tsv 0.2.0 +# agat_convert_sp_gff2tsv v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_sp_gff2tsv 0.2.0" + echo "agat_convert_sp_gff2tsv v0.2.0" echo "" echo "The script aims to convert gtf/gff file into tabulated file. Attribute's" echo "tags from the 9th column become column titles." @@ -484,10 +484,10 @@ 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="2024-09-12T13:23:23Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:18Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -623,7 +623,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_sp_gff2tsv 0.2.0" + echo "agat_convert_sp_gff2tsv v0.2.0" exit ;; --gff) @@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gff2tsv:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gff2tsv:v0.2.0' fi # print dockerfile diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index d1d3866a..bd576f78 100644 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gxf2gxf" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -195,11 +195,11 @@ 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" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -209,7 +209,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf index 96c68859..b2017a7e 100755 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# agat_convert_sp_gxf2gxf 0.2.0 +# agat_convert_sp_gxf2gxf v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "agat_convert_sp_gxf2gxf 0.2.0" + echo "agat_convert_sp_gxf2gxf v0.2.0" echo "" echo "This script fixes and/or standardizes any GTF/GFF file into full sorted" echo "GTF/GFF file. It AGAT parser removes duplicate features, fixes" @@ -493,10 +493,10 @@ 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="2024-09-12T13:23:22Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:18Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -632,7 +632,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "agat_convert_sp_gxf2gxf 0.2.0" + echo "agat_convert_sp_gxf2gxf v0.2.0" exit ;; --gxf) @@ -786,7 +786,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gxf2gxf:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/agat/agat_convert_sp_gxf2gxf:v0.2.0' fi # print dockerfile diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index 2296f8d4..db6fa968 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "arriba" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -688,7 +688,7 @@ engines: id: "docker" image: "quay.io/biocontainers/arriba:2.4.0--h0033a41_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -706,11 +706,11 @@ build_info: output: "target/executable/arriba" executable: "target/executable/arriba/arriba" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -720,7 +720,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index 880c6c8a..fe768ab8 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# arriba 0.2.0 +# arriba v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "arriba 0.2.0" + echo "arriba v0.2.0" echo "" echo "Detect gene fusions from RNA-Seq data" echo "" @@ -754,10 +754,10 @@ 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="2024-09-12T13:23:25Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:20Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -893,7 +893,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "arriba 0.2.0" + echo "arriba v0.2.0" exit ;; --bam) @@ -1619,7 +1619,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/arriba:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/arriba:v0.2.0' fi # print dockerfile diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml index a50f7a27..a6ac9fe3 100644 --- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcftools_sort" namespace: "bcftools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -162,7 +162,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -185,11 +185,11 @@ build_info: output: "target/executable/bcftools/bcftools_sort" executable: "target/executable/bcftools/bcftools_sort/bcftools_sort" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -199,7 +199,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort index 92451663..8af3d9bb 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bcftools_sort 0.2.0 +# bcftools_sort v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcftools_sort 0.2.0" + echo "bcftools_sort v0.2.0" echo "" echo "Sorts VCF/BCF files." echo "" @@ -483,10 +483,10 @@ 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="2024-09-12T13:23:18Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:14Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcftools_sort 0.2.0" + echo "bcftools_sort v0.2.0" exit ;; --input) @@ -764,7 +764,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcftools/bcftools_sort:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcftools/bcftools_sort:v0.2.0' fi # print dockerfile diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index 62449adf..c25e99d2 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bcl_convert" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -386,7 +386,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -418,11 +418,11 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -432,7 +432,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index f59040f8..6211e388 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bcl_convert 0.2.0 +# bcl_convert v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcl_convert 0.2.0" + echo "bcl_convert v0.2.0" echo "" echo "Convert bcl files to fastq files using bcl-convert." echo "Information about upgrading from bcl2fastq via" @@ -599,10 +599,10 @@ 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="2024-09-12T13:23:24Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -738,7 +738,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcl_convert 0.2.0" + echo "bcl_convert v0.2.0" exit ;; --bcl_input_directory) @@ -1100,7 +1100,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcl_convert:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcl_convert:v0.2.0' fi # print dockerfile diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index ce6f84b8..3e937d5f 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody_make_reference" namespace: "bd_rhapsody" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -243,7 +243,7 @@ engines: id: "docker" image: "bdgenomics/rhapsody:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -270,11 +270,11 @@ 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" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -284,7 +284,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git 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 index 68699da2..85847106 100755 --- 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 @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bd_rhapsody_make_reference 0.2.0 +# bd_rhapsody_make_reference v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bd_rhapsody_make_reference 0.2.0" + echo "bd_rhapsody_make_reference v0.2.0" echo "" echo "The Reference Files Generator creates an archive containing Genome Index" echo "and Transcriptome annotation files needed for the BD Rhapsody Sequencing" @@ -549,10 +549,10 @@ 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="2024-09-12T13:23:27Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:22Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -688,7 +688,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bd_rhapsody_make_reference 0.2.0" + echo "bd_rhapsody_make_reference v0.2.0" exit ;; --genome_fasta) @@ -879,7 +879,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bd_rhapsody/bd_rhapsody_make_reference:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bd_rhapsody/bd_rhapsody_make_reference:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml index 81cb8fd8..eac2128d 100644 --- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bamtofastq" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -164,7 +164,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -187,11 +187,11 @@ build_info: output: "target/executable/bedtools/bedtools_bamtofastq" executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -201,7 +201,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index 81e65254..a62a90dd 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_bamtofastq 0.2.0 +# bedtools_bamtofastq v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_bamtofastq 0.2.0" + echo "bedtools_bamtofastq v0.2.0" echo "" echo "Conversion tool for extracting FASTQ records from sequence alignments in BAM" echo "format." @@ -483,10 +483,10 @@ 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="2024-09-12T13:23:12Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:07Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_bamtofastq 0.2.0" + echo "bedtools_bamtofastq v0.2.0" exit ;; --input) @@ -769,7 +769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bamtofastq:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bamtofastq:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 3e240fab..990ebc4b 100644 --- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bed12tobed6" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -176,11 +176,11 @@ build_info: output: "target/executable/bedtools/bedtools_bed12tobed6" executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -190,7 +190,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index 75b5e8a1..7f280cb0 100755 --- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 +++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_bed12tobed6 0.2.0 +# bedtools_bed12tobed6 v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_bed12tobed6 0.2.0" + echo "bedtools_bed12tobed6 v0.2.0" echo "" echo "Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to" echo "discrete BED6 features." @@ -480,10 +480,10 @@ 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="2024-09-12T13:23:10Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:06Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -619,7 +619,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_bed12tobed6 0.2.0" + echo "bedtools_bed12tobed6 v0.2.0" exit ;; --input) @@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bed12tobed6:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bed12tobed6:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml index 8a99759a..b95e0645 100644 --- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bedtobam" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -186,7 +186,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -214,11 +214,11 @@ build_info: output: "target/executable/bedtools/bedtools_bedtobam" executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -228,7 +228,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index ea07841b..f075d624 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_bedtobam 0.2.0 +# bedtools_bedtobam v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_bedtobam 0.2.0" + echo "bedtools_bedtobam v0.2.0" echo "" echo "Converts feature records (bed/gff/vcf) to BAM format." echo "" @@ -496,10 +496,10 @@ 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="2024-09-12T13:23:13Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:08Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_bedtobam 0.2.0" + echo "bedtools_bedtobam v0.2.0" exit ;; --input) @@ -809,7 +809,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bedtobam:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_bedtobam:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index 7f674a27..ae4bc370 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_getfasta" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dries Schaumont" roles: @@ -209,7 +209,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -232,11 +232,11 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -246,7 +246,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index b63954c0..34332bfa 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_getfasta 0.2.0 +# bedtools_getfasta v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_getfasta 0.2.0" + echo "bedtools_getfasta v0.2.0" echo "" echo "Extract sequences from a FASTA file for each of the intervals defined in a" echo "BED/GFF/VCF file." @@ -526,10 +526,10 @@ 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="2024-09-12T13:23:11Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:06Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -665,7 +665,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_getfasta 0.2.0" + echo "bedtools_getfasta v0.2.0" exit ;; --input_fasta) @@ -840,7 +840,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_getfasta:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_getfasta:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index 8a813def..6c49376c 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_groupby" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -250,7 +250,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -273,11 +273,11 @@ build_info: output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -287,7 +287,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index 9df637a2..7f5379fd 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_groupby 0.2.0 +# bedtools_groupby v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_groupby 0.2.0" + echo "bedtools_groupby v0.2.0" echo "" echo "Summarizes a dataset column based upon common column groupings." echo "Akin to the SQL \"group by\" command." @@ -552,10 +552,10 @@ 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="2024-09-12T13:23:12Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:08Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -691,7 +691,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_groupby 0.2.0" + echo "bedtools_groupby v0.2.0" exit ;; --input) @@ -938,7 +938,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_groupby:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_groupby:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml index 23529582..7f61309f 100644 --- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_intersect" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -387,7 +387,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -410,11 +410,11 @@ build_info: output: "target/executable/bedtools/bedtools_intersect" executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -424,7 +424,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index 47f7ab5f..611ddcf0 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_intersect 0.2.0 +# bedtools_intersect v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_intersect 0.2.0" + echo "bedtools_intersect v0.2.0" echo "" echo "bedtools intersect allows one to screen for overlaps between two sets of genomic" echo "features." @@ -633,10 +633,10 @@ 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="2024-09-12T13:23:11Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:07Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -772,7 +772,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_intersect 0.2.0" + echo "bedtools_intersect v0.2.0" exit ;; --input_a) @@ -1171,7 +1171,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_intersect:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_intersect:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index 6dd22666..24fd73d6 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_links" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -187,7 +187,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -210,11 +210,11 @@ build_info: output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -224,7 +224,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index 3d95793f..0d521af6 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_links 0.2.0 +# bedtools_links v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_links 0.2.0" + echo "bedtools_links v0.2.0" echo "" echo "Creates an HTML file with links to an instance of the UCSC Genome Browser for" echo "all features / intervals in a file." @@ -500,10 +500,10 @@ 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="2024-09-12T13:23:11Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:07Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_links 0.2.0" + echo "bedtools_links v0.2.0" exit ;; --input) @@ -815,7 +815,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_links:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_links:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml index 5e2a176c..69e5568d 100644 --- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_merge" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -256,7 +256,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,11 @@ build_info: output: "target/executable/bedtools/bedtools_merge" executable: "target/executable/bedtools/bedtools_merge/bedtools_merge" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -293,7 +293,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge index ca603176..e172ea62 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_merge 0.2.0 +# bedtools_merge v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_merge 0.2.0" + echo "bedtools_merge v0.2.0" echo "" echo "Merges overlapping BED/GFF/VCF entries into a single interval." echo "" @@ -558,10 +558,10 @@ 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="2024-09-12T13:23:10Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:06Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -697,7 +697,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_merge 0.2.0" + echo "bedtools_merge v0.2.0" exit ;; --input) @@ -948,7 +948,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_merge:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_merge:v0.2.0' fi # print dockerfile diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index 4e2522ca..6d545a68 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_sort" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -199,7 +199,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -222,11 +222,11 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -236,7 +236,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index 0a849ac7..45aaab89 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bedtools_sort 0.2.0 +# bedtools_sort v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bedtools_sort 0.2.0" + echo "bedtools_sort v0.2.0" echo "" echo "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria." echo "" @@ -509,10 +509,10 @@ 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="2024-09-12T13:23:12Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:08Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_sort 0.2.0" + echo "bedtools_sort v0.2.0" exit ;; --input) @@ -836,7 +836,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_sort:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_sort:v0.2.0' fi # print dockerfile diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index 3ab46e38..5bebf680 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_download_datasets" namespace: "busco" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -141,7 +141,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -158,11 +158,11 @@ build_info: output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -172,7 +172,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index f8f8faa4..36aadced 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# busco_download_datasets 0.2.0 +# busco_download_datasets v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "busco_download_datasets 0.2.0" + echo "busco_download_datasets v0.2.0" echo "" echo "Downloads available busco datasets" echo "" @@ -475,10 +475,10 @@ 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="2024-09-12T13:23:21Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:16Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -614,7 +614,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "busco_download_datasets 0.2.0" + echo "busco_download_datasets v0.2.0" exit ;; --download) @@ -727,7 +727,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_download_datasets:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_download_datasets:v0.2.0' fi # print dockerfile diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml index fde9e6a2..1cc5a66b 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_list_datasets" namespace: "busco" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -128,7 +128,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -145,11 +145,11 @@ build_info: output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -159,7 +159,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index 5e3d21f1..569d8894 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# busco_list_datasets 0.2.0 +# busco_list_datasets v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "busco_list_datasets 0.2.0" + echo "busco_list_datasets v0.2.0" echo "" echo "Lists the available busco datasets" echo "" @@ -465,10 +465,10 @@ 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="2024-09-12T13:23:21Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:17Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -604,7 +604,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "busco_list_datasets 0.2.0" + echo "busco_list_datasets v0.2.0" exit ;; --output) @@ -712,7 +712,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_list_datasets:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_list_datasets:v0.2.0' fi # print dockerfile diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml index 90209d89..36d9ab30 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_run" namespace: "busco" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -406,7 +406,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -423,11 +423,11 @@ build_info: output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -437,7 +437,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index 708498d6..dabf2b91 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# busco_run 0.2.0 +# busco_run v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "busco_run 0.2.0" + echo "busco_run v0.2.0" echo "" echo "Assessment of genome assembly and annotation completeness with single copy" echo "orthologs" @@ -632,10 +632,10 @@ 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="2024-09-12T13:23:21Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:17Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -771,7 +771,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "busco_run 0.2.0" + echo "busco_run v0.2.0" exit ;; --input) @@ -1126,7 +1126,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_run:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_run:v0.2.0' fi # print dockerfile diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 864464d5..fbb4c6e3 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "cutadapt" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -718,7 +718,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "python" @@ -740,11 +740,11 @@ build_info: output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -754,7 +754,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index d7dd8908..f5e26ad7 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cutadapt 0.2.0 +# cutadapt v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cutadapt 0.2.0" + echo "cutadapt v0.2.0" echo "" echo "Cutadapt removes adapter sequences from high-throughput sequencing reads." echo "" @@ -831,10 +831,10 @@ 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="2024-09-12T13:23:26Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:21Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -970,7 +970,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cutadapt 0.2.0" + echo "cutadapt v0.2.0" exit ;; --adapter) @@ -1785,7 +1785,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/cutadapt:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/cutadapt:v0.2.0' fi # print dockerfile diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index b6aceb89..b5b71f76 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "falco" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -287,7 +287,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -317,11 +317,11 @@ build_info: output: "target/executable/falco" executable: "target/executable/falco/falco" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -331,7 +331,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index 8c4e44dd..6e8e0c4f 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# falco 0.2.0 +# falco v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "falco 0.2.0" + echo "falco v0.2.0" echo "" echo "A C++ drop-in replacement of FastQC to assess the quality of sequence read data" echo "" @@ -589,10 +589,10 @@ 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="2024-09-12T13:23:27Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:22Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -728,7 +728,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "falco 0.2.0" + echo "falco v0.2.0" exit ;; --input) @@ -996,7 +996,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/falco:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/falco:v0.2.0' fi # print dockerfile diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index 0300f8a8..c3f248ab 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastp" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -1066,7 +1066,7 @@ engines: id: "docker" image: "quay.io/biocontainers/fastp:0.23.4--hadf994f_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -1083,11 +1083,11 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -1097,7 +1097,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index d5ec27e3..66537ec3 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# fastp 0.2.0 +# fastp v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "fastp 0.2.0" + echo "fastp v0.2.0" echo "" echo "An ultra-fast all-in-one FASTQ preprocessor" echo "(QC/adapters/trimming/filtering/splitting/merging...)." @@ -1028,10 +1028,10 @@ 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="2024-09-12T13:23:24Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:19Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -1167,7 +1167,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "fastp 0.2.0" + echo "fastp v0.2.0" exit ;; --in1) @@ -2183,7 +2183,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/fastp:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/fastp:v0.2.0' fi # print dockerfile diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 757c0da0..3bac9f5f 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastqc" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -323,7 +323,7 @@ engines: id: "docker" image: "biocontainers/fastqc:v0.11.9_cv8" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -340,11 +340,11 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -354,7 +354,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 23ba5bc0..eeec3035 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# fastqc 0.2.0 +# fastqc v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "fastqc 0.2.0" + echo "fastqc v0.2.0" echo "" echo "FastQC - A high throughput sequence QC analysis tool." echo "" @@ -601,10 +601,10 @@ 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="2024-09-12T13:23:17Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:12Z" LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -740,7 +740,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "fastqc 0.2.0" + echo "fastqc v0.2.0" exit ;; --input) @@ -1018,7 +1018,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/fastqc:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/fastqc:v0.2.0' fi # print dockerfile diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index 54657c64..6a7d66cc 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "featurecounts" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -627,7 +627,7 @@ engines: id: "docker" image: "quay.io/biocontainers/subread:2.0.6--he4a0461_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -645,11 +645,11 @@ build_info: output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -659,7 +659,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 2cb2cef2..355cd666 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# featurecounts 0.2.0 +# featurecounts v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "featurecounts 0.2.0" + echo "featurecounts v0.2.0" echo "" echo "featureCounts is a read summarization program for counting reads generated from" echo "either RNA or genomic DNA sequencing experiments by implementing highly" @@ -754,10 +754,10 @@ 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="2024-09-12T13:23:19Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:15Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -893,7 +893,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "featurecounts 0.2.0" + echo "featurecounts v0.2.0" exit ;; --annotation) @@ -1497,7 +1497,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/featurecounts:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/featurecounts:v0.2.0' fi # print dockerfile diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 07de39eb..9347135c 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gffread" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -668,7 +668,7 @@ engines: id: "docker" image: "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -685,11 +685,11 @@ build_info: output: "target/executable/gffread" executable: "target/executable/gffread/gffread" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -699,7 +699,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index e5219ed3..de0a430a 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# gffread 0.2.0 +# gffread v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "gffread 0.2.0" + echo "gffread v0.2.0" echo "" echo "Validate, filter, convert and perform various other operations on GFF files." echo "" @@ -807,10 +807,10 @@ 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="2024-09-12T13:23:10Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:05Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -946,7 +946,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "gffread 0.2.0" + echo "gffread v0.2.0" exit ;; --input) @@ -1685,7 +1685,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/gffread:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/gffread:v0.2.0' fi # print dockerfile diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index 5be6efd7..ee4fd1ec 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lofreq_call" namespace: "lofreq" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Kai Waldrant" roles: @@ -489,7 +489,7 @@ engines: id: "docker" image: "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -507,11 +507,11 @@ build_info: output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -521,7 +521,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index 3eb8b53f..758f98f6 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# lofreq_call 0.2.0 +# lofreq_call v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "lofreq_call 0.2.0" + echo "lofreq_call v0.2.0" echo "" echo "Call variants from a BAM file." echo "" @@ -656,10 +656,10 @@ 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="2024-09-12T13:23:19Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:14Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -795,7 +795,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "lofreq_call 0.2.0" + echo "lofreq_call v0.2.0" exit ;; --input) @@ -1319,7 +1319,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/lofreq/lofreq_call:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/lofreq/lofreq_call:v0.2.0' fi # print dockerfile diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index c74fd637..f8da3490 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lofreq_indelqual" namespace: "lofreq" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Kai Waldrant" roles: @@ -197,7 +197,7 @@ engines: id: "docker" image: "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -215,11 +215,11 @@ build_info: output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -229,7 +229,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index 18f8d759..8bb934d2 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# lofreq_indelqual 0.2.0 +# lofreq_indelqual v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "lofreq_indelqual 0.2.0" + echo "lofreq_indelqual v0.2.0" echo "" echo "Insert indel qualities into BAM file (required for indel predictions)." echo "" @@ -501,10 +501,10 @@ 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="2024-09-12T13:23:19Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:14Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -640,7 +640,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "lofreq_indelqual 0.2.0" + echo "lofreq_indelqual v0.2.0" exit ;; --input) @@ -803,7 +803,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/lofreq/lofreq_indelqual:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/lofreq/lofreq_indelqual:v0.2.0' fi # print dockerfile diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index aaadc5e6..5673bfcf 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "multiqc" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -433,7 +433,7 @@ engines: id: "docker" image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -456,11 +456,11 @@ build_info: output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -470,7 +470,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index bcec38c6..416a5d35 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# multiqc 0.2.0 +# multiqc v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "multiqc 0.2.0" + echo "multiqc v0.2.0" echo "" echo "MultiQC aggregates results from bioinformatics analyses across many samples into" echo "a single report." @@ -637,10 +637,10 @@ 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="2024-09-12T13:23:26Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -776,7 +776,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multiqc 0.2.0" + echo "multiqc v0.2.0" exit ;; --input) @@ -1185,7 +1185,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/multiqc:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/multiqc:v0.2.0' fi # print dockerfile diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index 5e9f7c81..064abdfe 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "pear" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Kai Waldrant" roles: @@ -380,7 +380,7 @@ engines: id: "docker" image: "quay.io/biocontainers/pear:0.9.6--h9d449c0_10" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -398,11 +398,11 @@ build_info: output: "target/executable/pear" executable: "target/executable/pear/pear" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -412,7 +412,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index c530b2ec..fb4a1380 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# pear 0.2.0 +# pear v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "pear 0.2.0" + echo "pear v0.2.0" echo "" echo "PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger." echo "It is fully parallelized and can run with as low as just a few kilobytes of" @@ -597,10 +597,10 @@ 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="2024-09-12T13:23:13Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:09Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -736,7 +736,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "pear 0.2.0" + echo "pear v0.2.0" exit ;; --forward_fastq) @@ -1112,7 +1112,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/pear:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/pear:v0.2.0' fi # print dockerfile diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml index 87d84267..b98d2a8f 100644 --- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "qualimap_rnaseq" namespace: "qualimap" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -247,7 +247,7 @@ engines: id: "docker" image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -264,11 +264,11 @@ build_info: output: "target/executable/qualimap/qualimap_rnaseq" executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -278,7 +278,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index ef0e8824..8ce593cd 100755 --- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq +++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# qualimap_rnaseq 0.2.0 +# qualimap_rnaseq v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "qualimap_rnaseq 0.2.0" + echo "qualimap_rnaseq v0.2.0" echo "" echo "Qualimap RNA-seq QC reports quality control metrics and bias estimations" echo "which are specific for whole transcriptome sequencing, including reads genomic" @@ -527,10 +527,10 @@ 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="2024-09-12T13:23:17Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:12Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -666,7 +666,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "qualimap_rnaseq 0.2.0" + echo "qualimap_rnaseq v0.2.0" exit ;; --bam) @@ -877,7 +877,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/qualimap/qualimap_rnaseq:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/qualimap/qualimap_rnaseq:v0.2.0' fi # print dockerfile diff --git a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml index d6a4216e..21dcd8ba 100644 --- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rsem_prepare_reference" namespace: "rsem" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -352,7 +352,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -416,11 +416,11 @@ build_info: output: "target/executable/rsem/rsem_prepare_reference" executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -430,7 +430,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference index 4d767518..76a6f6b6 100755 --- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference +++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# rsem_prepare_reference 0.2.0 +# rsem_prepare_reference v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "rsem_prepare_reference 0.2.0" + echo "rsem_prepare_reference v0.2.0" echo "" echo "RSEM is a software package for estimating gene and isoform expression levels" echo "from RNA-Seq data. This component prepares transcript references for RSEM." @@ -656,10 +656,10 @@ 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="2024-09-12T13:23:22Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:17Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -795,7 +795,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rsem_prepare_reference 0.2.0" + echo "rsem_prepare_reference v0.2.0" exit ;; --reference_fasta_files) @@ -1092,7 +1092,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/rsem/rsem_prepare_reference:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/rsem/rsem_prepare_reference:v0.2.0' fi # print dockerfile diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index dbe29cd1..c8c01661 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "salmon_index" namespace: "salmon" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -260,7 +260,7 @@ engines: id: "docker" image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -277,11 +277,11 @@ build_info: output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -291,7 +291,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index eeb42d3f..77ad07bb 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# salmon_index 0.2.0 +# salmon_index v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "salmon_index 0.2.0" + echo "salmon_index v0.2.0" echo "" echo "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It" echo "can either make use of pre-computed alignments (in the form of a SAM/BAM file)" @@ -546,10 +546,10 @@ 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="2024-09-12T13:23:25Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:20Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -685,7 +685,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "salmon_index 0.2.0" + echo "salmon_index v0.2.0" exit ;; --genome) @@ -919,7 +919,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/salmon/salmon_index:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/salmon/salmon_index:v0.2.0' fi # print dockerfile diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index eecc02c0..c1a23fc9 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "salmon_quant" namespace: "salmon" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -1156,7 +1156,7 @@ engines: id: "docker" image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -1173,11 +1173,11 @@ build_info: output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -1187,7 +1187,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index a2cac963..20374a74 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# salmon_quant 0.2.0 +# salmon_quant v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "salmon_quant 0.2.0" + echo "salmon_quant v0.2.0" echo "" echo "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It" echo "can either make use of pre-computed alignments (in the form of a SAM/BAM file)" @@ -1168,10 +1168,10 @@ 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="2024-09-12T13:23:25Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:21Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -1307,7 +1307,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "salmon_quant 0.2.0" + echo "salmon_quant v0.2.0" exit ;; --lib_type) @@ -2274,7 +2274,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/salmon/salmon_quant:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/salmon/salmon_quant:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index 4d9bf2ff..1610c58b 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_collate" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -246,7 +246,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -264,11 +264,11 @@ build_info: output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -278,7 +278,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index cee0efba..6878c72f 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_collate 0.2.0 +# samtools_collate v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_collate 0.2.0" + echo "samtools_collate v0.2.0" echo "" echo "Shuffles and groups reads in SAM/BAM/CRAM files together by their names." echo "" @@ -519,10 +519,10 @@ 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="2024-09-12T13:23:15Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:11Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_collate 0.2.0" + echo "samtools_collate v0.2.0" exit ;; --input) @@ -914,7 +914,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_collate:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_collate:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml index 8f8e42a9..b7bb48cc 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_faidx" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -225,7 +225,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -243,11 +243,11 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -257,7 +257,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index 8590b714..9118756e 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_faidx 0.2.0 +# samtools_faidx v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_faidx 0.2.0" + echo "samtools_faidx v0.2.0" echo "" echo "Indexes FASTA files to enable random access to fasta and fastq files." echo "" @@ -512,10 +512,10 @@ 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="2024-09-12T13:23:15Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:10Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -651,7 +651,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_faidx 0.2.0" + echo "samtools_faidx v0.2.0" exit ;; --input) @@ -857,7 +857,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_faidx:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_faidx:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml index cb99b077..3330c523 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_fasta" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -415,7 +415,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -433,11 +433,11 @@ build_info: output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -447,7 +447,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index c4181b8c..abb8f803 100755 --- a/target/executable/samtools/samtools_fasta/samtools_fasta +++ b/target/executable/samtools/samtools_fasta/samtools_fasta @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_fasta 0.2.0 +# samtools_fasta v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_fasta 0.2.0" + echo "samtools_fasta v0.2.0" echo "" echo "Converts a SAM, BAM or CRAM to FASTA format." echo "" @@ -625,10 +625,10 @@ 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="2024-09-12T13:23:16Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:11Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -764,7 +764,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_fasta 0.2.0" + echo "samtools_fasta v0.2.0" exit ;; --input) @@ -1215,7 +1215,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_fasta:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_fasta:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml index 4fda082e..992f2ccb 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_fastq" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -415,7 +415,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -433,11 +433,11 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -447,7 +447,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index 69322d42..590ec15b 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_fastq 0.2.0 +# samtools_fastq v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_fastq 0.2.0" + echo "samtools_fastq v0.2.0" echo "" echo "Converts a SAM, BAM or CRAM to FASTQ format." echo "" @@ -626,10 +626,10 @@ 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="2024-09-12T13:23:15Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:10Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -765,7 +765,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_fastq 0.2.0" + echo "samtools_fastq v0.2.0" exit ;; --input) @@ -1216,7 +1216,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_fastq:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_fastq:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml index f8b4a9fa..6884f517 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_flagstat" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -155,7 +155,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -173,11 +173,11 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -187,7 +187,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index daf04311..d7493866 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_flagstat 0.2.0 +# samtools_flagstat v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_flagstat 0.2.0" + echo "samtools_flagstat v0.2.0" echo "" echo "Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type." echo "" @@ -474,10 +474,10 @@ 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="2024-09-12T13:23:14Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:10Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -613,7 +613,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_flagstat 0.2.0" + echo "samtools_flagstat v0.2.0" exit ;; --bam) @@ -737,7 +737,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_flagstat:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_flagstat:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml index ca34c12b..7b7b8083 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_idxstats" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -165,7 +165,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -183,11 +183,11 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -197,7 +197,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index da52e779..691d4178 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_idxstats 0.2.0 +# samtools_idxstats v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_idxstats 0.2.0" + echo "samtools_idxstats v0.2.0" echo "" echo "Reports alignment summary statistics for a BAM file." echo "" @@ -478,10 +478,10 @@ 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="2024-09-12T13:23:14Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:09Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -617,7 +617,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_idxstats 0.2.0" + echo "samtools_idxstats v0.2.0" exit ;; --bam) @@ -752,7 +752,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_idxstats:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_idxstats:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml index 26be7fd1..1f054a1d 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_index" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -171,7 +171,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -189,11 +189,11 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -203,7 +203,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index dd3ae2ce..8d1877b2 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_index 0.2.0 +# samtools_index v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_index 0.2.0" + echo "samtools_index v0.2.0" echo "" echo "Index SAM/BAM/CRAM files." echo "" @@ -485,10 +485,10 @@ 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="2024-09-12T13:23:13Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:09Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -624,7 +624,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_index 0.2.0" + echo "samtools_index v0.2.0" exit ;; --input) @@ -780,7 +780,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_index:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_index:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml index 6ed05fe0..74b4d815 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_sort" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -314,7 +314,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -332,11 +332,11 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -346,7 +346,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index 06550e40..9b0bc73d 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_sort 0.2.0 +# samtools_sort v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_sort 0.2.0" + echo "samtools_sort v0.2.0" echo "" echo "Sort SAM/BAM/CRAM file." echo "" @@ -556,10 +556,10 @@ 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="2024-09-12T13:23:16Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:11Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -695,7 +695,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_sort 0.2.0" + echo "samtools_sort v0.2.0" exit ;; --input) @@ -1035,7 +1035,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_sort:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_sort:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml index f85292ea..0a7210b7 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_stats" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -383,7 +383,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -401,11 +401,11 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -415,7 +415,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index 5aa676d2..c2f26a8f 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_stats 0.2.0 +# samtools_stats v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_stats 0.2.0" + echo "samtools_stats v0.2.0" echo "" echo "Reports alignment summary statistics for a BAM file." echo "" @@ -575,10 +575,10 @@ 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="2024-09-12T13:23:16Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:12Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -714,7 +714,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_stats 0.2.0" + echo "samtools_stats v0.2.0" exit ;; --input) @@ -1158,7 +1158,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_stats:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_stats:v0.2.0' fi # print dockerfile diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml index 836c41b6..386e4ad7 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_view" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -647,7 +647,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -665,11 +665,11 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -679,7 +679,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index d0b2ae30..a7a1a458 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_view 0.2.0 +# samtools_view v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_view 0.2.0" + echo "samtools_view v0.2.0" echo "" echo "Views and converts SAM/BAM/CRAM files." echo "" @@ -825,10 +825,10 @@ 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="2024-09-12T13:23:14Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:09Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -964,7 +964,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_view 0.2.0" + echo "samtools_view v0.2.0" exit ;; --input) @@ -1636,7 +1636,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_view:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/samtools/samtools_view:v0.2.0' fi # print dockerfile diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml index c7ef2b11..dcb48e12 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "seqtk_sample" namespace: "seqtk" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Jakub Majercik" roles: @@ -160,7 +160,7 @@ engines: id: "docker" image: "quay.io/biocontainers/seqtk:1.4--he4a0461_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" entrypoint: [] cmd: null @@ -173,11 +173,11 @@ build_info: output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -187,7 +187,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index 2d93d9c9..be7485a0 100755 --- a/target/executable/seqtk/seqtk_sample/seqtk_sample +++ b/target/executable/seqtk/seqtk_sample/seqtk_sample @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# seqtk_sample 0.2.0 +# seqtk_sample v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "seqtk_sample 0.2.0" + echo "seqtk_sample v0.2.0" echo "" echo "Subsamples sequences from FASTA/Q files." echo "" @@ -481,10 +481,10 @@ 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="2024-09-12T13:23:28Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:23Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -620,7 +620,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "seqtk_sample 0.2.0" + echo "seqtk_sample v0.2.0" exit ;; --input) @@ -760,7 +760,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/seqtk/seqtk_sample:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/seqtk/seqtk_sample:v0.2.0' fi # print dockerfile diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml index f81e9a22..50e0fc15 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "seqtk_subseq" namespace: "seqtk" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -179,7 +179,7 @@ engines: id: "docker" image: "quay.io/biocontainers/seqtk:1.4--he4a0461_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -196,11 +196,11 @@ build_info: output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -210,7 +210,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index 27922475..cfff812b 100755 --- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq +++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# seqtk_subseq 0.2.0 +# seqtk_subseq v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "seqtk_subseq 0.2.0" + echo "seqtk_subseq v0.2.0" echo "" echo "Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a" echo "name.lst (sequence ids file) or a reg.bed (genomic regions file)." @@ -491,10 +491,10 @@ 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="2024-09-12T13:23:27Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:23Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -630,7 +630,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "seqtk_subseq 0.2.0" + echo "seqtk_subseq v0.2.0" exit ;; --input) @@ -797,7 +797,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/seqtk/seqtk_subseq:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/seqtk/seqtk_subseq:v0.2.0' fi # print dockerfile diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml index a00e3a29..7fe0db4d 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_align_reads" namespace: "star" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Angela Oliveira Pisco" roles: @@ -2624,7 +2624,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -2663,11 +2663,11 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -2677,7 +2677,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index cbe464ff..8f205251 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# star_align_reads 0.2.0 +# star_align_reads v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_align_reads 0.2.0" + echo "star_align_reads v0.2.0" echo "" echo "Aligns reads to a reference genome using STAR." echo "" @@ -1920,10 +1920,10 @@ 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="2024-09-12T13:23:20Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:15Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -2059,7 +2059,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_align_reads 0.2.0" + echo "star_align_reads v0.2.0" exit ;; --run_rng_seed) @@ -4542,7 +4542,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/star/star_align_reads:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/star/star_align_reads:v0.2.0' fi # print dockerfile diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index b04babe7..a3e7c42e 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_genome_generate" namespace: "star" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -305,7 +305,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -333,11 +333,11 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -347,7 +347,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index 56e99286..38157dd4 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# star_genome_generate 0.2.0 +# star_genome_generate v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_genome_generate 0.2.0" + echo "star_genome_generate v0.2.0" echo "" echo "Create index for STAR" echo "" @@ -577,10 +577,10 @@ 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="2024-09-12T13:23:20Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:15Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -716,7 +716,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_genome_generate 0.2.0" + echo "star_genome_generate v0.2.0" exit ;; --genome_fasta_files) @@ -1012,7 +1012,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/star/star_genome_generate:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/star/star_genome_generate:v0.2.0' fi # print dockerfile diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml index bad69ea0..6755dded 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umi_tools_dedup" namespace: "umi_tools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -594,7 +594,7 @@ engines: id: "docker" image: "quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -611,11 +611,11 @@ 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" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -625,7 +625,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup index 546d71e9..51b321d9 100755 --- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup +++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# umi_tools_dedup 0.2.0 +# umi_tools_dedup v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "umi_tools_dedup 0.2.0" + echo "umi_tools_dedup v0.2.0" echo "" echo "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the" echo "read." @@ -770,10 +770,10 @@ 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="2024-09-12T13:23:18Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:13Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -909,7 +909,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umi_tools_dedup 0.2.0" + echo "umi_tools_dedup v0.2.0" exit ;; --input) @@ -1475,7 +1475,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/umi_tools/umi_tools_dedup:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/umi_tools/umi_tools_dedup:v0.2.0' fi # print dockerfile diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml index 54ab9ed6..0efb5c0e 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umi_tools_extract" namespace: "umi_tools" -version: "0.2.0" +version: "v0.2.0" argument_groups: - name: "Input" arguments: @@ -432,7 +432,7 @@ engines: id: "docker" image: "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -449,11 +449,11 @@ build_info: output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -463,7 +463,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract index ad067d9f..21f29cc8 100755 --- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract +++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# umi_tools_extract 0.2.0 +# umi_tools_extract v0.2.0 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "umi_tools_extract 0.2.0" + echo "umi_tools_extract v0.2.0" echo "" echo "Flexible removal of UMI sequences from fastq reads." echo "UMIs are removed and appended to the read name. Any other barcode, for example a" @@ -637,10 +637,10 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract" -LABEL org.opencontainers.image.created="2024-09-12T13:23:17Z" +LABEL org.opencontainers.image.created="2024-09-13T12:35:13Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="5526b3e939030daea80595fa98387b469329bbfa" -LABEL org.opencontainers.image.version="0.2.0" +LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5" +LABEL org.opencontainers.image.version="v0.2.0" VIASHDOCKER fi @@ -776,7 +776,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umi_tools_extract 0.2.0" + echo "umi_tools_extract v0.2.0" exit ;; --input) @@ -1189,7 +1189,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/umi_tools/umi_tools_extract:0.2.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/umi_tools/umi_tools_extract:v0.2.0' fi # print dockerfile diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml index 14a5457d..a0a473b9 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_bed2gff" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -218,7 +218,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -235,11 +235,11 @@ build_info: output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -249,7 +249,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index 40ed988a..e456ee1e 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -1,4 +1,4 @@ -// agat_convert_bed2gff 0.2.0 +// agat_convert_bed2gff v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_bed2gff", "namespace" : "agat", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3070,7 +3070,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3092,12 +3092,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_bed2gff", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3106,7 +3106,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3540,7 +3540,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_bed2gff", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_bed2gff/nextflow.config b/target/nextflow/agat/agat_convert_bed2gff/nextflow.config index d0abfb6b..610df73b 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/nextflow.config +++ b/target/nextflow/agat/agat_convert_bed2gff/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_bed2gff' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index b534591d..59e8dede 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_embl2gff" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -208,7 +208,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -225,11 +225,11 @@ build_info: output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -239,7 +239,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index ac0c9682..283b8e0d 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -1,4 +1,4 @@ -// agat_convert_embl2gff 0.2.0 +// agat_convert_embl2gff v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_embl2gff", "namespace" : "agat", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3063,7 +3063,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3085,12 +3085,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_embl2gff", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3099,7 +3099,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3536,7 +3536,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_embl2gff", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_embl2gff/nextflow.config b/target/nextflow/agat/agat_convert_embl2gff/nextflow.config index 5660e990..db5a62cb 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/nextflow.config +++ b/target/nextflow/agat/agat_convert_embl2gff/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_embl2gff' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'The script takes an EMBL file as input, and will translate it in gff format.\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 28cb1e30..b181013d 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gff2gtf" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -211,7 +211,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -228,11 +228,11 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -242,7 +242,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index a76022a2..e54a85e3 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -1,4 +1,4 @@ -// agat_convert_sp_gff2gtf 0.2.0 +// agat_convert_sp_gff2gtf v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_sp_gff2gtf", "namespace" : "agat", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3046,7 +3046,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3068,12 +3068,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3082,7 +3082,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3503,7 +3503,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_sp_gff2gtf", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow.config b/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow.config index 72b08431..163588af 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow.config +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_sp_gff2gtf' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'The script aims to convert any GTF/GFF file into a proper GTF file. Full\ninformation about the format can be found here:\nhttps://agat.readthedocs.io/en/latest/gxf.html You can choose among 7\ndifferent GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the\nversion selected the script will filter out the features that are not\naccepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene\npseudogene) will be converted into gene feature and every level2 feature\n(e.g mRNA ncRNA) will be converted into transcript feature. Using the\n"relax" option you will produce a GTF-like output keeping all original\nfeature types (3rd column). No modification will occur e.g. mRNA to\ntranscript.\n\nTo be fully GTF compliant all feature have a gene_id and a transcript_id\nattribute. The gene_id is unique identifier for the genomic source of\nthe transcript, which is used to group transcripts into genes. The\ntranscript_id is a unique identifier for the predicted transcript, which\nis used to group features into transcripts.\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index f01745fc..94cc894c 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gff2tsv" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -171,7 +171,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -188,11 +188,11 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -202,7 +202,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index 4e9e9e6f..aea60cc0 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -1,4 +1,4 @@ -// agat_convert_sp_gff2tsv 0.2.0 +// agat_convert_sp_gff2tsv v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_sp_gff2tsv", "namespace" : "agat", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3024,7 +3024,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3046,12 +3046,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3060,7 +3060,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3479,7 +3479,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_sp_gff2tsv", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow.config b/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow.config index 897aedaa..93439a39 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow.config +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_sp_gff2tsv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'The script aims to convert gtf/gff file into tabulated file. Attribute\'s\ntags from the 9th column become column titles.\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index a7631567..d77bb58e 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "agat_convert_sp_gxf2gxf" namespace: "agat" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Leïla Paquay" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -195,11 +195,11 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -209,7 +209,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index ba693e23..fe05ff2b 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -1,4 +1,4 @@ -// agat_convert_sp_gxf2gxf 0.2.0 +// agat_convert_sp_gxf2gxf v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "agat_convert_sp_gxf2gxf", "namespace" : "agat", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Leïla Paquay", @@ -3024,7 +3024,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3046,12 +3046,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3060,7 +3060,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3479,7 +3479,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/agat/agat_convert_sp_gxf2gxf", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow.config b/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow.config index 18b64ccd..11694179 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow.config +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'agat/agat_convert_sp_gxf2gxf' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'This script fixes and/or standardizes any GTF/GFF file into full sorted\nGTF/GFF file. It AGAT parser removes duplicate features, fixes\nduplicated IDs, adds missing ID and/or Parent attributes, deflates\nfactorized attributes (attributes with several parents are duplicated\nwith uniq ID), add missing features when possible (e.g. add exon if only\nCDS described, add UTR if CDS and exon described), fix feature locations\n(e.g. check exon is embedded in the parent features mRNA, gene), etc...\n\nAll AGAT\'s scripts with the _sp_ prefix use the AGAT parser, before to\nperform any supplementary task. So, it is not necessary to run this\nscript prior the use of any other _sp_ script.\n' author = 'Leïla Paquay' } diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index 8217fd3e..b4c880e1 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "arriba" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -688,7 +688,7 @@ engines: id: "docker" image: "quay.io/biocontainers/arriba:2.4.0--h0033a41_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -706,11 +706,11 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -720,7 +720,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index 5ee98bcc..9002f126 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -1,4 +1,4 @@ -// arriba 0.2.0 +// arriba v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "arriba", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3570,7 +3570,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/arriba:2.4.0--h0033a41_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3592,12 +3592,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/arriba", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3606,7 +3606,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4104,7 +4104,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/arriba", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "cpus" : 1, "tag" : "$id" diff --git a/target/nextflow/arriba/nextflow.config b/target/nextflow/arriba/nextflow.config index 826ff39a..2bb9eb7f 100644 --- a/target/nextflow/arriba/nextflow.config +++ b/target/nextflow/arriba/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'arriba' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Detect gene fusions from RNA-Seq data' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index 0354f8c4..b8f1f5c0 100644 --- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcftools_sort" namespace: "bcftools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -162,7 +162,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -185,11 +185,11 @@ build_info: output: "target/nextflow/bcftools/bcftools_sort" executable: "target/nextflow/bcftools/bcftools_sort/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -199,7 +199,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf index 62e80ab8..2cfb4b76 100644 --- a/target/nextflow/bcftools/bcftools_sort/main.nf +++ b/target/nextflow/bcftools/bcftools_sort/main.nf @@ -1,4 +1,4 @@ -// bcftools_sort 0.2.0 +// bcftools_sort v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bcftools_sort", "namespace" : "bcftools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3018,7 +3018,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3048,12 +3048,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_sort", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3062,7 +3062,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3487,7 +3487,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bcftools/bcftools_sort", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bcftools/bcftools_sort/nextflow.config b/target/nextflow/bcftools/bcftools_sort/nextflow.config index eb45701b..3f8b56d3 100644 --- a/target/nextflow/bcftools/bcftools_sort/nextflow.config +++ b/target/nextflow/bcftools/bcftools_sort/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bcftools/bcftools_sort' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Sorts VCF/BCF files.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 6aba9f98..1eb5edcd 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bcl_convert" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -386,7 +386,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -418,11 +418,11 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -432,7 +432,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index eb1c214c..4c068af2 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -1,4 +1,4 @@ -// bcl_convert 0.2.0 +// bcl_convert v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "bcl_convert", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Toni Verbeiren", @@ -3289,7 +3289,7 @@ meta = [ "id" : "docker", "image" : "debian:trixie-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3329,12 +3329,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3343,7 +3343,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3815,7 +3815,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bcl_convert", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bcl_convert/nextflow.config b/target/nextflow/bcl_convert/nextflow.config index 0f8797a3..20ea31b2 100644 --- a/target/nextflow/bcl_convert/nextflow.config +++ b/target/nextflow/bcl_convert/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bcl_convert' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n' author = 'Toni Verbeiren, Dorien Roosen' } diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index bfe7e16e..4452208b 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody_make_reference" namespace: "bd_rhapsody" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -243,7 +243,7 @@ engines: id: "docker" image: "bdgenomics/rhapsody:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -270,11 +270,11 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -284,7 +284,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf index 295ad3bb..3a81a5da 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -1,4 +1,4 @@ -// bd_rhapsody_make_reference 0.2.0 +// bd_rhapsody_make_reference v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bd_rhapsody_make_reference", "namespace" : "bd_rhapsody", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3104,7 +3104,7 @@ meta = [ "id" : "docker", "image" : "bdgenomics/rhapsody:2.2.1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3142,12 +3142,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3156,7 +3156,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3722,7 +3722,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bd_rhapsody/bd_rhapsody_make_reference", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow.config b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow.config index 365dc66f..700101d8 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow.config +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bd_rhapsody/bd_rhapsody_make_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'The Reference Files Generator creates an archive containing Genome Index\nand Transcriptome annotation files needed for the BD Rhapsody Sequencing\nAnalysis Pipeline. The app takes as input one or more FASTA and GTF files\nand produces a compressed archive in the form of a tar.gz file. The \narchive contains:\n\n- STAR index\n- Filtered GTF file\n' author = 'Robrecht Cannoodt, Weiwei Schultz' } diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index ca6fe156..f048d8eb 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bamtofastq" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -164,7 +164,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -187,11 +187,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -201,7 +201,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index 0a531f3a..ece1a816 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -1,4 +1,4 @@ -// bedtools_bamtofastq 0.2.0 +// bedtools_bamtofastq v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_bamtofastq", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3020,7 +3020,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3050,12 +3050,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtofastq", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3064,7 +3064,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3493,7 +3493,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_bamtofastq", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow.config b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow.config index 0fd48169..a784b41e 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow.config +++ b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_bamtofastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Conversion tool for extracting FASTQ records from sequence alignments in BAM format.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 32069829..573540b1 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bed12tobed6" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -176,11 +176,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_bed12tobed6" executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -190,7 +190,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf index 6f037a8e..7beca0aa 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf @@ -1,4 +1,4 @@ -// bedtools_bed12tobed6 0.2.0 +// bedtools_bed12tobed6 v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_bed12tobed6", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3005,7 +3005,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3035,12 +3035,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bed12tobed6", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3049,7 +3049,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3474,7 +3474,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_bed12tobed6", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow.config b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow.config index 014a4714..d4105da1 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow.config +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_bed12tobed6' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features.\nFor example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index 4e2e9304..630febb1 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_bedtobam" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -186,7 +186,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -214,11 +214,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -228,7 +228,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index 0154fffb..68aad721 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -1,4 +1,4 @@ -// bedtools_bedtobam 0.2.0 +// bedtools_bedtobam v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_bedtobam", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3044,7 +3044,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3083,12 +3083,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedtobam", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3097,7 +3097,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3529,7 +3529,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_bedtobam", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_bedtobam/nextflow.config b/target/nextflow/bedtools/bedtools_bedtobam/nextflow.config index 661578e0..934d2eaa 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/nextflow.config +++ b/target/nextflow/bedtools/bedtools_bedtobam/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_bedtobam' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Converts feature records (bed/gff/vcf) to BAM format.' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index 173d9a32..9663a47d 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_getfasta" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dries Schaumont" roles: @@ -209,7 +209,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -232,11 +232,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -246,7 +246,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index 00de8d13..6a668941 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -1,4 +1,4 @@ -// bedtools_getfasta 0.2.0 +// bedtools_getfasta v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_getfasta", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Dries Schaumont", @@ -3056,7 +3056,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3086,12 +3086,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3100,7 +3100,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3541,7 +3541,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_getfasta", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_getfasta/nextflow.config b/target/nextflow/bedtools/bedtools_getfasta/nextflow.config index f61b17d2..6a0dd3da 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/nextflow.config +++ b/target/nextflow/bedtools/bedtools_getfasta/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_getfasta' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.' author = 'Dries Schaumont' } diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml index c606163f..f1fe0ff3 100644 --- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_groupby" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -250,7 +250,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -273,11 +273,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_groupby" executable: "target/nextflow/bedtools/bedtools_groupby/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -287,7 +287,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf index 08eaacb7..f720f0ef 100644 --- a/target/nextflow/bedtools/bedtools_groupby/main.nf +++ b/target/nextflow/bedtools/bedtools_groupby/main.nf @@ -1,4 +1,4 @@ -// bedtools_groupby 0.2.0 +// bedtools_groupby v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_groupby", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3100,7 +3100,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3130,12 +3130,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_groupby", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3144,7 +3144,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3599,7 +3599,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_groupby", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_groupby/nextflow.config b/target/nextflow/bedtools/bedtools_groupby/nextflow.config index c4a24801..d29e78cf 100644 --- a/target/nextflow/bedtools/bedtools_groupby/nextflow.config +++ b/target/nextflow/bedtools/bedtools_groupby/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_groupby' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Summarizes a dataset column based upon common column groupings. \nAkin to the SQL "group by" command.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index 16cda546..b9a58b77 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_intersect" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -387,7 +387,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -410,11 +410,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -424,7 +424,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index 0a2c9580..c6b09772 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -1,4 +1,4 @@ -// bedtools_intersect 0.2.0 +// bedtools_intersect v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_intersect", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3252,7 +3252,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3282,12 +3282,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_intersect", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3296,7 +3296,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3801,7 +3801,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_intersect", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_intersect/nextflow.config b/target/nextflow/bedtools/bedtools_intersect/nextflow.config index 1b08d2b2..05965590 100644 --- a/target/nextflow/bedtools/bedtools_intersect/nextflow.config +++ b/target/nextflow/bedtools/bedtools_intersect/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_intersect' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'bedtools intersect allows one to screen for overlaps between two sets of genomic features. \nMoreover, it allows one to have fine control as to how the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF and BAM files as input.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml index b9d4b930..1a655174 100644 --- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_links" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -187,7 +187,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -210,11 +210,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_links" executable: "target/nextflow/bedtools/bedtools_links/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -224,7 +224,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf index ea91e5f5..b51d4a52 100644 --- a/target/nextflow/bedtools/bedtools_links/main.nf +++ b/target/nextflow/bedtools/bedtools_links/main.nf @@ -1,4 +1,4 @@ -// bedtools_links 0.2.0 +// bedtools_links v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_links", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3043,7 +3043,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3073,12 +3073,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_links", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3087,7 +3087,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3513,7 +3513,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_links", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_links/nextflow.config b/target/nextflow/bedtools/bedtools_links/nextflow.config index 33eb36ff..b7408642 100644 --- a/target/nextflow/bedtools/bedtools_links/nextflow.config +++ b/target/nextflow/bedtools/bedtools_links/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_links' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. \nThis is useful for cases when one wants to manually inspect through a large set of annotations or features.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml index 1f3fa6de..592c9a22 100644 --- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_merge" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -256,7 +256,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_merge" executable: "target/nextflow/bedtools/bedtools_merge/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -293,7 +293,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf index 6cd59548..dcc26b55 100644 --- a/target/nextflow/bedtools/bedtools_merge/main.nf +++ b/target/nextflow/bedtools/bedtools_merge/main.nf @@ -1,4 +1,4 @@ -// bedtools_merge 0.2.0 +// bedtools_merge v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_merge", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3104,7 +3104,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3134,12 +3134,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_merge", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3148,7 +3148,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3602,7 +3602,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_merge", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_merge/nextflow.config b/target/nextflow/bedtools/bedtools_merge/nextflow.config index a7523a1c..ce74b742 100644 --- a/target/nextflow/bedtools/bedtools_merge/nextflow.config +++ b/target/nextflow/bedtools/bedtools_merge/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_merge' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Merges overlapping BED/GFF/VCF entries into a single interval.\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index a5240910..398fb731 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedtools_sort" namespace: "bedtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -199,7 +199,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -222,11 +222,11 @@ build_info: output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -236,7 +236,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index 156f6127..bc232851 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -1,4 +1,4 @@ -// bedtools_sort 0.2.0 +// bedtools_sort v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedtools_sort", "namespace" : "bedtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3062,7 +3062,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3092,12 +3092,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sort", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3106,7 +3106,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3558,7 +3558,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bedtools/bedtools_sort", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools/bedtools_sort/nextflow.config b/target/nextflow/bedtools/bedtools_sort/nextflow.config index 81c566cf..5c6ffab4 100644 --- a/target/nextflow/bedtools/bedtools_sort/nextflow.config +++ b/target/nextflow/bedtools/bedtools_sort/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools/bedtools_sort' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Sorts a feature file (bed/gff/vcf) by chromosome and other criteria.' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index 04b03d38..b160ef5f 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_download_datasets" namespace: "busco" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -141,7 +141,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -158,11 +158,11 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -172,7 +172,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index 9e13a282..0270877a 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -1,4 +1,4 @@ -// busco_download_datasets 0.2.0 +// busco_download_datasets v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "busco_download_datasets", "namespace" : "busco", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -2989,7 +2989,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3011,12 +3011,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3025,7 +3025,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3448,7 +3448,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/busco/busco_download_datasets", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/busco/busco_download_datasets/nextflow.config b/target/nextflow/busco/busco_download_datasets/nextflow.config index 98e282f1..b4b4b4a4 100644 --- a/target/nextflow/busco/busco_download_datasets/nextflow.config +++ b/target/nextflow/busco/busco_download_datasets/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'busco/busco_download_datasets' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Downloads available busco datasets' author = 'Dorien Roosen' } diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index 4632e840..b79be5d5 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_list_datasets" namespace: "busco" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -128,7 +128,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -145,11 +145,11 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -159,7 +159,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index b077980e..31d967b1 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -1,4 +1,4 @@ -// busco_list_datasets 0.2.0 +// busco_list_datasets v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "busco_list_datasets", "namespace" : "busco", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -2975,7 +2975,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -2997,12 +2997,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3011,7 +3011,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3425,7 +3425,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/busco/busco_list_datasets", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/busco/busco_list_datasets/nextflow.config b/target/nextflow/busco/busco_list_datasets/nextflow.config index c41da094..e96befa8 100644 --- a/target/nextflow/busco/busco_list_datasets/nextflow.config +++ b/target/nextflow/busco/busco_list_datasets/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'busco/busco_list_datasets' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Lists the available busco datasets' author = 'Dorien Roosen' } diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index 893c319a..6b7b051f 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "busco_run" namespace: "busco" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -406,7 +406,7 @@ engines: id: "docker" image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -423,11 +423,11 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -437,7 +437,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index 438de8c2..b5110fc6 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -1,4 +1,4 @@ -// busco_run 0.2.0 +// busco_run v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "busco_run", "namespace" : "busco", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -3287,7 +3287,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3309,12 +3309,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3323,7 +3323,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3835,7 +3835,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/busco/busco_run", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/busco/busco_run/nextflow.config b/target/nextflow/busco/busco_run/nextflow.config index 93634eaf..7a4379d6 100644 --- a/target/nextflow/busco/busco_run/nextflow.config +++ b/target/nextflow/busco/busco_run/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'busco/busco_run' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Assessment of genome assembly and annotation completeness with single copy orthologs' author = 'Dorien Roosen' } diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index 259949cd..70a7c69d 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "cutadapt" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -718,7 +718,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "python" @@ -740,11 +740,11 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -754,7 +754,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index 4468bef5..a84d5cab 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -1,4 +1,4 @@ -// cutadapt 0.2.0 +// cutadapt v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "cutadapt", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Toni Verbeiren", @@ -3589,7 +3589,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3619,12 +3619,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cutadapt", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3633,7 +3633,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4346,7 +4346,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/cutadapt", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/cutadapt/nextflow.config b/target/nextflow/cutadapt/nextflow.config index 2aa5ef3b..4c7cf1bf 100644 --- a/target/nextflow/cutadapt/nextflow.config +++ b/target/nextflow/cutadapt/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'cutadapt' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Cutadapt removes adapter sequences from high-throughput sequencing reads.\n' author = 'Toni Verbeiren' } diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index 71b2d68f..b503611e 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "falco" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Toni Verbeiren" roles: @@ -287,7 +287,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -317,11 +317,11 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -331,7 +331,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index b0bdf8e2..cebc361b 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -1,4 +1,4 @@ -// falco 0.2.0 +// falco v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "falco", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Toni Verbeiren", @@ -3131,7 +3131,7 @@ meta = [ "id" : "docker", "image" : "debian:trixie-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3170,12 +3170,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/falco", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3184,7 +3184,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3630,7 +3630,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/falco", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/falco/nextflow.config b/target/nextflow/falco/nextflow.config index 9251d236..af116d2a 100644 --- a/target/nextflow/falco/nextflow.config +++ b/target/nextflow/falco/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'falco' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'A C++ drop-in replacement of FastQC to assess the quality of sequence read data' author = 'Toni Verbeiren' } diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index 401926d6..ff26464a 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastp" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Robrecht Cannoodt" roles: @@ -1066,7 +1066,7 @@ engines: id: "docker" image: "quay.io/biocontainers/fastp:0.23.4--hadf994f_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -1083,11 +1083,11 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -1097,7 +1097,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index 571d8b58..6c942989 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -1,4 +1,4 @@ -// fastp 0.2.0 +// fastp v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "fastp", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -4001,7 +4001,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/fastp:0.23.4--hadf994f_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -4023,12 +4023,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -4037,7 +4037,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4632,7 +4632,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/fastp", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/fastp/nextflow.config b/target/nextflow/fastp/nextflow.config index 3e1cb67e..8c035703 100644 --- a/target/nextflow/fastp/nextflow.config +++ b/target/nextflow/fastp/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'fastp' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...).\n\nFeatures:\n\n - comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents...)\n - filter out bad reads (too low quality, too short, or too many N...)\n - cut low quality bases for per read in its 5\' and 3\' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).\n - trim all reads in front and tail\n - cut adapters. Adapter sequences can be automatically detected, which means you don\'t have to input the adapter sequences to trim them.\n - correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality\n - trim polyG in 3\' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3\' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n - preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name.\n - report JSON format result for further interpreting.\n - visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).\n - split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.\n - support long reads (data from PacBio / Nanopore devices).\n - support reading from STDIN and writing to STDOUT\n - support interleaved input\n - support ultra-fast FASTQ-level deduplication\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index eae52449..c6916648 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastqc" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -323,7 +323,7 @@ engines: id: "docker" image: "biocontainers/fastqc:v0.11.9_cv8" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -340,11 +340,11 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -354,7 +354,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 8949a8b2..33e37e1f 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -1,4 +1,4 @@ -// fastqc 0.2.0 +// fastqc v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "fastqc", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3160,7 +3160,7 @@ meta = [ "id" : "docker", "image" : "biocontainers/fastqc:v0.11.9_cv8", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3182,12 +3182,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3196,7 +3196,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3704,7 +3704,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/fastqc", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/fastqc/nextflow.config b/target/nextflow/fastqc/nextflow.config index 780f1235..3b23f591 100644 --- a/target/nextflow/fastqc/nextflow.config +++ b/target/nextflow/fastqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'fastqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'FastQC - A high throughput sequence QC analysis tool.' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 79e96a83..3a72e207 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "featurecounts" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -627,7 +627,7 @@ engines: id: "docker" image: "quay.io/biocontainers/subread:2.0.6--he4a0461_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -645,11 +645,11 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -659,7 +659,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index f39e7133..1be82887 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -1,4 +1,4 @@ -// featurecounts 0.2.0 +// featurecounts v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "featurecounts", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3527,7 +3527,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/subread:2.0.6--he4a0461_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3549,12 +3549,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3563,7 +3563,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4115,7 +4115,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/featurecounts", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/featurecounts/nextflow.config b/target/nextflow/featurecounts/nextflow.config index 346054a3..02f0e8bc 100644 --- a/target/nextflow/featurecounts/nextflow.config +++ b/target/nextflow/featurecounts/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'featurecounts' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.\n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index 8fdae94e..9603e2c3 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gffread" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -668,7 +668,7 @@ engines: id: "docker" image: "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -685,11 +685,11 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -699,7 +699,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index 4fa0e80f..04ee10d5 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -1,4 +1,4 @@ -// gffread 0.2.0 +// gffread v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "gffread", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3584,7 +3584,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3606,12 +3606,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3620,7 +3620,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4218,7 +4218,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/gffread", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/gffread/nextflow.config b/target/nextflow/gffread/nextflow.config index 18606584..c0fafa43 100644 --- a/target/nextflow/gffread/nextflow.config +++ b/target/nextflow/gffread/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'gffread' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Validate, filter, convert and perform various other operations on GFF files.' author = 'Emma Rousseau' } diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index e2d38a49..79564d8f 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lofreq_call" namespace: "lofreq" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Kai Waldrant" roles: @@ -489,7 +489,7 @@ engines: id: "docker" image: "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -507,11 +507,11 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -521,7 +521,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index f35859df..89872922 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -1,4 +1,4 @@ -// lofreq_call 0.2.0 +// lofreq_call v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "lofreq_call", "namespace" : "lofreq", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Kai Waldrant", @@ -3392,7 +3392,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3414,12 +3414,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3428,7 +3428,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3934,7 +3934,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/lofreq/lofreq_call", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/lofreq/lofreq_call/nextflow.config b/target/nextflow/lofreq/lofreq_call/nextflow.config index d424c8ec..8169abe6 100644 --- a/target/nextflow/lofreq/lofreq_call/nextflow.config +++ b/target/nextflow/lofreq/lofreq_call/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'lofreq/lofreq_call' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Call variants from a BAM file.\n\nLoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.\n\nLoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent or Pacbio) since no machine- or sequencing-technology dependent thresholds are used. It automatically adapts to changes in coverage and sequencing quality and can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or somatic data.\n\nLoFreq* is very sensitive; most notably, it is able to predict variants below the average base-call quality (i.e. sequencing error rate). Each variant call is assigned a p-value which allows for rigorous false positive control. Even though it uses no approximations or heuristics, it is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel implementation. LoFreq* is generic and fast enough to be applied to high-coverage data and large genomes. On a single processor it takes a minute to analyze Dengue genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage human exome dataset.\n' author = 'Kai Waldrant' } diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index 5a4f21b5..fb88b1bc 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lofreq_indelqual" namespace: "lofreq" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Kai Waldrant" roles: @@ -197,7 +197,7 @@ engines: id: "docker" image: "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -215,11 +215,11 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -229,7 +229,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index 7c8bb8ce..ddc0b99c 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -1,4 +1,4 @@ -// lofreq_indelqual 0.2.0 +// lofreq_indelqual v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "lofreq_indelqual", "namespace" : "lofreq", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Kai Waldrant", @@ -3055,7 +3055,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3077,12 +3077,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3091,7 +3091,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3521,7 +3521,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/lofreq/lofreq_indelqual", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/lofreq/lofreq_indelqual/nextflow.config b/target/nextflow/lofreq/lofreq_indelqual/nextflow.config index 4a81e6c2..c6050951 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/nextflow.config +++ b/target/nextflow/lofreq/lofreq_indelqual/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'lofreq/lofreq_indelqual' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK\'s BQSR (>=2) If that\'s not possible, use this subcommand.\nThe command has two modes: \'uniform\' and \'dindel\':\n- \'uniform\' will assign a given value uniformly, whereas\n- \'dindel\' will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n' author = 'Kai Waldrant' } diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index 245ef5c6..4223169a 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "multiqc" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -433,7 +433,7 @@ engines: id: "docker" image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -456,11 +456,11 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -470,7 +470,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index 7e0282b5..be592a2d 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -1,4 +1,4 @@ -// multiqc 0.2.0 +// multiqc v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "multiqc", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -3335,7 +3335,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3366,12 +3366,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3380,7 +3380,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3961,7 +3961,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/multiqc", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/multiqc/nextflow.config b/target/nextflow/multiqc/nextflow.config index 2fe3a6a0..2400f6ac 100644 --- a/target/nextflow/multiqc/nextflow.config +++ b/target/nextflow/multiqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'multiqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index a825f32e..d0a4febc 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "pear" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Kai Waldrant" roles: @@ -380,7 +380,7 @@ engines: id: "docker" image: "quay.io/biocontainers/pear:0.9.6--h9d449c0_10" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -398,11 +398,11 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -412,7 +412,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index 2b8ae602..e5c73419 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -1,4 +1,4 @@ -// pear 0.2.0 +// pear v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2808,7 +2808,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "pear", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Kai Waldrant", @@ -3237,7 +3237,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/pear:0.9.6--h9d449c0_10", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3259,12 +3259,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/pear", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3273,7 +3273,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3764,7 +3764,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/pear", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/pear/nextflow.config b/target/nextflow/pear/nextflow.config index e4633bd2..77f064e9 100644 --- a/target/nextflow/pear/nextflow.config +++ b/target/nextflow/pear/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'pear' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.\n\nPEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.\n' author = 'Kai Waldrant' } diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index 29bdd909..b5a4955e 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "qualimap_rnaseq" namespace: "qualimap" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Dorien Roosen" roles: @@ -247,7 +247,7 @@ engines: id: "docker" image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -264,11 +264,11 @@ build_info: output: "target/nextflow/qualimap/qualimap_rnaseq" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -278,7 +278,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf index b2cb1e41..b79020d6 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -1,4 +1,4 @@ -// qualimap_rnaseq 0.2.0 +// qualimap_rnaseq v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "qualimap_rnaseq", "namespace" : "qualimap", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Dorien Roosen", @@ -3107,7 +3107,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/qualimap:2.3--hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3129,12 +3129,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/qualimap/qualimap_rnaseq", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3143,7 +3143,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3614,7 +3614,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/qualimap/qualimap_rnaseq", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config b/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config index 906a2486..bb4b1f17 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config +++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qualimap/qualimap_rnaseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Qualimap RNA-seq QC reports quality control metrics and bias estimations \nwhich are specific for whole transcriptome sequencing, including reads genomic \norigin, junction analysis, transcript coverage and 5’-3’ bias computation.\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 76883ee3..30c9243f 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rsem_prepare_reference" namespace: "rsem" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -352,7 +352,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -416,11 +416,11 @@ build_info: output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -430,7 +430,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf index 3fd602ed..43864736 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf @@ -1,4 +1,4 @@ -// rsem_prepare_reference 0.2.0 +// rsem_prepare_reference v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rsem_prepare_reference", "namespace" : "rsem", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3185,7 +3185,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3245,12 +3245,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3259,7 +3259,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3731,7 +3731,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/rsem/rsem_prepare_reference", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rsem/rsem_prepare_reference/nextflow.config b/target/nextflow/rsem/rsem_prepare_reference/nextflow.config index 02146110..07266bba 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/nextflow.config +++ b/target/nextflow/rsem/rsem_prepare_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rsem/rsem_prepare_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. This component prepares transcript references for RSEM.\n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index f4b3e353..307951a7 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "salmon_index" namespace: "salmon" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -260,7 +260,7 @@ engines: id: "docker" image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -277,11 +277,11 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -291,7 +291,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index 6633d73b..3cfeb696 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -1,4 +1,4 @@ -// salmon_index 0.2.0 +// salmon_index v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "salmon_index", "namespace" : "salmon", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3107,7 +3107,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/salmon:1.10.2--hecfa306_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3129,12 +3129,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3143,7 +3143,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3619,7 +3619,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/salmon/salmon_index", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/salmon/salmon_index/nextflow.config b/target/nextflow/salmon/salmon_index/nextflow.config index d036a17d..230622c9 100644 --- a/target/nextflow/salmon/salmon_index/nextflow.config +++ b/target/nextflow/salmon/salmon_index/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'salmon/salmon_index' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. This component creates a salmon index for the transcriptome to use Salmon in the mapping-based mode. It is generally recommend that you build a decoy-aware transcriptome file. This is done using the entire genome of the organism as the decoy sequence by concatenating the genome to the end of the transcriptome to be indexed and populating the decoys.txt file with the chromosome names.\n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index 2e84d6c5..fffba6ce 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "salmon_quant" namespace: "salmon" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -1156,7 +1156,7 @@ engines: id: "docker" image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -1173,11 +1173,11 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -1187,7 +1187,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index 4c415267..074d4fba 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -1,4 +1,4 @@ -// salmon_quant 0.2.0 +// salmon_quant v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "salmon_quant", "namespace" : "salmon", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3942,7 +3942,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/salmon:1.10.2--hecfa306_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3964,12 +3964,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3978,7 +3978,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4634,7 +4634,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/salmon/salmon_quant", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/salmon/salmon_quant/nextflow.config b/target/nextflow/salmon/salmon_quant/nextflow.config index 34252791..fcf59f97 100644 --- a/target/nextflow/salmon/salmon_quant/nextflow.config +++ b/target/nextflow/salmon/salmon_quant/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'salmon/salmon_quant' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. \n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index 8907edb3..f19a100c 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_collate" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -246,7 +246,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -264,11 +264,11 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -278,7 +278,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index 60b6acd3..9dd85f5d 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -1,4 +1,4 @@ -// samtools_collate 0.2.0 +// samtools_collate v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_collate", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3118,7 +3118,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3140,12 +3140,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3154,7 +3154,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3601,7 +3601,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_collate", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_collate/nextflow.config b/target/nextflow/samtools/samtools_collate/nextflow.config index 29f6c620..ac02ac86 100644 --- a/target/nextflow/samtools/samtools_collate/nextflow.config +++ b/target/nextflow/samtools/samtools_collate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_collate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Shuffles and groups reads in SAM/BAM/CRAM files together by their names.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index 721d15f3..9d2dbc95 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_faidx" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -225,7 +225,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -243,11 +243,11 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -257,7 +257,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index 201839f3..4db6cac3 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -1,4 +1,4 @@ -// samtools_faidx 0.2.0 +// samtools_faidx v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_faidx", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3090,7 +3090,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3112,12 +3112,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3126,7 +3126,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3567,7 +3567,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_faidx", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_faidx/nextflow.config b/target/nextflow/samtools/samtools_faidx/nextflow.config index 5955ef93..e23a353d 100644 --- a/target/nextflow/samtools/samtools_faidx/nextflow.config +++ b/target/nextflow/samtools/samtools_faidx/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_faidx' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Indexes FASTA files to enable random access to fasta and fastq files.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index 5f15bdda..e860f3f0 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_fasta" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -415,7 +415,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -433,11 +433,11 @@ build_info: output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -447,7 +447,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index 10bba4d7..0fde4203 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -1,4 +1,4 @@ -// samtools_fasta 0.2.0 +// samtools_fasta v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_fasta", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3282,7 +3282,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3304,12 +3304,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3318,7 +3318,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3803,7 +3803,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_fasta", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_fasta/nextflow.config b/target/nextflow/samtools/samtools_fasta/nextflow.config index 1d278ef7..12ad35c6 100644 --- a/target/nextflow/samtools/samtools_fasta/nextflow.config +++ b/target/nextflow/samtools/samtools_fasta/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_fasta' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Converts a SAM, BAM or CRAM to FASTA format.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index ba2532e3..fd2be83a 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_fastq" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -415,7 +415,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -433,11 +433,11 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -447,7 +447,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index fd4314fe..8b1044a0 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -1,4 +1,4 @@ -// samtools_fastq 0.2.0 +// samtools_fastq v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_fastq", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3282,7 +3282,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3304,12 +3304,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3318,7 +3318,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3803,7 +3803,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_fastq", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_fastq/nextflow.config b/target/nextflow/samtools/samtools_fastq/nextflow.config index 9fff574e..059094d4 100644 --- a/target/nextflow/samtools/samtools_fastq/nextflow.config +++ b/target/nextflow/samtools/samtools_fastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_fastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Converts a SAM, BAM or CRAM to FASTQ format.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 85c50eac..38551657 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_flagstat" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -155,7 +155,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -173,11 +173,11 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -187,7 +187,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index 4e8d8e99..53551c00 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -1,4 +1,4 @@ -// samtools_flagstat 0.2.0 +// samtools_flagstat v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_flagstat", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3006,7 +3006,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3028,12 +3028,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3042,7 +3042,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3463,7 +3463,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_flagstat", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_flagstat/nextflow.config b/target/nextflow/samtools/samtools_flagstat/nextflow.config index 17007f7c..b86e4a75 100644 --- a/target/nextflow/samtools/samtools_flagstat/nextflow.config +++ b/target/nextflow/samtools/samtools_flagstat/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_flagstat' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index 48743292..3b7a698f 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_idxstats" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -165,7 +165,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -183,11 +183,11 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -197,7 +197,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index 15ce9495..c0a1257f 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -1,4 +1,4 @@ -// samtools_idxstats 0.2.0 +// samtools_idxstats v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_idxstats", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3018,7 +3018,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3040,12 +3040,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3054,7 +3054,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3473,7 +3473,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_idxstats", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_idxstats/nextflow.config b/target/nextflow/samtools/samtools_idxstats/nextflow.config index c53aaa5d..5829e7cf 100644 --- a/target/nextflow/samtools/samtools_idxstats/nextflow.config +++ b/target/nextflow/samtools/samtools_idxstats/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_idxstats' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Reports alignment summary statistics for a BAM file.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index 36e112f3..31a2a95a 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_index" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -171,7 +171,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -189,11 +189,11 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -203,7 +203,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index d8b6b241..af7a6e8d 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -1,4 +1,4 @@ -// samtools_index 0.2.0 +// samtools_index v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_index", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3031,7 +3031,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3053,12 +3053,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3067,7 +3067,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3497,7 +3497,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_index", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_index/nextflow.config b/target/nextflow/samtools/samtools_index/nextflow.config index 0ce06ea1..ea5a5996 100644 --- a/target/nextflow/samtools/samtools_index/nextflow.config +++ b/target/nextflow/samtools/samtools_index/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_index' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Index SAM/BAM/CRAM files.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index a37efeb4..d9e93a70 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_sort" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -314,7 +314,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -332,11 +332,11 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -346,7 +346,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index 7525e025..4b698e34 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -1,4 +1,4 @@ -// samtools_sort 0.2.0 +// samtools_sort v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_sort", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3203,7 +3203,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3225,12 +3225,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3239,7 +3239,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3717,7 +3717,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_sort", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_sort/nextflow.config b/target/nextflow/samtools/samtools_sort/nextflow.config index ea64c8c9..005ab61f 100644 --- a/target/nextflow/samtools/samtools_sort/nextflow.config +++ b/target/nextflow/samtools/samtools_sort/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_sort' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Sort SAM/BAM/CRAM file.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index ee7dd489..f1e1e329 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_stats" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -383,7 +383,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -401,11 +401,11 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -415,7 +415,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index 1f8595f4..58c15508 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -1,4 +1,4 @@ -// samtools_stats 0.2.0 +// samtools_stats v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_stats", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3273,7 +3273,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3295,12 +3295,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3309,7 +3309,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3779,7 +3779,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_stats", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_stats/nextflow.config b/target/nextflow/samtools/samtools_stats/nextflow.config index 8b99052a..70ea9cf4 100644 --- a/target/nextflow/samtools/samtools_stats/nextflow.config +++ b/target/nextflow/samtools/samtools_stats/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_stats' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Reports alignment summary statistics for a BAM file.' author = 'Emma Rousseau' } diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index 0c2c0ad4..815cd5fc 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_view" namespace: "samtools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -647,7 +647,7 @@ engines: id: "docker" image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -665,11 +665,11 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -679,7 +679,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index db7caab5..cb5b6f86 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -1,4 +1,4 @@ -// samtools_view 0.2.0 +// samtools_view v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_view", "namespace" : "samtools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3454,7 +3454,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3476,12 +3476,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3490,7 +3490,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4021,7 +4021,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/samtools/samtools_view", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/samtools/samtools_view/nextflow.config b/target/nextflow/samtools/samtools_view/nextflow.config index d8931428..66da9a21 100644 --- a/target/nextflow/samtools/samtools_view/nextflow.config +++ b/target/nextflow/samtools/samtools_view/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'samtools/samtools_view' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Views and converts SAM/BAM/CRAM files.' author = 'Emma Rousseau' } diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index 6cf7ed30..38ad5370 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "seqtk_sample" namespace: "seqtk" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Jakub Majercik" roles: @@ -160,7 +160,7 @@ engines: id: "docker" image: "quay.io/biocontainers/seqtk:1.4--he4a0461_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" entrypoint: [] cmd: null @@ -173,11 +173,11 @@ build_info: output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -187,7 +187,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index 2170955f..a65557b1 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -1,4 +1,4 @@ -// seqtk_sample 0.2.0 +// seqtk_sample v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "seqtk_sample", "namespace" : "seqtk", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Jakub Majercik", @@ -3016,7 +3016,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/seqtk:1.4--he4a0461_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/" }, { @@ -3030,12 +3030,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3044,7 +3044,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3467,7 +3467,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/seqtk/seqtk_sample", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/seqtk/seqtk_sample/nextflow.config b/target/nextflow/seqtk/seqtk_sample/nextflow.config index abd614f8..d1989f58 100644 --- a/target/nextflow/seqtk/seqtk_sample/nextflow.config +++ b/target/nextflow/seqtk/seqtk_sample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'seqtk/seqtk_sample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Subsamples sequences from FASTA/Q files.' author = 'Jakub Majercik' } diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index 115571b9..0da64890 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "seqtk_subseq" namespace: "seqtk" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -179,7 +179,7 @@ engines: id: "docker" image: "quay.io/biocontainers/seqtk:1.4--he4a0461_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -196,11 +196,11 @@ build_info: output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -210,7 +210,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index a2554f16..29bf723b 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -1,4 +1,4 @@ -// seqtk_subseq 0.2.0 +// seqtk_subseq v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "seqtk_subseq", "namespace" : "seqtk", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3038,7 +3038,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/seqtk:1.4--he4a0461_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3060,12 +3060,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3074,7 +3074,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3502,7 +3502,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/seqtk/seqtk_subseq", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/seqtk/seqtk_subseq/nextflow.config b/target/nextflow/seqtk/seqtk_subseq/nextflow.config index 20088033..63c2e8d8 100644 --- a/target/nextflow/seqtk/seqtk_subseq/nextflow.config +++ b/target/nextflow/seqtk/seqtk_subseq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'seqtk/seqtk_subseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a name.lst (sequence ids file) or a reg.bed (genomic regions file).\n' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index caf1001d..90e0e245 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_align_reads" namespace: "star" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Angela Oliveira Pisco" roles: @@ -2624,7 +2624,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -2663,11 +2663,11 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -2677,7 +2677,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index a205d8a2..a4d7acbd 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -1,4 +1,4 @@ -// star_align_reads 0.2.0 +// star_align_reads v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "star_align_reads", "namespace" : "star", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -4570,7 +4570,7 @@ meta = [ { "type" : "integer", "name" : "--seed_split_min", - "description" : "min length of the seed seque''' + '''nces split by Ns or mate gap", + "description" : "min length of the seed sequ''' + '''ences split by Ns or mate gap", "info" : { "orig_name" : "--seedSplitMin" }, @@ -5894,7 +5894,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -5943,12 +5943,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -5957,7 +5957,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -6671,7 +6671,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/star/star_align_reads", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/star/star_align_reads/nextflow.config b/target/nextflow/star/star_align_reads/nextflow.config index 9406e869..e0452727 100644 --- a/target/nextflow/star/star_align_reads/nextflow.config +++ b/target/nextflow/star/star_align_reads/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'star/star_align_reads' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Aligns reads to a reference genome using STAR.\n' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index 0280082e..251fe74f 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_genome_generate" namespace: "star" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Sai Nirmayi Yasa" roles: @@ -305,7 +305,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -333,11 +333,11 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -347,7 +347,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index 68618010..b73db0f3 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -1,4 +1,4 @@ -// star_genome_generate 0.2.0 +// star_genome_generate v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "star_genome_generate", "namespace" : "star", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Sai Nirmayi Yasa", @@ -3163,7 +3163,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3195,12 +3195,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3209,7 +3209,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3662,7 +3662,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/star/star_genome_generate", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/star/star_genome_generate/nextflow.config b/target/nextflow/star/star_genome_generate/nextflow.config index 19e916a3..ebbf1bbe 100644 --- a/target/nextflow/star/star_genome_generate/nextflow.config +++ b/target/nextflow/star/star_genome_generate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'star/star_genome_generate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Create index for STAR\n' author = 'Sai Nirmayi Yasa' } diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml index f7d709cd..fd503d29 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umi_tools_dedup" namespace: "umi_tools" -version: "0.2.0" +version: "v0.2.0" authors: - name: "Emma Rousseau" roles: @@ -594,7 +594,7 @@ engines: id: "docker" image: "quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -611,11 +611,11 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -625,7 +625,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index 8e92cce9..45b9f098 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -1,4 +1,4 @@ -// umi_tools_dedup 0.2.0 +// umi_tools_dedup v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "umi_tools_dedup", "namespace" : "umi_tools", - "version" : "0.2.0", + "version" : "v0.2.0", "authors" : [ { "name" : "Emma Rousseau", @@ -3465,7 +3465,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3487,12 +3487,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3501,7 +3501,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -4034,7 +4034,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/umi_tools/umi_tools_dedup", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/umi_tools/umi_tools_dedup/nextflow.config b/target/nextflow/umi_tools/umi_tools_dedup/nextflow.config index 4a9124a0..10e2cc5e 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/nextflow.config +++ b/target/nextflow/umi_tools/umi_tools_dedup/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'umi_tools/umi_tools_dedup' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.\n' author = 'Emma Rousseau' } diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index 5807149d..ef8d1db3 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umi_tools_extract" namespace: "umi_tools" -version: "0.2.0" +version: "v0.2.0" argument_groups: - name: "Input" arguments: @@ -432,7 +432,7 @@ engines: id: "docker" image: "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2" target_registry: "images.viash-hub.com" - target_tag: "0.2.0" + target_tag: "v0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -449,11 +449,11 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.0" - git_commit: "5526b3e939030daea80595fa98387b469329bbfa" - git_remote: "https://github.com/viash-hub/biobox" + git_commit: "7e530218844c373048bc33de58f021b6460642e5" + git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" package_config: name: "biobox" - version: "0.2.0" + version: "v0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null viash_version: "0.9.0" @@ -463,7 +463,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := '0.2.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index 6bc9d6a0..6fc55be5 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -1,4 +1,4 @@ -// umi_tools_extract 0.2.0 +// umi_tools_extract v0.2.0 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "umi_tools_extract", "namespace" : "umi_tools", - "version" : "0.2.0", + "version" : "v0.2.0", "argument_groups" : [ { "name" : "Input", @@ -3294,7 +3294,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2", "target_registry" : "images.viash-hub.com", - "target_tag" : "0.2.0", + "target_tag" : "v0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3316,12 +3316,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "viash_version" : "0.9.0", - "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", - "git_remote" : "https://github.com/viash-hub/biobox" + "git_commit" : "7e530218844c373048bc33de58f021b6460642e5", + "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "0.2.0", + "version" : "v0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", "viash_version" : "0.9.0", "source" : "src", @@ -3330,7 +3330,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := '0.2.0'" + ".engines[.type == 'docker'].target_tag := 'v0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3861,7 +3861,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/umi_tools/umi_tools_extract", - "tag" : "0.2.0" + "tag" : "v0.2.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/umi_tools/umi_tools_extract/nextflow.config b/target/nextflow/umi_tools/umi_tools_extract/nextflow.config index d1ede51c..3b230df5 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/nextflow.config +++ b/target/nextflow/umi_tools/umi_tools_extract/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'umi_tools/umi_tools_extract' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '0.2.0' + version = 'v0.2.0' description = 'Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n' }