diff --git a/_viash.yaml b/_viash.yaml index 31b3f98..11dffa4 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -11,3 +11,13 @@ info: config_mods: | .requirements.commands := ['ps'] .runners[.type == 'nextflow'].directives.tag := '$id' + +repositories: + - name: biobox + type: vsh + repo: vsh/biobox + tag: v0.2.0 + - name: craftbox + type: vsh + repo: craftbox + tag: v0.1.0 diff --git a/src/workflows/genome_alignment_and_quant/config.vsh.yaml b/src/workflows/genome_alignment_and_quant/config.vsh.yaml index 6e79592..d93b916 100644 --- a/src/workflows/genome_alignment_and_quant/config.vsh.yaml +++ b/src/workflows/genome_alignment_and_quant/config.vsh.yaml @@ -173,13 +173,6 @@ dependencies: - name: rsem/rsem_calculate_expression # repository: biobox -repositories: - - name: biobox - type: vsh - repo: vsh/biobox - tag: v0.2.0 - - runners: - type: executable - type: nextflow diff --git a/src/workflows/post_processing/config.vsh.yaml b/src/workflows/post_processing/config.vsh.yaml index 778b69a..50b52e9 100644 --- a/src/workflows/post_processing/config.vsh.yaml +++ b/src/workflows/post_processing/config.vsh.yaml @@ -155,12 +155,6 @@ dependencies: - name: ucsc/bedclip - name: ucsc/bedgraphtobigwig -repositories: - - name: biobox - type: vsh - repo: vsh/biobox - tag: v0.2.0 - runners: - type: executable - type: nextflow diff --git a/src/workflows/pre_processing/config.vsh.yaml b/src/workflows/pre_processing/config.vsh.yaml index 6535dde..b4868d1 100644 --- a/src/workflows/pre_processing/config.vsh.yaml +++ b/src/workflows/pre_processing/config.vsh.yaml @@ -266,13 +266,7 @@ dependencies: - name: fq_subsample - name: salmon/salmon_quant repository: biobox - -repositories: - - name: biobox - type: vsh - repo: vsh/biobox - tag: v0.2.0 - + runners: - type: executable - type: nextflow diff --git a/src/workflows/prepare_genome/config.vsh.yaml b/src/workflows/prepare_genome/config.vsh.yaml index 4bd9bc0..0d1816e 100644 --- a/src/workflows/prepare_genome/config.vsh.yaml +++ b/src/workflows/prepare_genome/config.vsh.yaml @@ -164,16 +164,6 @@ dependencies: repository: biobox - name: kallisto/kallisto_index -repositories: - - name: biobox - type: vsh - repo: biobox - tag: v0.2.0 - - name: craftbox - type: vsh - repo: craftbox - tag: v0.1.0 - runners: - type: executable - type: nextflow diff --git a/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml b/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml index 586c472..7a67ba8 100644 --- a/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml +++ b/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml @@ -83,12 +83,6 @@ dependencies: repository: biobox - name: kallisto/kallisto_quant -repositories: - - name: biobox - type: vsh - repo: vsh/biobox - tag: v0.2.0 - runners: - type: executable - type: nextflow diff --git a/src/workflows/quality_control/config.vsh.yaml b/src/workflows/quality_control/config.vsh.yaml index b615e7a..072d347 100644 --- a/src/workflows/quality_control/config.vsh.yaml +++ b/src/workflows/quality_control/config.vsh.yaml @@ -652,13 +652,6 @@ dependencies: repository: biobox - name: workflows/merge_quant_results -repositories: - - name: biobox - type: vsh - repo: vsh/biobox - tag: v0.2.0 - - runners: - type: executable - type: nextflow diff --git a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/.config.vsh.yaml index 401926d..ff26464 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf index 571d8b5..6c94298 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/nextflow.config index 3e1cb67..8c03570 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/.config.vsh.yaml index 79e96a8..3a72e20 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf index f39e713..1be8288 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/nextflow.config index 346054a..02f0e8b 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/.config.vsh.yaml index 8fdae94..9603e2c 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf index 4fa0e80..04ee10d 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/nextflow.config index 1860658..c0fafa4 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml index 245ef5c..4223169 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf index 7e0282b..be592a2 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config index 2fe3a6a..2400f6a 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 76883ee..30c9243 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf index 3fd602e..4386473 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/nextflow.config index 0214611..07266bb 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/.config.vsh.yaml index f4b3e35..307951a 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf index 6633d73..3cfeb69 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/nextflow.config index d036a17..230622c 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/.config.vsh.yaml index 2e84d6c..fffba6c 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf index 4c41526..074d4fb 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/nextflow.config index 3425279..fcf59f9 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 85c50ea..3855165 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf index 4e8d8e9..53551c0 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/nextflow.config index 17007f7..b86e4a7 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index 4874329..3b7a698 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf index 15ce949..c0a1257 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/nextflow.config index c53aaa5..5829e7c 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/.config.vsh.yaml index 36e112f..31a2a95 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf index d8b6b24..af7a6e8 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/nextflow.config index 0ce06ea..ea5a599 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/.config.vsh.yaml index a37efeb..d9e93a7 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf index 7525e02..4b698e3 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/nextflow.config index ea64c8c..005ab61 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/.config.vsh.yaml index ee7dd48..f1e1e32 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf index 1f8595f..58c1550 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/nextflow.config index 8b99052..70ea9cf 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/.config.vsh.yaml index caf1001..90e0e24 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf index a205d8a..a4d7acb 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/nextflow.config index 9406e86..e045272 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/.config.vsh.yaml index 0280082..251fe74 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf index 6861801..b73db0f 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/nextflow.config index 19e916a..ebbf1bb 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/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/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index 3fae3fe..515b84e 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -140,6 +140,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -229,14 +238,23 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index 031080b..e81a4df 100755 --- a/target/executable/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit @@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \ cp -r bbmap/* /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit" -LABEL org.opencontainers.image.created="2024-09-13T10:19:10Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index 9f59ebe..87ad222 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -80,6 +80,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -169,14 +178,23 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index 3f50d69..5b7f612 100755 --- a/target/executable/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools_genomecov/bedtools_genomecov @@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \ chmod a+x /usr/local/bin/bedtools LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov" -LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index 3bd1930..cbcb0a3 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -90,6 +90,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -173,14 +182,23 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index c822cb2..000b11a 100755 --- a/target/executable/cat_additional_fasta/cat_additional_fasta +++ b/target/executable/cat_additional_fasta/cat_additional_fasta @@ -480,9 +480,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta" -LABEL org.opencontainers.image.created="2024-09-13T10:19:17Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index 601beec..70002ff 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -77,6 +77,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -160,14 +169,23 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index 2a56225..cc2e7ee 100755 --- a/target/executable/cat_fastq/cat_fastq +++ b/target/executable/cat_fastq/cat_fastq @@ -472,9 +472,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_fastq" -LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 4321520..09f6f79 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -126,6 +126,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -228,14 +237,23 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index 832e0f3..36f0eb8 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-09-13T10:19:30Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index a8b8891..d789cfc 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -165,6 +165,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -257,14 +266,23 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index a918549..d91f558 100755 --- a/target/executable/dupradar/dupradar +++ b/target/executable/dupradar/dupradar @@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")' LABEL org.opencontainers.image.description="Companion container for running component dupradar" -LABEL org.opencontainers.image.created="2024-09-13T10:19:19Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 03a38f3..cbacc30 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -101,6 +101,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -189,14 +198,23 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index b49ba34..3105e1e 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -490,9 +490,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index efd46c8..5473004 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -74,6 +74,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -168,14 +177,23 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index 20a34c5..79abf75 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -485,9 +485,9 @@ cargo install --locked --path . && \ mv /usr/local/fq/target/release/fq /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" -LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index 4e7500c..a4ec956 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -67,6 +67,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -158,14 +167,23 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index 8eb748c..1ff792e 100755 --- a/target/executable/getchromsizes/getchromsizes +++ b/target/executable/getchromsizes/getchromsizes @@ -480,9 +480,9 @@ make && \ make install LABEL org.opencontainers.image.description="Companion container for running component getchromsizes" -LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index 7bda08c..3907b59 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -48,6 +48,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -136,14 +145,23 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index ac61544..a127eae 100755 --- a/target/executable/gtf2bed/gtf2bed +++ b/target/executable/gtf2bed/gtf2bed @@ -466,9 +466,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component gtf2bed" -LABEL org.opencontainers.image.created="2024-09-13T10:19:25Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 3af4651..9bb4e93 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -63,6 +63,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -146,14 +155,23 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index 6b1aba6..e671d74 100755 --- a/target/executable/gtf_filter/gtf_filter +++ b/target/executable/gtf_filter/gtf_filter @@ -470,9 +470,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component gtf_filter" -LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index 36ed156..2e6d099 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -47,6 +47,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -135,14 +144,23 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index a86c9ac..d209231 100755 --- a/target/executable/gunzip/gunzip +++ b/target/executable/gunzip/gunzip @@ -466,9 +466,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component gunzip" -LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 3f1c9ac..bf8cc0c 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -56,6 +56,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -146,14 +155,23 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index 0ba7108..99303bc 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" -LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index bea6c21..2fe71b1 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -154,6 +154,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -244,14 +253,23 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index c7b17ed..530357d 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" -LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index efb6502..3b73edb 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -70,6 +70,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -161,14 +170,23 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 1037e37..c31ede0 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -481,9 +481,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" -LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index 3dbcbf3..c2dc4e3 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -107,6 +107,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -198,14 +207,23 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index bc1e96f..b5c9d5d 100755 --- a/target/executable/picard_markduplicates/picard_markduplicates +++ b/target/executable/picard_markduplicates/picard_markduplicates @@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do mv picard.jar /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates" -LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index cf39721..429f7a9 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -317,6 +317,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -400,14 +409,23 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 9bfff9f..f6a079c 100755 --- a/target/executable/prepare_multiqc_input/prepare_multiqc_input +++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input @@ -557,9 +557,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input" -LABEL org.opencontainers.image.created="2024-09-13T10:19:24Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index ef6a1af..5cd97f3 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -46,6 +46,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -129,14 +138,23 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index 7509d8b..8d0c5ab 100755 --- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta +++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta @@ -462,9 +462,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta" -LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index de7d3a3..a6faf22 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -67,6 +67,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -182,14 +191,23 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index 27068d1..c9b4ce8 100755 --- a/target/executable/preseq_lcextrap/preseq_lcextrap +++ b/target/executable/preseq_lcextrap/preseq_lcextrap @@ -495,9 +495,9 @@ mkdir build && cd build && \ make && make install && make HAVE_HTSLIB=1 all LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap" -LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index 092f429..29c7c13 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -158,6 +158,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -262,14 +271,23 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index c057e77..9dc5e16 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component qualimap" -LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index a910e0e..d183602 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -181,6 +181,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -299,14 +308,23 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index caa65a5..4798d5b 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -545,9 +545,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \ /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index 8950881..75d73b7 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -110,6 +110,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -193,14 +202,23 @@ build_info: output: "target/executable/rsem/rsem_merge_counts" executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index fd8ad5f..6a012b4 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -490,9 +490,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts" -LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index 28b499b..6ecb4df 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -61,6 +61,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -154,14 +163,23 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 62c24b1..f87170d 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 0a0011d..888e05d 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -84,6 +84,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -177,14 +186,23 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index 8168042..b93a8a5 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index a9b70a3..755f02d 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -169,6 +169,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -263,14 +272,23 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index 58cb253..e9e5731 100755 --- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance +++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance @@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance" -LABEL org.opencontainers.image.created="2024-09-13T10:19:22Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index ec7c9ea..69ef173 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -157,6 +157,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -251,14 +260,23 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index 0694b61..8b490c5 100755 --- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation +++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation @@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation" -LABEL org.opencontainers.image.created="2024-09-13T10:19:22Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index b3cd479..8e19d43 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -146,6 +146,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -240,14 +249,23 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index a1742be..b950c1c 100755 --- a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation +++ b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation @@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation" -LABEL org.opencontainers.image.created="2024-09-13T10:19:21Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index 0c7498a..fd9f000 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -60,6 +60,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -153,14 +162,23 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index c7c55eb..2b5bed4 100755 --- a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution +++ b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution @@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution" -LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index e3c513d..8972cf4 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -108,6 +108,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -202,14 +211,23 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index 6edeaaa..5291077 100755 --- a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication +++ b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication @@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication" -LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index 26d3e5b..548d63d 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -114,6 +114,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -205,14 +214,23 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index 844666e..c34cf90 100755 --- a/target/executable/rseqc/rseqc_tin/rseqc_tin +++ b/target/executable/rseqc/rseqc_tin/rseqc_tin @@ -501,9 +501,9 @@ RUN apt-get update && \ RUN pip3 install RSeQC LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin" -LABEL org.opencontainers.image.created="2024-09-13T10:19:21Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 9385587..f06e481 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -100,6 +100,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -189,14 +198,23 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index a6f50cf..bcaff1a 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down bash sortmerna-4.3.6-Linux.sh --skip-license LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 36ec788..0df051f 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -117,6 +117,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -207,14 +216,23 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 88d13dc..ddde1c9 100755 --- a/target/executable/stringtie/stringtie +++ b/target/executable/stringtie/stringtie @@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \ cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component stringtie" -LABEL org.opencontainers.image.created="2024-09-13T10:19:25Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index f11cd7f..74c6f66 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -96,6 +96,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -190,14 +199,23 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index a4ee416..7d799e1 100755 --- a/target/executable/summarizedexperiment/summarizedexperiment +++ b/target/executable/summarizedexperiment/summarizedexperiment @@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")' LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment" -LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index f49b024..4b17d4b 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -683,6 +683,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" keywords: - "trimming" - "adapters" @@ -779,14 +788,23 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 4ba0640..41e5f43 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -858,9 +858,9 @@ ENTRYPOINT [] RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z" +LABEL org.opencontainers.image.created="2024-09-14T08:49:19Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index 9c29f8f..8e34886 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -91,6 +91,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -183,14 +192,23 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 17fc024..dde1103 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -487,9 +487,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component tx2gene" -LABEL org.opencontainers.image.created="2024-09-13T10:19:24Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index b5a0420..1a23642 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -139,6 +139,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -238,14 +247,23 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 2a23bfd..b3f6613 100755 --- a/target/executable/tximport/tximport +++ b/target/executable/tximport/tximport @@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component tximport" -LABEL org.opencontainers.image.created="2024-09-13T10:19:17Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index dae5f3c..34feccb 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -62,6 +62,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -155,14 +164,23 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index d66243b..b2da9a4 100755 --- a/target/executable/ucsc/bedclip/bedclip +++ b/target/executable/ucsc/bedclip/bedclip @@ -473,9 +473,9 @@ RUN apt-get update && \ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip" -LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 255ada5..4510afc 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -62,6 +62,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -155,14 +164,23 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index ba2f940..42f2cb9 100755 --- a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig +++ b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig @@ -473,9 +473,9 @@ RUN apt-get update && \ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig" -LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index 25edc91..97df5f0 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -93,6 +93,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -186,14 +195,23 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index cfd1758..304c02b 100755 --- a/target/executable/umitools/umitools_dedup/umitools_dedup +++ b/target/executable/umitools/umitools_dedup/umitools_dedup @@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup" -LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index 909dedc..aff16b3 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -151,6 +151,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -244,14 +253,23 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index b4c1699..261d576 100755 --- a/target/executable/umitools/umitools_extract/umitools_extract +++ b/target/executable/umitools/umitools_extract/umitools_extract @@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract" -LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index 5ee07e8..08bf466 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -53,6 +53,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -147,14 +156,23 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index 7cf0e3e..be96010 100755 --- a/target/executable/umitools_prepareforquant/umitools_prepareforquant +++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant @@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" "pysam" LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant" -LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z" -LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c" +LABEL org.opencontainers.image.created="2024-09-14T08:49:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml index 18ba3d5..e2d23bc 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -443,6 +443,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -518,8 +522,8 @@ build_info: output: "target/executable/workflows/genome_alignment_and_quant" executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" @@ -537,6 +541,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index 03a7d31..f8704c4 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -194,6 +194,15 @@ dependencies: - name: "summarizedexperiment" repository: type: "local" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -269,8 +278,8 @@ build_info: output: "target/executable/workflows/merge_quant_results" executable: "target/executable/workflows/merge_quant_results/merge_quant_results" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" @@ -281,6 +290,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/workflows/post_processing/.config.vsh.yaml b/target/executable/workflows/post_processing/.config.vsh.yaml index 291477f..cb29c14 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -407,6 +407,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -482,8 +486,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" @@ -501,6 +505,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index 11420c9..0b4b7b5 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -565,6 +565,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -640,8 +644,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" @@ -657,6 +661,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index fe5953f..a1e62e4 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -369,7 +369,7 @@ dependencies: - name: "gffread" repository: type: "vsh" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - name: "cat_additional_fasta" repository: @@ -386,7 +386,7 @@ dependencies: - name: "rsem/rsem_prepare_reference" repository: type: "vsh" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - name: "getchromsizes" repository: @@ -399,7 +399,7 @@ dependencies: - name: "star/star_genome_generate" repository: type: "vsh" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - name: "bbmap_bbsplit" repository: @@ -407,7 +407,7 @@ dependencies: - name: "salmon/salmon_index" repository: type: "vsh" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - name: "kallisto/kallisto_index" repository: @@ -415,7 +415,7 @@ dependencies: repositories: - type: "vsh" name: "biobox" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - type: "vsh" name: "craftbox" @@ -496,8 +496,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" @@ -518,6 +518,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index a5785a2..9c3dd5c 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -206,6 +206,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -281,8 +285,8 @@ build_info: output: "target/executable/workflows/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" @@ -292,6 +296,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index 05f4c9c..2a8d785 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1513,6 +1513,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -1588,8 +1592,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" @@ -1614,6 +1618,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 9657d82..7ecb4f7 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -1881,6 +1881,15 @@ dependencies: - name: "workflows/quality_control" repository: type: "local" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -1956,8 +1965,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" @@ -1972,6 +1981,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 616aeda..33d70df 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -140,6 +140,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -229,14 +238,23 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index 384f02f..a6da168 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -2988,6 +2988,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3090,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3103,6 +3117,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index 10ee3ed..0207914 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -80,6 +80,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -169,14 +178,23 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index 20f8c8d..1e4c561 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -2915,6 +2915,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3017,8 +3031,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3030,6 +3044,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index 5946f6f..cb8671a 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -90,6 +90,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -173,14 +182,23 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index c884808..441b4fb 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -2924,6 +2924,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3018,8 +3032,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3031,6 +3045,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index 351ac9b..3e39bec 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -77,6 +77,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -160,14 +169,23 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index ccc6da6..17f2230 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -2915,6 +2915,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3009,8 +3023,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3022,6 +3036,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index b09c9ce..afc3df5 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -126,6 +126,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -228,14 +237,23 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index 7fddc9b..4b35d37 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -2974,6 +2974,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3096,8 +3110,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3109,6 +3123,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index 93f78ff..20d4598 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -165,6 +165,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -257,14 +266,23 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index 3ee50e9..29c67aa 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -3012,6 +3012,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3122,8 +3136,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3135,6 +3149,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index c663236..035421f 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -101,6 +101,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -189,14 +198,23 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 15eca1f..a01299d 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -2939,6 +2939,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3042,8 +3056,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3055,6 +3069,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index c90c5e0..552ae85 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -74,6 +74,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -168,14 +177,23 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 797e2a0..64a3f87 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -2908,6 +2908,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3013,8 +3027,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3026,6 +3040,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index 0fc2066..2d726cc 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -67,6 +67,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -158,14 +167,23 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index f22f708..808374e 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -2897,6 +2897,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -2999,8 +3013,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3012,6 +3026,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index 4c5d521..fa20291 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -48,6 +48,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -136,14 +145,23 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 7ee9152..85cd58b 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -2878,6 +2878,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -2981,8 +2995,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -2994,6 +3008,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index a86123b..1ad0607 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -63,6 +63,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -146,14 +155,23 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index ba2211c..963a628 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -2895,6 +2895,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -2989,8 +3003,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3002,6 +3016,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index 62205f5..cfde6ac 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -47,6 +47,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -135,14 +144,23 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index a12bdb4..fbd2a90 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -2875,6 +2875,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -2978,8 +2992,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -2991,6 +3005,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index 3f5cd66..818ab98 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -56,6 +56,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -146,14 +155,23 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index c91d680..19ac654 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -2886,6 +2886,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -2988,8 +3002,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3001,6 +3015,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index e57419c..18ae671 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -154,6 +154,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -244,14 +253,23 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 95343b8..8abdbd4 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -2998,6 +2998,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3100,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3113,6 +3127,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 98da44d..8086d24 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -70,6 +70,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -161,14 +170,23 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index a3dc566..03957b0 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -2898,6 +2898,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3006,8 +3020,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3019,6 +3033,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index 1807801..5611b63 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -107,6 +107,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -198,14 +207,23 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index 473f9e5..ed870ec 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -2944,6 +2944,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3049,8 +3063,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3062,6 +3076,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index ed3b567..5038103 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -317,6 +317,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -400,14 +409,23 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index b2ed4a8..5e0d835 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -3169,6 +3169,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3263,8 +3277,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3276,6 +3290,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index d95a24f..e430781 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -46,6 +46,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -129,14 +138,23 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index ec11355..b7b5280 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -2874,6 +2874,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -2968,8 +2982,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -2981,6 +2995,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index e496a6d..d4b8cd8 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -67,6 +67,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -182,14 +191,23 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index 8298fdf..ac51f5c 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -2898,6 +2898,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3021,8 +3035,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3034,6 +3048,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index 5216011..e2d825d 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -158,6 +158,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -262,14 +271,23 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index e39c337..d79ee45 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3006,6 +3006,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3130,8 +3144,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3143,6 +3157,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 9bca5e1..6d01064 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -181,6 +181,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -299,14 +308,23 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index 3165b4e..b061a82 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3033,6 +3033,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3159,8 +3173,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3172,6 +3186,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index 0ba87ad..d8237ab 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -110,6 +110,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -193,14 +202,23 @@ build_info: output: "target/nextflow/rsem/rsem_merge_counts" executable: "target/nextflow/rsem/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index 9665aad..00da3ff 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -2943,6 +2943,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3037,8 +3051,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3050,6 +3064,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index 1fa8cd0..0e16cf4 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -61,6 +61,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -154,14 +163,23 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index a3673a2..df4c049 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -2891,6 +2891,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3002,8 +3016,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3015,6 +3029,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 9e272f3..4e440d0 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -84,6 +84,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -177,14 +186,23 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index 8d93323..7471372 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -2919,6 +2919,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3030,8 +3044,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3043,6 +3057,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index 87262c5..d634cef 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -169,6 +169,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -263,14 +272,23 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index db1b60a..e17d1c3 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -3011,6 +3011,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3123,8 +3137,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3136,6 +3150,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 269b9c7..f1a7ae4 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -157,6 +157,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -251,14 +260,23 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index 26e4303..cdb4475 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -3002,6 +3002,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3114,8 +3128,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3127,6 +3141,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 3cb8eca..a07bbfd 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -146,6 +146,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -240,14 +249,23 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index 0b94404..eb3f03f 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -2987,6 +2987,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3099,8 +3113,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3112,6 +3126,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index de51055..f786a8d 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -60,6 +60,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -153,14 +162,23 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 9f2f857..b8e4a39 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -2892,6 +2892,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3003,8 +3017,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3016,6 +3030,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index 83be962..b078e3a 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -108,6 +108,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -202,14 +211,23 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index 28359f5..b5baaf1 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -2945,6 +2945,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3057,8 +3071,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3070,6 +3084,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index b41e51e..08be1ee 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -114,6 +114,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -205,14 +214,23 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index aa05bc3..da4796c 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -2953,6 +2953,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3062,8 +3076,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3075,6 +3089,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index d60daf4..4ccc1ea 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -100,6 +100,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -189,14 +198,23 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 22ea85f..319745a 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -2934,6 +2934,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3036,8 +3050,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3049,6 +3063,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index 5447c92..3c0adbe 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -117,6 +117,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -207,14 +216,23 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 4011a29..9171ea8 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -2957,6 +2957,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3059,8 +3073,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3072,6 +3086,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index cf33d20..ad51409 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -96,6 +96,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -190,14 +199,23 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index f7db9e2..eac1854 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -2928,6 +2928,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3040,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3053,6 +3067,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index c100d59..da2ceb2 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -683,6 +683,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" keywords: - "trimming" - "adapters" @@ -779,14 +788,23 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index 80c1c30..0fd48e1 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3450,6 +3450,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "keywords" : [ "trimming", "adapters" @@ -3562,8 +3576,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3575,6 +3589,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index 9bf565a..8e5b485 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -91,6 +91,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -183,14 +192,23 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index e812cd3..cf181e3 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -2926,6 +2926,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3035,8 +3049,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3048,6 +3062,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index 5c2a703..14df736 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -139,6 +139,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -238,14 +247,23 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index 3caada6..8a059f1 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -2982,6 +2982,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3100,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3113,6 +3127,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index d351628..230fdd1 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -62,6 +62,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -155,14 +164,23 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index 86f1601..494b255 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -2894,6 +2894,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3004,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3017,6 +3031,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index 4e642b3..a7806cf 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -62,6 +62,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -155,14 +164,23 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index a20f80d..fc3c288 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -2894,6 +2894,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3004,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3017,6 +3031,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index f7d0992..901f128 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -93,6 +93,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -186,14 +195,23 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index ae52e1a..6337ddd 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -2929,6 +2929,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3040,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3053,6 +3067,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index c1937ed..e87f302 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -151,6 +151,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -244,14 +253,23 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index 7ec5ea4..96e62b9 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -2994,6 +2994,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3105,8 +3119,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3118,6 +3132,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index 9437d39..8d55921 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -53,6 +53,15 @@ status: "enabled" requirements: commands: - "ps" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -147,14 +156,23 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" package_config: version: "main" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index 9e5c365..37bec02 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -2881,6 +2881,20 @@ meta = [ "ps" ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -2993,8 +3007,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3006,6 +3020,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml index 144f973..25175be 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -443,6 +443,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -518,8 +522,8 @@ build_info: output: "target/nextflow/workflows/genome_alignment_and_quant" executable: "target/nextflow/workflows/genome_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" @@ -537,6 +541,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/workflows/genome_alignment_and_quant/main.nf b/target/nextflow/workflows/genome_alignment_and_quant/main.nf index 6e8d097..03fc08e 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3343,6 +3343,12 @@ meta = [ "name" : "biobox", "repo" : "vsh/biobox", "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" } ], "runners" : [ @@ -3431,8 +3437,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3444,6 +3450,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index 706204f..6ed8743 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -194,6 +194,15 @@ dependencies: - name: "summarizedexperiment" repository: type: "local" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -269,8 +278,8 @@ build_info: output: "target/nextflow/workflows/merge_quant_results" executable: "target/nextflow/workflows/merge_quant_results/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" @@ -281,6 +290,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/workflows/merge_quant_results/main.nf b/target/nextflow/workflows/merge_quant_results/main.nf index 572b4c0..1e4e635 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -3049,6 +3049,20 @@ meta = [ } } ], + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -3135,8 +3149,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3148,6 +3162,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index 6857119..44536e2 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -407,6 +407,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -482,8 +486,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" @@ -501,6 +505,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index b022e4a..c4f1f78 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3303,6 +3303,12 @@ meta = [ "name" : "biobox", "repo" : "vsh/biobox", "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" } ], "runners" : [ @@ -3391,8 +3397,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3404,6 +3410,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index d7d35ec..6d4413f 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -565,6 +565,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -640,8 +644,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" @@ -657,6 +661,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index 17d30b1..e7e6725 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3497,6 +3497,12 @@ meta = [ "name" : "biobox", "repo" : "vsh/biobox", "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" } ], "runners" : [ @@ -3585,8 +3591,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3598,6 +3604,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index e1b1cbc..d1125ef 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -369,7 +369,7 @@ dependencies: - name: "gffread" repository: type: "vsh" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - name: "cat_additional_fasta" repository: @@ -386,7 +386,7 @@ dependencies: - name: "rsem/rsem_prepare_reference" repository: type: "vsh" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - name: "getchromsizes" repository: @@ -399,7 +399,7 @@ dependencies: - name: "star/star_genome_generate" repository: type: "vsh" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - name: "bbmap_bbsplit" repository: @@ -407,7 +407,7 @@ dependencies: - name: "salmon/salmon_index" repository: type: "vsh" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - name: "kallisto/kallisto_index" repository: @@ -415,7 +415,7 @@ dependencies: repositories: - type: "vsh" name: "biobox" - repo: "biobox" + repo: "vsh/biobox" tag: "v0.2.0" - type: "vsh" name: "craftbox" @@ -496,8 +496,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" @@ -518,6 +518,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index 61a9b72..f79c2ef 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3228,7 +3228,7 @@ meta = [ "name" : "gffread", "repository" : { "type" : "vsh", - "repo" : "biobox", + "repo" : "vsh/biobox", "tag" : "v0.2.0" } }, @@ -3260,7 +3260,7 @@ meta = [ "name" : "rsem/rsem_prepare_reference", "repository" : { "type" : "vsh", - "repo" : "biobox", + "repo" : "vsh/biobox", "tag" : "v0.2.0" } }, @@ -3282,7 +3282,7 @@ meta = [ "name" : "star/star_genome_generate", "repository" : { "type" : "vsh", - "repo" : "biobox", + "repo" : "vsh/biobox", "tag" : "v0.2.0" } }, @@ -3296,7 +3296,7 @@ meta = [ "name" : "salmon/salmon_index", "repository" : { "type" : "vsh", - "repo" : "biobox", + "repo" : "vsh/biobox", "tag" : "v0.2.0" } }, @@ -3311,7 +3311,7 @@ meta = [ { "type" : "vsh", "name" : "biobox", - "repo" : "biobox", + "repo" : "vsh/biobox", "tag" : "v0.2.0" }, { @@ -3407,8 +3407,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3420,6 +3420,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index bf4c943..3dc54ca 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -206,6 +206,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -281,8 +285,8 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" @@ -292,6 +296,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index 250b3c9..11d3143 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3052,6 +3052,12 @@ meta = [ "name" : "biobox", "repo" : "vsh/biobox", "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" } ], "runners" : [ @@ -3140,8 +3146,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -3153,6 +3159,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index 5f3e609..12fd152 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1513,6 +1513,10 @@ repositories: name: "biobox" repo: "vsh/biobox" tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -1588,8 +1592,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" @@ -1614,6 +1618,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index 97392a9..8012b7c 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4575,6 +4575,12 @@ meta = [ "name" : "biobox", "repo" : "vsh/biobox", "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" } ], "runners" : [ @@ -4663,8 +4669,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -4676,6 +4682,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target", diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 5a75178..6a43fe0 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -1881,6 +1881,15 @@ dependencies: - name: "workflows/quality_control" repository: type: "local" +repositories: +- type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" +- type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" runners: - type: "executable" id: "executable" @@ -1956,8 +1965,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "cb9b32883494c48f394213551a82e9103f2e620c" - git_remote: "https://github.com/viash-hub/rnaseq" + git_commit: "64aad6a006818388eceffe024b1701b3eae06bee" + git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" @@ -1972,6 +1981,15 @@ package_config: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" dest: "testData" + repositories: + - type: "vsh" + name: "biobox" + repo: "vsh/biobox" + tag: "v0.2.0" + - type: "vsh" + name: "craftbox" + repo: "craftbox" + tag: "v0.1.0" viash_version: "0.9.0" source: "src" target: "target" diff --git a/target/nextflow/workflows/rnaseq/main.nf b/target/nextflow/workflows/rnaseq/main.nf index 533d062..f10fe12 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -5003,6 +5003,20 @@ meta = [ } } ], + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "runners" : [ { "type" : "executable", @@ -5089,8 +5103,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "cb9b32883494c48f394213551a82e9103f2e620c", - "git_remote" : "https://github.com/viash-hub/rnaseq" + "git_commit" : "64aad6a006818388eceffe024b1701b3eae06bee", + "git_remote" : "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", @@ -5102,6 +5116,20 @@ meta = [ } ] }, + "repositories" : [ + { + "type" : "vsh", + "name" : "biobox", + "repo" : "vsh/biobox", + "tag" : "v0.2.0" + }, + { + "type" : "vsh", + "name" : "craftbox", + "repo" : "craftbox", + "tag" : "v0.1.0" + } + ], "viash_version" : "0.9.0", "source" : "/workdir/root/repo/src", "target" : "/workdir/root/repo/target",