From a0d4b1dd21a63e4d09ff7c14809ba35e59bf2ab0 Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 3 Oct 2025 14:05:09 +0000 Subject: [PATCH] Build branch demultiplex/v0.6 with version v0.6.1 to demultiplex on branch v0.6 (edbd04b) Build pipeline: viash-hub.demultiplex.v0.6-mrtf2 Source commit: https://github.com/viash-hub/demultiplex/commit/edbd04b6b129080fe2fac4d123af9ce7f1ae57ea Source message: Bump version to v0.6.1 --- CHANGELOG.md | 9 ++++++ _viash.yaml | 2 +- src/demultiplex/config.vsh.yaml | 2 +- src/demultiplex/main.nf | 1 + .../nextflow/bases2fastq/.config.vsh.yaml | 12 ++++---- .../nextflow/bases2fastq/main.nf | 16 +++++----- .../nextflow/bases2fastq/nextflow.config | 2 +- .../nextflow/bases2fastq/nextflow_schema.json | 0 .../nextflow/bcl_convert/.config.vsh.yaml | 10 +++---- .../nextflow/bcl_convert/main.nf | 14 ++++----- .../nextflow/bcl_convert/nextflow.config | 2 +- .../nextflow/bcl_convert/nextflow_schema.json | 0 .../nextflow/fastqc/.config.vsh.yaml | 10 +++---- .../nextflow/fastqc/main.nf | 14 ++++----- .../nextflow/fastqc/nextflow.config | 2 +- .../nextflow/fastqc/nextflow_schema.json | 0 .../nextflow/multiqc/.config.vsh.yaml | 10 +++---- .../nextflow/multiqc/main.nf | 14 ++++----- .../nextflow/multiqc/nextflow.config | 2 +- .../nextflow/multiqc/nextflow_schema.json | 0 .../interop_summary_to_csv/.config.vsh.yaml | 10 +++---- .../io/interop_summary_to_csv/_viash.yaml | 2 +- .../interop_summary_to_csv | 14 ++++----- target/executable/io/publish/.config.vsh.yaml | 10 +++---- target/executable/io/publish/_viash.yaml | 2 +- target/executable/io/publish/publish | 14 ++++----- target/executable/io/untar/.config.vsh.yaml | 10 +++---- target/executable/io/untar/_viash.yaml | 2 +- target/executable/io/untar/untar | 14 ++++----- .../dataflow/combine_samples/.config.vsh.yaml | 8 ++--- .../dataflow/combine_samples/_viash.yaml | 2 +- .../nextflow/dataflow/combine_samples/main.nf | 10 +++---- .../dataflow/combine_samples/nextflow.config | 2 +- .../.config.vsh.yaml | 8 ++--- .../gather_fastqs_and_validate/_viash.yaml | 2 +- .../gather_fastqs_and_validate/main.nf | 10 +++---- .../nextflow.config | 2 +- target/nextflow/demultiplex/.config.vsh.yaml | 26 ++++++++--------- target/nextflow/demultiplex/_viash.yaml | 2 +- target/nextflow/demultiplex/main.nf | 29 ++++++++++--------- target/nextflow/demultiplex/nextflow.config | 2 +- .../detect_demultiplexer/.config.vsh.yaml | 8 ++--- .../nextflow/detect_demultiplexer/_viash.yaml | 2 +- target/nextflow/detect_demultiplexer/main.nf | 10 +++---- .../detect_demultiplexer/nextflow.config | 2 +- .../interop_summary_to_csv/.config.vsh.yaml | 10 +++---- .../io/interop_summary_to_csv/_viash.yaml | 2 +- .../io/interop_summary_to_csv/main.nf | 14 ++++----- .../io/interop_summary_to_csv/nextflow.config | 2 +- target/nextflow/io/publish/.config.vsh.yaml | 10 +++---- target/nextflow/io/publish/_viash.yaml | 2 +- target/nextflow/io/publish/main.nf | 14 ++++----- target/nextflow/io/publish/nextflow.config | 2 +- target/nextflow/io/untar/.config.vsh.yaml | 10 +++---- target/nextflow/io/untar/_viash.yaml | 2 +- target/nextflow/io/untar/main.nf | 14 ++++----- target/nextflow/io/untar/nextflow.config | 2 +- target/nextflow/runner/.config.vsh.yaml | 8 ++--- target/nextflow/runner/_viash.yaml | 2 +- target/nextflow/runner/main.nf | 10 +++---- target/nextflow/runner/nextflow.config | 2 +- 61 files changed, 221 insertions(+), 210 deletions(-) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/bases2fastq/.config.vsh.yaml (98%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/bases2fastq/main.nf (99%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/bases2fastq/nextflow.config (99%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/bases2fastq/nextflow_schema.json (100%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/bcl_convert/.config.vsh.yaml (98%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/bcl_convert/main.nf (99%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/bcl_convert/nextflow.config (99%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/bcl_convert/nextflow_schema.json (100%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/fastqc/.config.vsh.yaml (98%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/fastqc/main.nf (99%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/fastqc/nextflow.config (99%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/fastqc/nextflow_schema.json (100%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/multiqc/.config.vsh.yaml (98%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/multiqc/main.nf (99%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/multiqc/nextflow.config (99%) rename target/dependencies/vsh/vsh/biobox/{v0.4.0 => v0.4.1}/nextflow/multiqc/nextflow_schema.json (100%) diff --git a/CHANGELOG.md b/CHANGELOG.md index f2b13ca..6d6d465 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,12 @@ +# demultiplex v0.6.1 + +## Minor changes + +* Disable native `bases2fastq` MultiQC report because the workflow generates one itself (PR #66). + +* Bump biobox to `v0.4.1`. This updates `bases2fastq` to version `2.2.1` (PR #67). + + # demultiplex v0.6.0 # New functionality diff --git a/_viash.yaml b/_viash.yaml index e8b0900..6f82e74 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/src/demultiplex/config.vsh.yaml b/src/demultiplex/config.vsh.yaml index 304ebc7..b501014 100644 --- a/src/demultiplex/config.vsh.yaml +++ b/src/demultiplex/config.vsh.yaml @@ -106,7 +106,7 @@ repositories: - name: bb type: vsh repo: biobox - tag: v0.4.0 + tag: v0.4.1 runners: - type: nextflow diff --git a/src/demultiplex/main.nf b/src/demultiplex/main.nf index 8e47c7a..50eeb42 100644 --- a/src/demultiplex/main.nf +++ b/src/demultiplex/main.nf @@ -89,6 +89,7 @@ workflow run_wf { //"split_lanes": true, "legacy_fastq": true, // Illumina style output names "group_fastq": true, // No subdir per sample + "skip_multi_qc": true // This pipeline generates its own MultiQC report ], toState: {id, result, state -> def toAdd = [ diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/.config.vsh.yaml rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/.config.vsh.yaml index 3f6a1b1..07b60f9 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bases2fastq" -version: "v0.4.0" +version: "v0.4.1" authors: - name: "Dries Schaumont" roles: @@ -432,9 +432,9 @@ runners: engines: - type: "docker" id: "docker" - image: "elembio/bases2fastq:2.2" + image: "elembio/bases2fastq:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "v0.4.0" + target_tag: "v0.4.1" namespace_separator: "/" setup: - type: "docker" @@ -452,11 +452,11 @@ build_info: output: "target/nextflow/bases2fastq" executable: "target/nextflow/bases2fastq/main.nf" viash_version: "0.9.4" - git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262" + git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.4.0" + version: "v0.4.1" summary: "A curated collection of high-quality, standalone bioinformatics components\ \ built with [Viash](https://viash.io).\n" description: "`biobox` offers a suite of reliable bioinformatics components, similar\ @@ -477,7 +477,7 @@ package_config: - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.1'" keywords: - "bioinformatics" - "modules" diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/main.nf b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/main.nf rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/main.nf index c888066..5721360 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/main.nf @@ -1,4 +1,4 @@ -// bases2fastq v0.4.0 +// bases2fastq v0.4.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3034,7 +3034,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "bases2fastq", - "version" : "v0.4.0", + "version" : "v0.4.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3545,9 +3545,9 @@ meta = [ { "type" : "docker", "id" : "docker", - "image" : "elembio/bases2fastq:2.2", + "image" : "elembio/bases2fastq:2.2.1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.4.0", + "target_tag" : "v0.4.1", "namespace_separator" : "/", "setup" : [ { @@ -3569,12 +3569,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bases2fastq", "viash_version" : "0.9.4", - "git_commit" : "666507c86de9150bfbdffdb2dbabc1dbde3c3262", + "git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.4.0", + "version" : "v0.4.1", "summary" : "A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).\n", "description" : "`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation for components and parameters.\n * Full exposure of underlying tool arguments.\n * Containerized (Docker) for dependency management and reproducibility.\n * Unit tested for verified functionality.\n", "viash_version" : "0.9.4", @@ -3584,7 +3584,7 @@ meta = [ ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.0'" + ".engines[.type == 'docker'].target_tag := 'v0.4.1'" ], "keywords" : [ "bioinformatics", @@ -4186,7 +4186,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bases2fastq", - "tag" : "v0.4.0" + "tag" : "v0.4.1" }, "tag" : "$id" }'''), diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/nextflow.config rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow.config index b7c5223..8d24894 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bases2fastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.0' + version = 'v0.4.1' description = 'Bases2Fastq demultiplexes sequencing data generated by Element Biosciences instruments and converts base calls into FASTQ files.\n' author = 'Dries Schaumont' } diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/nextflow_schema.json b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/nextflow_schema.json rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/.config.vsh.yaml rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/.config.vsh.yaml index cefd93a..79438e2 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bcl_convert" -version: "v0.4.0" +version: "v0.4.1" authors: - name: "Toni Verbeiren" roles: @@ -399,7 +399,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.4.0" + target_tag: "v0.4.1" namespace_separator: "/" setup: - type: "apt" @@ -431,11 +431,11 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.4" - git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262" + git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.4.0" + version: "v0.4.1" summary: "A curated collection of high-quality, standalone bioinformatics components\ \ built with [Viash](https://viash.io).\n" description: "`biobox` offers a suite of reliable bioinformatics components, similar\ @@ -456,7 +456,7 @@ package_config: - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.1'" keywords: - "bioinformatics" - "modules" diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/main.nf b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/main.nf rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/main.nf index f528870..fd7d582 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/main.nf @@ -1,4 +1,4 @@ -// bcl_convert v0.4.0 +// bcl_convert v0.4.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "bcl_convert", - "version" : "v0.4.0", + "version" : "v0.4.1", "authors" : [ { "name" : "Toni Verbeiren", @@ -3531,7 +3531,7 @@ meta = [ "id" : "docker", "image" : "debian:trixie-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.4.0", + "target_tag" : "v0.4.1", "namespace_separator" : "/", "setup" : [ { @@ -3571,12 +3571,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.4", - "git_commit" : "666507c86de9150bfbdffdb2dbabc1dbde3c3262", + "git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.4.0", + "version" : "v0.4.1", "summary" : "A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).\n", "description" : "`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation for components and parameters.\n * Full exposure of underlying tool arguments.\n * Containerized (Docker) for dependency management and reproducibility.\n * Unit tested for verified functionality.\n", "viash_version" : "0.9.4", @@ -3586,7 +3586,7 @@ meta = [ ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.0'" + ".engines[.type == 'docker'].target_tag := 'v0.4.1'" ], "keywords" : [ "bioinformatics", @@ -4084,7 +4084,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bcl_convert", - "tag" : "v0.4.0" + "tag" : "v0.4.1" }, "tag" : "$id" }'''), diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/nextflow.config rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow.config index 8688f18..9016fa2 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bcl_convert' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.0' + version = 'v0.4.1' description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n' author = 'Toni Verbeiren, Dorien Roosen' } diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/nextflow_schema.json b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/nextflow_schema.json rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/.config.vsh.yaml rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/.config.vsh.yaml index 5f9a9bd..74d1c1b 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastqc" -version: "v0.4.0" +version: "v0.4.1" authors: - name: "Theodoro Gasperin Terra Camargo" roles: @@ -334,7 +334,7 @@ engines: id: "docker" image: "biocontainers/fastqc:v0.11.9_cv8" target_registry: "images.viash-hub.com" - target_tag: "v0.4.0" + target_tag: "v0.4.1" namespace_separator: "/" setup: - type: "docker" @@ -351,11 +351,11 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.4" - git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262" + git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.4.0" + version: "v0.4.1" summary: "A curated collection of high-quality, standalone bioinformatics components\ \ built with [Viash](https://viash.io).\n" description: "`biobox` offers a suite of reliable bioinformatics components, similar\ @@ -376,7 +376,7 @@ package_config: - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.1'" keywords: - "bioinformatics" - "modules" diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/main.nf b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/main.nf rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/main.nf index d6751b8..7ba6c48 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/main.nf @@ -1,4 +1,4 @@ -// fastqc v0.4.0 +// fastqc v0.4.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3034,7 +3034,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "fastqc", - "version" : "v0.4.0", + "version" : "v0.4.1", "authors" : [ { "name" : "Theodoro Gasperin Terra Camargo", @@ -3397,7 +3397,7 @@ meta = [ "id" : "docker", "image" : "biocontainers/fastqc:v0.11.9_cv8", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.4.0", + "target_tag" : "v0.4.1", "namespace_separator" : "/", "setup" : [ { @@ -3419,12 +3419,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastqc", "viash_version" : "0.9.4", - "git_commit" : "666507c86de9150bfbdffdb2dbabc1dbde3c3262", + "git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.4.0", + "version" : "v0.4.1", "summary" : "A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).\n", "description" : "`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation for components and parameters.\n * Full exposure of underlying tool arguments.\n * Containerized (Docker) for dependency management and reproducibility.\n * Unit tested for verified functionality.\n", "viash_version" : "0.9.4", @@ -3434,7 +3434,7 @@ meta = [ ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.0'" + ".engines[.type == 'docker'].target_tag := 'v0.4.1'" ], "keywords" : [ "bioinformatics", @@ -3989,7 +3989,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/fastqc", - "tag" : "v0.4.0" + "tag" : "v0.4.1" }, "tag" : "$id" }'''), diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/nextflow.config rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow.config index 8c03257..935e9b2 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'fastqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.0' + version = 'v0.4.1' description = 'FastQC - A high throughput sequence QC analysis tool.' author = 'Theodoro Gasperin Terra Camargo' } diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/nextflow_schema.json b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/nextflow_schema.json rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/.config.vsh.yaml rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/.config.vsh.yaml index 23f9180..19e4f6b 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "multiqc" -version: "v0.4.0" +version: "v0.4.1" authors: - name: "Dorien Roosen" roles: @@ -436,7 +436,7 @@ engines: id: "docker" image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.4.0" + target_tag: "v0.4.1" namespace_separator: "/" setup: - type: "docker" @@ -459,11 +459,11 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.4" - git_commit: "666507c86de9150bfbdffdb2dbabc1dbde3c3262" + git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.4.0" + version: "v0.4.1" summary: "A curated collection of high-quality, standalone bioinformatics components\ \ built with [Viash](https://viash.io).\n" description: "`biobox` offers a suite of reliable bioinformatics components, similar\ @@ -484,7 +484,7 @@ package_config: - ".requirements.commands += ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.1'" keywords: - "bioinformatics" - "modules" diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/main.nf b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/main.nf rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/main.nf index cda44a6..26db6f2 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/main.nf @@ -1,4 +1,4 @@ -// multiqc v0.4.0 +// multiqc v0.4.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3034,7 +3034,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "multiqc", - "version" : "v0.4.0", + "version" : "v0.4.1", "authors" : [ { "name" : "Dorien Roosen", @@ -3565,7 +3565,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.4.0", + "target_tag" : "v0.4.1", "namespace_separator" : "/", "setup" : [ { @@ -3596,12 +3596,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.4", - "git_commit" : "666507c86de9150bfbdffdb2dbabc1dbde3c3262", + "git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.4.0", + "version" : "v0.4.1", "summary" : "A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).\n", "description" : "`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation for components and parameters.\n * Full exposure of underlying tool arguments.\n * Containerized (Docker) for dependency management and reproducibility.\n * Unit tested for verified functionality.\n", "viash_version" : "0.9.4", @@ -3611,7 +3611,7 @@ meta = [ ".requirements.commands += ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.0'" + ".engines[.type == 'docker'].target_tag := 'v0.4.1'" ], "keywords" : [ "bioinformatics", @@ -4213,7 +4213,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/multiqc", - "tag" : "v0.4.0" + "tag" : "v0.4.1" }, "tag" : "$id" }'''), diff --git a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/nextflow.config rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow.config index e3680e5..2b28ce1 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'multiqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.0' + version = 'v0.4.1' 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/v0.4.0/nextflow/multiqc/nextflow_schema.json b/target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/nextflow_schema.json rename to target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/nextflow_schema.json diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml index 1436db2..3f3bd01 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "interop_summary_to_csv" namespace: "io" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -135,7 +135,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.6.0" + target_tag: "v0.6.1" namespace_separator: "/" setup: - type: "apt" @@ -160,11 +160,11 @@ build_info: output: "target/executable/io/interop_summary_to_csv" executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -180,7 +180,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/interop_summary_to_csv/_viash.yaml b/target/executable/io/interop_summary_to_csv/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/executable/io/interop_summary_to_csv/_viash.yaml +++ b/target/executable/io/interop_summary_to_csv/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv index 260186d..fd5ae37 100755 --- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv +++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# interop_summary_to_csv v0.6.0 +# interop_summary_to_csv v0.6.1 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \ mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv" -LABEL org.opencontainers.image.created="2025-09-17T14:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T13:21:51Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="b9fa5488ac04b1add4b31c986060979a58aa1a78" -LABEL org.opencontainers.image.version="v0.6.0" +LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" +LABEL org.opencontainers.image.version="v0.6.1" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "interop_summary_to_csv v0.6.0" + echo "interop_summary_to_csv v0.6.1" echo "" echo "Input arguments:" echo " --input" @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "interop_summary_to_csv v0.6.0" + echo "interop_summary_to_csv v0.6.1" exit ;; --input) @@ -759,7 +759,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.6.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.6.1' fi # print dockerfile diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index d1c5abe..f582249 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish" namespace: "io" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -204,7 +204,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.6.0" + target_tag: "v0.6.1" namespace_separator: "/" setup: - type: "apt" @@ -222,11 +222,11 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -242,7 +242,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish/_viash.yaml b/target/executable/io/publish/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/executable/io/publish/_viash.yaml +++ b/target/executable/io/publish/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index 0df4c9a..14cc0e1 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish v0.6.0 +# publish v0.6.1 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish" -LABEL org.opencontainers.image.created="2025-09-17T14:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T13:21:51Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="b9fa5488ac04b1add4b31c986060979a58aa1a78" -LABEL org.opencontainers.image.version="v0.6.0" +LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" +LABEL org.opencontainers.image.version="v0.6.1" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish v0.6.0" + echo "publish v0.6.1" echo "" echo "Publish the processed results of the run" echo "" @@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish v0.6.0" + echo "publish v0.6.1" exit ;; --input) @@ -869,7 +869,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.6.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.6.1' fi # print dockerfile diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index 8672f7e..fd4cfac 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "untar" namespace: "io" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -141,7 +141,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.6.0" + target_tag: "v0.6.1" namespace_separator: "/" setup: - type: "apt" @@ -159,11 +159,11 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -179,7 +179,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/untar/_viash.yaml b/target/executable/io/untar/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/executable/io/untar/_viash.yaml +++ b/target/executable/io/untar/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 2a9b4ff..6919ec2 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# untar v0.6.0 +# untar v0.6.1 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io untar" -LABEL org.opencontainers.image.created="2025-09-17T14:02:47Z" +LABEL org.opencontainers.image.created="2025-10-03T13:21:52Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="b9fa5488ac04b1add4b31c986060979a58aa1a78" -LABEL org.opencontainers.image.version="v0.6.0" +LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" +LABEL org.opencontainers.image.version="v0.6.1" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "untar v0.6.0" + echo "untar v0.6.1" echo "" echo "Unpack a .tar file. When the contents of the .tar file is just a single" echo "directory," @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "untar v0.6.0" + echo "untar v0.6.1" exit ;; --input) @@ -771,7 +771,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.6.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.6.1' fi # print dockerfile diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index 0591691..d45d8d3 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_samples" namespace: "dataflow" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -168,11 +168,11 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -188,7 +188,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/combine_samples/_viash.yaml b/target/nextflow/dataflow/combine_samples/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/nextflow/dataflow/combine_samples/_viash.yaml +++ b/target/nextflow/dataflow/combine_samples/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index 51e6383..580c436 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -1,4 +1,4 @@ -// combine_samples v0.6.0 +// combine_samples v0.6.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "combine_samples", "namespace" : "dataflow", - "version" : "v0.6.0", + "version" : "v0.6.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3235,12 +3235,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.4", - "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78", + "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3257,7 +3257,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + ".engines[.type == 'docker'].target_tag := 'v0.6.1'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config index 7b7833c..faa8b3a 100644 --- a/target/nextflow/dataflow/combine_samples/nextflow.config +++ b/target/nextflow/dataflow/combine_samples/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/combine_samples' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.6.0' + version = 'v0.6.1' description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.' } diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml index d9942b9..3991bf6 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "gather_fastqs_and_validate" namespace: "dataflow" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -159,11 +159,11 @@ build_info: output: "target/nextflow/dataflow/gather_fastqs_and_validate" executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -179,7 +179,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index b9a6b9f..d636fc9 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -1,4 +1,4 @@ -// gather_fastqs_and_validate v0.6.0 +// gather_fastqs_and_validate v0.6.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "gather_fastqs_and_validate", "namespace" : "dataflow", - "version" : "v0.6.0", + "version" : "v0.6.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3232,12 +3232,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.4", - "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78", + "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3254,7 +3254,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + ".engines[.type == 'docker'].target_tag := 'v0.6.1'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config index e640395..0e9a1d4 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/gather_fastqs_and_validate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.6.0' + version = 'v0.6.1' description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n' } diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 9ae9a5f..5b490b5 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "demultiplex" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -165,22 +165,22 @@ dependencies: repository: type: "vsh" repo: "biobox" - tag: "v0.4.0" + tag: "v0.4.1" - name: "bases2fastq" repository: type: "vsh" repo: "biobox" - tag: "v0.4.0" + tag: "v0.4.1" - name: "fastqc" repository: type: "vsh" repo: "biobox" - tag: "v0.4.0" + tag: "v0.4.1" - name: "multiqc" repository: type: "vsh" repo: "biobox" - tag: "v0.4.0" + tag: "v0.4.1" - name: "detect_demultiplexer" repository: type: "local" @@ -188,7 +188,7 @@ repositories: - type: "vsh" name: "bb" repo: "biobox" - tag: "v0.4.0" + tag: "v0.4.1" license: "MIT" links: repository: "https://github.com/viash-hub/demultiplex" @@ -268,21 +268,21 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" dependencies: - "target/nextflow/io/untar" - "target/nextflow/dataflow/gather_fastqs_and_validate" - "target/nextflow/io/interop_summary_to_csv" - "target/nextflow/dataflow/combine_samples" - - "target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert" - - "target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq" - - "target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc" - - "target/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc" + - "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert" + - "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq" + - "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc" + - "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc" - "target/nextflow/detect_demultiplexer" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -298,7 +298,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/demultiplex/_viash.yaml b/target/nextflow/demultiplex/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/nextflow/demultiplex/_viash.yaml +++ b/target/nextflow/demultiplex/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index 94b4687..96ba3eb 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -1,4 +1,4 @@ -// demultiplex v0.6.0 +// demultiplex v0.6.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3031,7 +3031,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3246,7 +3246,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "biobox", - "tag" : "v0.4.0" + "tag" : "v0.4.1" } }, { @@ -3254,7 +3254,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "biobox", - "tag" : "v0.4.0" + "tag" : "v0.4.1" } }, { @@ -3262,7 +3262,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "biobox", - "tag" : "v0.4.0" + "tag" : "v0.4.1" } }, { @@ -3270,7 +3270,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "biobox", - "tag" : "v0.4.0" + "tag" : "v0.4.1" } }, { @@ -3285,7 +3285,7 @@ meta = [ "type" : "vsh", "name" : "bb", "repo" : "biobox", - "tag" : "v0.4.0" + "tag" : "v0.4.1" } ], "license" : "MIT", @@ -3380,12 +3380,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.4", - "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78", + "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3402,7 +3402,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + ".engines[.type == 'docker'].target_tag := 'v0.6.1'" ], "keywords" : [ "bioinformatics", @@ -3426,10 +3426,10 @@ include { untar } from "${meta.resources_dir}/../../nextflow/io/untar/main.nf" include { gather_fastqs_and_validate } from "${meta.resources_dir}/../../nextflow/dataflow/gather_fastqs_and_validate/main.nf" include { interop_summary_to_csv } from "${meta.resources_dir}/../../nextflow/io/interop_summary_to_csv/main.nf" include { combine_samples } from "${meta.resources_dir}/../../nextflow/dataflow/combine_samples/main.nf" -include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bcl_convert/main.nf" -include { bases2fastq } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/bases2fastq/main.nf" -include { fastqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/fastqc/main.nf" -include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.0/nextflow/multiqc/main.nf" +include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/main.nf" +include { bases2fastq } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/main.nf" +include { fastqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/main.nf" +include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/main.nf" include { detect_demultiplexer } from "${meta.resources_dir}/../../nextflow/detect_demultiplexer/main.nf" // inner workflow @@ -3525,6 +3525,7 @@ workflow run_wf { //"split_lanes": true, "legacy_fastq": true, // Illumina style output names "group_fastq": true, // No subdir per sample + "skip_multi_qc": true // This pipeline generates its own MultiQC report ], toState: {id, result, state -> def toAdd = [ diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config index 663c376..b28b34d 100644 --- a/target/nextflow/demultiplex/nextflow.config +++ b/target/nextflow/demultiplex/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demultiplex' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.6.0' + version = 'v0.6.1' description = 'Demultiplexing of raw sequencing data' } diff --git a/target/nextflow/detect_demultiplexer/.config.vsh.yaml b/target/nextflow/detect_demultiplexer/.config.vsh.yaml index 1219eb9..bbe050f 100644 --- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml +++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "detect_demultiplexer" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Arguments" arguments: @@ -168,11 +168,11 @@ build_info: output: "target/nextflow/detect_demultiplexer" executable: "target/nextflow/detect_demultiplexer/main.nf" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -188,7 +188,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/detect_demultiplexer/_viash.yaml b/target/nextflow/detect_demultiplexer/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/nextflow/detect_demultiplexer/_viash.yaml +++ b/target/nextflow/detect_demultiplexer/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/detect_demultiplexer/main.nf b/target/nextflow/detect_demultiplexer/main.nf index 09f08e3..514eaf0 100644 --- a/target/nextflow/detect_demultiplexer/main.nf +++ b/target/nextflow/detect_demultiplexer/main.nf @@ -1,4 +1,4 @@ -// detect_demultiplexer v0.6.0 +// detect_demultiplexer v0.6.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3031,7 +3031,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "detect_demultiplexer", - "version" : "v0.6.0", + "version" : "v0.6.1", "argument_groups" : [ { "name" : "Arguments", @@ -3224,12 +3224,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/detect_demultiplexer", "viash_version" : "0.9.4", - "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78", + "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3246,7 +3246,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + ".engines[.type == 'docker'].target_tag := 'v0.6.1'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/detect_demultiplexer/nextflow.config b/target/nextflow/detect_demultiplexer/nextflow.config index 94b3064..eed9c81 100644 --- a/target/nextflow/detect_demultiplexer/nextflow.config +++ b/target/nextflow/detect_demultiplexer/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'detect_demultiplexer' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.6.0' + version = 'v0.6.1' description = 'Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n' } diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml index 1c966a1..0f069d3 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "interop_summary_to_csv" namespace: "io" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -135,7 +135,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.6.0" + target_tag: "v0.6.1" namespace_separator: "/" setup: - type: "apt" @@ -160,11 +160,11 @@ build_info: output: "target/nextflow/io/interop_summary_to_csv" executable: "target/nextflow/io/interop_summary_to_csv/main.nf" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -180,7 +180,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/interop_summary_to_csv/_viash.yaml b/target/nextflow/io/interop_summary_to_csv/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/nextflow/io/interop_summary_to_csv/_viash.yaml +++ b/target/nextflow/io/interop_summary_to_csv/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index 98135f4..ffb527a 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -1,4 +1,4 @@ -// interop_summary_to_csv v0.6.0 +// interop_summary_to_csv v0.6.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "interop_summary_to_csv", "namespace" : "io", - "version" : "v0.6.0", + "version" : "v0.6.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3203,7 +3203,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.6.0", + "target_tag" : "v0.6.1", "namespace_separator" : "/", "setup" : [ { @@ -3233,12 +3233,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.4", - "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78", + "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3255,7 +3255,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + ".engines[.type == 'docker'].target_tag := 'v0.6.1'" ], "keywords" : [ "bioinformatics", @@ -3699,7 +3699,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/interop_summary_to_csv", - "tag" : "v0.6.0" + "tag" : "v0.6.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow.config b/target/nextflow/io/interop_summary_to_csv/nextflow.config index eae0284..113b242 100644 --- a/target/nextflow/io/interop_summary_to_csv/nextflow.config +++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/interop_summary_to_csv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.6.0' + version = 'v0.6.1' } process.container = 'nextflow/bash:latest' diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index 746d818..288b3a5 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish" namespace: "io" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -204,7 +204,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.6.0" + target_tag: "v0.6.1" namespace_separator: "/" setup: - type: "apt" @@ -222,11 +222,11 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -242,7 +242,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish/_viash.yaml b/target/nextflow/io/publish/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/nextflow/io/publish/_viash.yaml +++ b/target/nextflow/io/publish/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index 3d4c2e8..8a99bea 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -1,4 +1,4 @@ -// publish v0.6.0 +// publish v0.6.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish", "namespace" : "io", - "version" : "v0.6.0", + "version" : "v0.6.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3279,7 +3279,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.6.0", + "target_tag" : "v0.6.1", "namespace_separator" : "/", "setup" : [ { @@ -3302,12 +3302,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.4", - "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78", + "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3324,7 +3324,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + ".engines[.type == 'docker'].target_tag := 'v0.6.1'" ], "keywords" : [ "bioinformatics", @@ -3799,7 +3799,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/publish", - "tag" : "v0.6.0" + "tag" : "v0.6.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish/nextflow.config b/target/nextflow/io/publish/nextflow.config index fd84193..10d9efc 100644 --- a/target/nextflow/io/publish/nextflow.config +++ b/target/nextflow/io/publish/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.6.0' + version = 'v0.6.1' description = 'Publish the processed results of the run' } diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 4a5170b..c77b288 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "untar" namespace: "io" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -141,7 +141,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.6.0" + target_tag: "v0.6.1" namespace_separator: "/" setup: - type: "apt" @@ -159,11 +159,11 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -179,7 +179,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/untar/_viash.yaml b/target/nextflow/io/untar/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/nextflow/io/untar/_viash.yaml +++ b/target/nextflow/io/untar/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index e04fd93..b6fc098 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -1,4 +1,4 @@ -// untar v0.6.0 +// untar v0.6.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "untar", "namespace" : "io", - "version" : "v0.6.0", + "version" : "v0.6.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3209,7 +3209,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.6.0", + "target_tag" : "v0.6.1", "namespace_separator" : "/", "setup" : [ { @@ -3232,12 +3232,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.4", - "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78", + "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3254,7 +3254,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + ".engines[.type == 'docker'].target_tag := 'v0.6.1'" ], "keywords" : [ "bioinformatics", @@ -3728,7 +3728,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/untar", - "tag" : "v0.6.0" + "tag" : "v0.6.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config index 91da17b..0a7305a 100644 --- a/target/nextflow/io/untar/nextflow.config +++ b/target/nextflow/io/untar/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/untar' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.6.0' + version = 'v0.6.1' description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n' } diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index d6df5ed..a7adb50 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "runner" -version: "v0.6.0" +version: "v0.6.1" argument_groups: - name: "Input arguments" arguments: @@ -217,14 +217,14 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.4" - git_commit: "b9fa5488ac04b1add4b31c986060979a58aa1a78" + git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea" git_remote: "https://github.com/viash-hub/demultiplex" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" package_config: name: "demultiplex" - version: "v0.6.0" + version: "v0.6.1" description: "Demultiplexing pipeline\n" info: test_resources: @@ -240,7 +240,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.6.1'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/runner/_viash.yaml b/target/nextflow/runner/_viash.yaml index e8b0900..6f82e74 100644 --- a/target/nextflow/runner/_viash.yaml +++ b/target/nextflow/runner/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.6.0 +version: v0.6.1 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index 9e73276..16a5c08 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.6.0 +// runner v0.6.1 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3031,7 +3031,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "runner", - "version" : "v0.6.0", + "version" : "v0.6.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3301,12 +3301,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.4", - "git_commit" : "b9fa5488ac04b1add4b31c986060979a58aa1a78", + "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.6.0", + "version" : "v0.6.1", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3323,7 +3323,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.6.0'" + ".engines[.type == 'docker'].target_tag := 'v0.6.1'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/runner/nextflow.config b/target/nextflow/runner/nextflow.config index 55e761d..f2ab6bd 100644 --- a/target/nextflow/runner/nextflow.config +++ b/target/nextflow/runner/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'runner' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.6.0' + version = 'v0.6.1' description = 'Runner for demultiplexing of raw sequencing data' }