From ebd9b69856d4611e4fb93edde7793e77f7620c4e Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 13 Sep 2024 09:46:12 +0000 Subject: [PATCH] Build branch main with version main (399e469) Build pipeline: viash-hub.demultiplex.main-f55jt Source commit: https://github.com/viash-hub/demultiplex/commit/399e46901d6ce882a7430842b0d74774736439e2 Source message: Add test_resources to .gitignore --- .gitignore | 3 +- CHANGELOG.md | 18 +- src/demultiplex/config.vsh.yaml | 2 +- .../nextflow/bcl_convert/.config.vsh.yaml | 48 ++++- .../nextflow/bcl_convert/main.nf | 149 +++++++++++--- .../nextflow/bcl_convert/nextflow.config | 3 +- .../nextflow/bcl_convert/nextflow_schema.json | 0 .../nextflow/falco/.config.vsh.yaml | 27 ++- .../{v0.1.0 => v0.2.0}/nextflow/falco/main.nf | 116 ++++++++--- .../nextflow/falco/nextflow.config | 3 +- .../nextflow/falco/nextflow_schema.json | 4 +- .../nextflow/multiqc/.config.vsh.yaml | 48 +++-- .../nextflow/multiqc/main.nf | 189 ++++++++++++------ .../nextflow/multiqc/nextflow.config | 3 +- .../nextflow/multiqc/nextflow_schema.json | 20 +- .../interop_summary_to_csv/.config.vsh.yaml | 2 +- .../interop_summary_to_csv | 4 +- target/executable/io/untar/.config.vsh.yaml | 2 +- target/executable/io/untar/untar | 4 +- .../dataflow/combine_samples/.config.vsh.yaml | 2 +- .../nextflow/dataflow/combine_samples/main.nf | 2 +- .../.config.vsh.yaml | 2 +- .../gather_fastqs_and_validate/main.nf | 2 +- target/nextflow/demultiplex/.config.vsh.yaml | 16 +- target/nextflow/demultiplex/main.nf | 16 +- .../interop_summary_to_csv/.config.vsh.yaml | 2 +- .../io/interop_summary_to_csv/main.nf | 2 +- target/nextflow/io/untar/.config.vsh.yaml | 2 +- target/nextflow/io/untar/main.nf | 2 +- test_resources | 1 - 30 files changed, 482 insertions(+), 212 deletions(-) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/bcl_convert/.config.vsh.yaml (91%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/bcl_convert/main.nf (97%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/bcl_convert/nextflow.config (98%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/bcl_convert/nextflow_schema.json (100%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/falco/.config.vsh.yaml (95%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/falco/main.nf (97%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/falco/nextflow.config (98%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/falco/nextflow_schema.json (98%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/multiqc/.config.vsh.yaml (94%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/multiqc/main.nf (97%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/multiqc/nextflow.config (98%) rename target/dependencies/vsh/vsh/biobox/{v0.1.0 => v0.2.0}/nextflow/multiqc/nextflow_schema.json (96%) delete mode 120000 test_resources diff --git a/.gitignore b/.gitignore index 78db699..2c35f84 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,8 @@ target testData +test_resources # Nextflow related files .nextflow .nextflow.log* -work \ No newline at end of file +work diff --git a/CHANGELOG.md b/CHANGELOG.md index 214204d..b76003b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,17 +1,13 @@ -# 0.1.2 +# Unreleased -## NEW FEATURES +## Minor updates + +* Bump viash to 0.9.0 (PR #14). + +* `demultiplex` workflow: use `v0.2.0` release instead of `main` branch for `biobox` dependencies (PR #11). * Renamed `biobase` repository to `biobox` (PR #13 and PR #15). -* Bump viash to 0.9.0-RC6 (PR #14). - -# v0.1.1 - -## NEW FEATURES - -* `demultiplex` workflow: use `v0.1.0` release instead of `main` branch for `biobase` dependencies (PR #11). - # v0.1.0 -Initial release \ No newline at end of file +Initial release diff --git a/src/demultiplex/config.vsh.yaml b/src/demultiplex/config.vsh.yaml index 97341bc..2e13d3a 100644 --- a/src/demultiplex/config.vsh.yaml +++ b/src/demultiplex/config.vsh.yaml @@ -61,7 +61,7 @@ repositories: - name: bb type: vsh repo: biobox - tag: v0.1.0 + tag: v0.2.0 runners: - type: nextflow diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/.config.vsh.yaml similarity index 91% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/.config.vsh.yaml rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/.config.vsh.yaml index 9fa8ed0..6aba9f9 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/.config.vsh.yaml @@ -1,5 +1,30 @@ name: "bcl_convert" -version: "v0.1.0" +version: "0.2.0" +authors: +- name: "Toni Verbeiren" + roles: + - "author" + - "maintainer" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" +- name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" argument_groups: - name: "Input arguments" arguments: @@ -281,9 +306,16 @@ status: "enabled" requirements: commands: - "ps" -license: "MIT" +keywords: +- "demultiplex" +- "fastq" +- "bcl" +- "illumina" +license: "Proprietary" links: repository: "https://github.com/viash-hub/biobox" + homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html" + documentation: "https://support.illumina.com/downloads/bcl-convert-user-guide.html" runners: - type: "executable" id: "executable" @@ -354,7 +386,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -385,22 +417,22 @@ build_info: engine: "docker|native" output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" - viash_version: "0.9.0-RC6" - git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.1.0" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC6" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf similarity index 97% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/main.nf rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf index 9ecfb1c..eb1c214 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf @@ -1,13 +1,17 @@ -// bcl_convert v0.1.0 +// bcl_convert 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// 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 +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such // files, or include a separate license file detailing the licenses of all included // files. +// +// Component authors: +// * Toni Verbeiren (author, maintainer) +// * Dorien Roosen (author) //////////////////////////// // VDSL3 helper functions // @@ -760,8 +764,11 @@ def runEach(Map args) { def fromState_ = args.fromState def toState_ = args.toState def filter_ = args.filter + def runIf_ = args.runIf def id_ = args.id + assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf." + workflow runEachWf { take: input_ch main: @@ -783,7 +790,20 @@ def runEach(Map args) { [new_id] + tup.drop(1) } : filter_ch - def data_ch = id_ch | map{tup -> + def chPassthrough = null + def chRun = null + if (runIf_) { + def idRunIfBranch = id_ch.branch{ tup -> + run: runIf_(tup[0], tup[1], comp_) + passthrough: true + } + chPassthrough = idRunIfBranch.passthrough + chRun = idRunIfBranch.run + } else { + chRun = id_ch + chPassthrough = Channel.empty() + } + def data_ch = chRun | map{tup -> def new_data = tup[1] if (fromState_ instanceof Map) { new_data = fromState_.collectEntries{ key0, key1 -> @@ -821,8 +841,11 @@ def runEach(Map args) { [tup[0], new_state] + tup.drop(3) } : out_ch + + def return_ch = post_ch + | concat(chPassthrough) - post_ch + return_ch } // mix all results @@ -1598,8 +1621,8 @@ def findStates(Map params, Map config) { // construct renameMap if (args.rename_keys) { def renameMap = args.rename_keys.collectEntries{renameString -> - def split = renameString.split(";") - assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'" + def split = renameString.split(":") + assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values" split } @@ -1709,7 +1732,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1780,7 +1805,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1822,7 +1849,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2626,30 +2655,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) { tuple } - def chModifiedFiltered = workflowArgs.filter ? - chModified | filter{workflowArgs.filter(it)} : - chModified def chRun = null def chPassthrough = null if (workflowArgs.runIf) { - def runIfBranch = chModifiedFiltered.branch{ tup -> + def runIfBranch = chModified.branch{ tup -> run: workflowArgs.runIf(tup[0], tup[1]) passthrough: true } chRun = runIfBranch.run chPassthrough = runIfBranch.passthrough } else { - chRun = chModifiedFiltered + chRun = chModified chPassthrough = Channel.empty() } + def chRunFiltered = workflowArgs.filter ? + chRun | filter{workflowArgs.filter(it)} : + chRun + def chArgs = workflowArgs.fromState ? - chRun | map{ + chRunFiltered | map{ def new_data = workflowArgs.fromState(it.take(2)) [it[0], new_data] } : - chRun | map {tup -> tup.take(2)} + chRunFiltered | map {tup -> tup.take(2)} // fill in defaults def chArgsWithDefaults = chArgs @@ -2720,7 +2750,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) { // | view{"chInitialOutput: ${it.take(3)}"} // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...] - def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_) + def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_) // input tuple format: [join_id, id, output, prev_state, ...] // output tuple format: [join_id, id, new_state, ...] | map{ tup -> @@ -2779,7 +2809,49 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "bcl_convert", - "version" : "v0.1.0", + "version" : "0.2.0", + "authors" : [ + { + "name" : "Toni Verbeiren", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + } + ], "argument_groups" : [ { "name" : "Input arguments", @@ -3125,9 +3197,17 @@ meta = [ "ps" ] }, - "license" : "MIT", + "keywords" : [ + "demultiplex", + "fastq", + "bcl", + "illumina" + ], + "license" : "Proprietary", "links" : { - "repository" : "https://github.com/viash-hub/biobox" + "repository" : "https://github.com/viash-hub/biobox", + "homepage" : "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html", + "documentation" : "https://support.illumina.com/downloads/bcl-convert-user-guide.html" }, "runners" : [ { @@ -3209,7 +3289,7 @@ meta = [ "id" : "docker", "image" : "debian:trixie-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3248,22 +3328,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", - "viash_version" : "0.9.0-RC6", - "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.1.0", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC6", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3454,7 +3534,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3585,7 +3669,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3593,8 +3678,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3631,6 +3716,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3642,10 +3728,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3730,7 +3815,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/bcl_convert", - "tag" : "v0.1.0" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow.config similarity index 98% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow.config rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow.config index 9444a22..0f8797a 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow.config @@ -2,8 +2,9 @@ manifest { name = 'bcl_convert' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = '0.2.0' description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n' + author = 'Toni Verbeiren, Dorien Roosen' } process.container = 'nextflow/bash:latest' diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow_schema.json b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow_schema.json rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/.config.vsh.yaml similarity index 95% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/.config.vsh.yaml rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/.config.vsh.yaml index c7e812b..71b2d68 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/.config.vsh.yaml @@ -1,5 +1,18 @@ name: "falco" -version: "v0.1.0" +version: "0.2.0" +authors: +- name: "Toni Verbeiren" + roles: + - "author" + - "maintainer" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" argument_groups: - name: "Input arguments" arguments: @@ -274,7 +287,7 @@ engines: id: "docker" image: "debian:trixie-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "apt" @@ -303,22 +316,22 @@ build_info: engine: "docker|native" output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" - viash_version: "0.9.0-RC6" - git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.1.0" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC6" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf similarity index 97% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/main.nf rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf index d0389df..b0bdf8e 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf @@ -1,13 +1,16 @@ -// falco v0.1.0 +// falco 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// 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 +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such // files, or include a separate license file detailing the licenses of all included // files. +// +// Component authors: +// * Toni Verbeiren (author, maintainer) //////////////////////////// // VDSL3 helper functions // @@ -760,8 +763,11 @@ def runEach(Map args) { def fromState_ = args.fromState def toState_ = args.toState def filter_ = args.filter + def runIf_ = args.runIf def id_ = args.id + assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf." + workflow runEachWf { take: input_ch main: @@ -783,7 +789,20 @@ def runEach(Map args) { [new_id] + tup.drop(1) } : filter_ch - def data_ch = id_ch | map{tup -> + def chPassthrough = null + def chRun = null + if (runIf_) { + def idRunIfBranch = id_ch.branch{ tup -> + run: runIf_(tup[0], tup[1], comp_) + passthrough: true + } + chPassthrough = idRunIfBranch.passthrough + chRun = idRunIfBranch.run + } else { + chRun = id_ch + chPassthrough = Channel.empty() + } + def data_ch = chRun | map{tup -> def new_data = tup[1] if (fromState_ instanceof Map) { new_data = fromState_.collectEntries{ key0, key1 -> @@ -821,8 +840,11 @@ def runEach(Map args) { [tup[0], new_state] + tup.drop(3) } : out_ch + + def return_ch = post_ch + | concat(chPassthrough) - post_ch + return_ch } // mix all results @@ -1598,8 +1620,8 @@ def findStates(Map params, Map config) { // construct renameMap if (args.rename_keys) { def renameMap = args.rename_keys.collectEntries{renameString -> - def split = renameString.split(";") - assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'" + def split = renameString.split(":") + assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values" split } @@ -1709,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1780,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1822,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2626,30 +2654,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) { tuple } - def chModifiedFiltered = workflowArgs.filter ? - chModified | filter{workflowArgs.filter(it)} : - chModified def chRun = null def chPassthrough = null if (workflowArgs.runIf) { - def runIfBranch = chModifiedFiltered.branch{ tup -> + def runIfBranch = chModified.branch{ tup -> run: workflowArgs.runIf(tup[0], tup[1]) passthrough: true } chRun = runIfBranch.run chPassthrough = runIfBranch.passthrough } else { - chRun = chModifiedFiltered + chRun = chModified chPassthrough = Channel.empty() } + def chRunFiltered = workflowArgs.filter ? + chRun | filter{workflowArgs.filter(it)} : + chRun + def chArgs = workflowArgs.fromState ? - chRun | map{ + chRunFiltered | map{ def new_data = workflowArgs.fromState(it.take(2)) [it[0], new_data] } : - chRun | map {tup -> tup.take(2)} + chRunFiltered | map {tup -> tup.take(2)} // fill in defaults def chArgsWithDefaults = chArgs @@ -2720,7 +2749,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) { // | view{"chInitialOutput: ${it.take(3)}"} // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...] - def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_) + def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_) // input tuple format: [join_id, id, output, prev_state, ...] // output tuple format: [join_id, id, new_state, ...] | map{ tup -> @@ -2779,7 +2808,29 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "falco", - "version" : "v0.1.0", + "version" : "0.2.0", + "authors" : [ + { + "name" : "Toni Verbeiren", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + } + ], "argument_groups" : [ { "name" : "Input arguments", @@ -3080,7 +3131,7 @@ meta = [ "id" : "docker", "image" : "debian:trixie-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3118,22 +3169,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/falco", - "viash_version" : "0.9.0-RC6", - "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.1.0", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC6", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3298,7 +3349,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3429,7 +3484,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3437,8 +3493,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3475,6 +3531,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3486,10 +3543,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3574,7 +3630,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/falco", - "tag" : "v0.1.0" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow.config similarity index 98% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow.config rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow.config index 3ac4103..9251d23 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow.config @@ -2,8 +2,9 @@ manifest { name = 'falco' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = '0.2.0' description = 'A C++ drop-in replacement of FastQC to assess the quality of sequence read data' + author = 'Toni Verbeiren' } process.container = 'nextflow/bash:latest' diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow_schema.json b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow_schema.json similarity index 98% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow_schema.json rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow_schema.json index 71b5872..22f431e 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow_schema.json +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow_schema.json @@ -17,8 +17,8 @@ "input": { "type": "string", - "description": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\":\"`. input fastq files", - "help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\":\"`. input fastq files" + "description": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files", + "help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files" } diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/.config.vsh.yaml b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml similarity index 94% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/.config.vsh.yaml rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml index fcf4762..245ef5c 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml @@ -1,5 +1,19 @@ name: "multiqc" -version: "v0.1.0" +version: "0.2.0" +authors: +- name: "Dorien Roosen" + roles: + - "author" + - "maintainer" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" argument_groups: - name: "Input" arguments: @@ -63,39 +77,43 @@ argument_groups: description: "Use only these module" info: null example: - - "fastqc,cutadapt" + - "fastqc" + - "cutadapt" required: false direction: "input" multiple: true - multiple_sep: "," + multiple_sep: ";" - type: "string" name: "--exclude_modules" description: "Do not use only these modules" info: null example: - - "fastqc,cutadapt" + - "fastqc" + - "cutadapt" required: false direction: "input" multiple: true - multiple_sep: "," + multiple_sep: ";" - type: "string" name: "--ignore_analysis" info: null example: - - "run_one/*,run_two/*" + - "run_one/*" + - "run_two/*" required: false direction: "input" multiple: true - multiple_sep: "," + multiple_sep: ";" - type: "string" name: "--ignore_samples" info: null example: - - "sample_1*,sample_3*" + - "sample_1*" + - "sample_3*" required: false direction: "input" multiple: true - multiple_sep: "," + multiple_sep: ";" - type: "boolean_true" name: "--ignore_symlinks" description: "Ignore symlinked directories and files" @@ -415,7 +433,7 @@ engines: id: "docker" image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "0.2.0" namespace_separator: "/" setup: - type: "docker" @@ -437,22 +455,22 @@ build_info: engine: "docker|native" output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" - viash_version: "0.9.0-RC6" - git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724" + viash_version: "0.9.0" + git_commit: "5526b3e939030daea80595fa98387b469329bbfa" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" - version: "v0.1.0" + version: "0.2.0" description: "A collection of bioinformatics tools for working with sequence data.\n" info: null - viash_version: "0.9.0-RC6" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := '0.2.0'" keywords: - "bioinformatics" - "modules" diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/main.nf b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf similarity index 97% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/main.nf rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf index d7f771d..7e0282b 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/main.nf +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf @@ -1,13 +1,16 @@ -// multiqc v0.1.0 +// multiqc 0.2.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// 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 +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such // files, or include a separate license file detailing the licenses of all included // files. +// +// Component authors: +// * Dorien Roosen (author, maintainer) //////////////////////////// // VDSL3 helper functions // @@ -760,8 +763,11 @@ def runEach(Map args) { def fromState_ = args.fromState def toState_ = args.toState def filter_ = args.filter + def runIf_ = args.runIf def id_ = args.id + assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf." + workflow runEachWf { take: input_ch main: @@ -783,7 +789,20 @@ def runEach(Map args) { [new_id] + tup.drop(1) } : filter_ch - def data_ch = id_ch | map{tup -> + def chPassthrough = null + def chRun = null + if (runIf_) { + def idRunIfBranch = id_ch.branch{ tup -> + run: runIf_(tup[0], tup[1], comp_) + passthrough: true + } + chPassthrough = idRunIfBranch.passthrough + chRun = idRunIfBranch.run + } else { + chRun = id_ch + chPassthrough = Channel.empty() + } + def data_ch = chRun | map{tup -> def new_data = tup[1] if (fromState_ instanceof Map) { new_data = fromState_.collectEntries{ key0, key1 -> @@ -821,8 +840,11 @@ def runEach(Map args) { [tup[0], new_state] + tup.drop(3) } : out_ch + + def return_ch = post_ch + | concat(chPassthrough) - post_ch + return_ch } // mix all results @@ -1598,8 +1620,8 @@ def findStates(Map params, Map config) { // construct renameMap if (args.rename_keys) { def renameMap = args.rename_keys.collectEntries{renameString -> - def split = renameString.split(";") - assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'" + def split = renameString.split(":") + assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values" split } @@ -1709,7 +1731,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1780,7 +1804,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1822,7 +1848,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2626,30 +2654,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) { tuple } - def chModifiedFiltered = workflowArgs.filter ? - chModified | filter{workflowArgs.filter(it)} : - chModified def chRun = null def chPassthrough = null if (workflowArgs.runIf) { - def runIfBranch = chModifiedFiltered.branch{ tup -> + def runIfBranch = chModified.branch{ tup -> run: workflowArgs.runIf(tup[0], tup[1]) passthrough: true } chRun = runIfBranch.run chPassthrough = runIfBranch.passthrough } else { - chRun = chModifiedFiltered + chRun = chModified chPassthrough = Channel.empty() } + def chRunFiltered = workflowArgs.filter ? + chRun | filter{workflowArgs.filter(it)} : + chRun + def chArgs = workflowArgs.fromState ? - chRun | map{ + chRunFiltered | map{ def new_data = workflowArgs.fromState(it.take(2)) [it[0], new_data] } : - chRun | map {tup -> tup.take(2)} + chRunFiltered | map {tup -> tup.take(2)} // fill in defaults def chArgsWithDefaults = chArgs @@ -2720,7 +2749,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) { // | view{"chInitialOutput: ${it.take(3)}"} // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...] - def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_) + def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_) // input tuple format: [join_id, id, output, prev_state, ...] // output tuple format: [join_id, id, new_state, ...] | map{ tup -> @@ -2779,7 +2808,30 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "multiqc", - "version" : "v0.1.0", + "version" : "0.2.0", + "authors" : [ + { + "name" : "Dorien Roosen", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + } + ], "argument_groups" : [ { "name" : "Input", @@ -2855,46 +2907,50 @@ meta = [ "name" : "--include_modules", "description" : "Use only these module", "example" : [ - "fastqc,cutadapt" + "fastqc", + "cutadapt" ], "required" : false, "direction" : "input", "multiple" : true, - "multiple_sep" : "," + "multiple_sep" : ";" }, { "type" : "string", "name" : "--exclude_modules", "description" : "Do not use only these modules", "example" : [ - "fastqc,cutadapt" + "fastqc", + "cutadapt" ], "required" : false, "direction" : "input", "multiple" : true, - "multiple_sep" : "," + "multiple_sep" : ";" }, { "type" : "string", "name" : "--ignore_analysis", "example" : [ - "run_one/*,run_two/*" + "run_one/*", + "run_two/*" ], "required" : false, "direction" : "input", "multiple" : true, - "multiple_sep" : "," + "multiple_sep" : ";" }, { "type" : "string", "name" : "--ignore_samples", "example" : [ - "sample_1*,sample_3*" + "sample_1*", + "sample_3*" ], "required" : false, "direction" : "input", "multiple" : true, - "multiple_sep" : "," + "multiple_sep" : ";" }, { "type" : "boolean_true", @@ -3279,7 +3335,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "0.2.0", "namespace_separator" : "/", "setup" : [ { @@ -3309,22 +3365,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/multiqc", - "viash_version" : "0.9.0-RC6", - "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724", + "viash_version" : "0.9.0", + "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { "name" : "biobox", - "version" : "v0.1.0", + "version" : "0.2.0", "description" : "A collection of bioinformatics tools for working with sequence data.\n", - "viash_version" : "0.9.0-RC6", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := '0.2.0'" ], "keywords" : [ "bioinformatics", @@ -3411,26 +3467,32 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" #!/bin/bash # disable flags -[[ "\\$par_ignore_symlinks" == "false" ]] && unset par_ignore_symlinks -[[ "\\$par_dirs" == "false" ]] && unset par_dirs -[[ "\\$par_full_names" == "false" ]] && unset par_full_names -[[ "\\$par_fn_as_s_name" == "false" ]] && unset par_fn_as_s_name -[[ "\\$par_profile_runtime" == "false" ]] && unset par_profile_runtime -[[ "\\$par_verbose" == "false" ]] && unset par_verbose -[[ "\\$par_quiet" == "false" ]] && unset par_quiet -[[ "\\$par_strict" == "false" ]] && unset par_strict -[[ "\\$par_development" == "false" ]] && unset par_development -[[ "\\$par_require_logs" == "false" ]] && unset par_require_logs -[[ "\\$par_no_megaqc_upload" == "false" ]] && unset par_no_megaqc_upload -[[ "\\$par_no_ansi" == "false" ]] && unset par_no_ansi -[[ "\\$par_flat" == "false" ]] && unset par_flat -[[ "\\$par_interactive" == "false" ]] && unset par_interactive -[[ "\\$par_static_plot_export" == "false" ]] && unset par_static_plot_export -[[ "\\$par_data_dir" == "false" ]] && unset par_data_dir -[[ "\\$par_no_data_dir" == "false" ]] && unset par_no_data_dir -[[ "\\$par_zip_data_dir" == "false" ]] && unset par_zip_data_dir -[[ "\\$par_pdf" == "false" ]] && unset par_pdf +unset_if_false=( + par_ignore_symlinks + par_dirs + par_full_names + par_fn_as_s_name + par_profile_runtime + par_verbose + par_quiet + par_strict + par_development + par_require_logs + par_no_megaqc_upload + par_no_ansi + par_flat + par_interactive + par_static_plot_export + par_data_dir + par_no_data_dir + par_zip_data_dir + par_pdf +) +for par in \\${unset_if_false[@]}; do + test_val="\\${!par}" + [[ "\\$test_val" == "false" ]] && unset \\$par +done # handle inputs out_dir=\\$(dirname "\\$par_output_report") @@ -3448,7 +3510,7 @@ IFS=";" read -ra inputs <<< \\$par_input if [[ -n "\\$par_include_modules" ]]; then include_modules="" - IFS="," read -ra incl_modules <<< \\$par_include_modules + IFS=";" read -ra incl_modules <<< \\$par_include_modules for i in "\\${incl_modules[@]}"; do include_modules+="--include \\$i " done @@ -3457,7 +3519,7 @@ fi if [[ -n "\\$par_exclude_modules" ]]; then exclude_modules="" - IFS="," read -ra excl_modules <<< \\$par_exclude_modules + IFS=";" read -ra excl_modules <<< \\$par_exclude_modules for i in "\\${excl_modules[@]}"; do exclude_modules+="--exclude \\$i" done @@ -3466,7 +3528,7 @@ fi if [[ -n "\\$par_ignore_analysis" ]]; then ignore="" - IFS="," read -ra ignore_analysis <<< \\$par_ignore_analysis + IFS=";" read -ra ignore_analysis <<< \\$par_ignore_analysis for i in "\\${ignore_analysis[@]}"; do ignore+="--ignore \\$i " done @@ -3475,7 +3537,7 @@ fi if [[ -n "\\$par_ignore_samples" ]]; then ignore_samples="" - IFS="," read -ra ign_samples <<< \\$par_ignore_samples + IFS=";" read -ra ign_samples <<< \\$par_ignore_samples for i in "\\${ign_samples[@]}"; do ignore_samples+="--ignore-samples \\$i" done @@ -3618,7 +3680,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3749,7 +3815,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3757,8 +3824,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3795,6 +3862,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3806,10 +3874,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3894,7 +3961,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/biobox/multiqc", - "tag" : "v0.1.0" + "tag" : "0.2.0" }, "tag" : "$id" }'''), diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow.config b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config similarity index 98% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow.config rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config index 2443ee9..2fe3a6a 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow.config +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config @@ -2,8 +2,9 @@ manifest { name = 'multiqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = '0.2.0' 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' } process.container = 'nextflow/bash:latest' diff --git a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow_schema.json b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow_schema.json similarity index 96% rename from target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow_schema.json rename to target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow_schema.json index daab1d2..5f3f25e 100644 --- a/target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow_schema.json +++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow_schema.json @@ -17,8 +17,8 @@ "input": { "type": "string", - "description": "Type: List of `file`, required, example: `data/results/`, multiple_sep: `\":\"`. File paths to be searched for analysis results to be included in the report", - "help_text": "Type: List of `file`, required, example: `data/results/`, multiple_sep: `\":\"`. File paths to be searched for analysis results to be included in the report.\n" + "description": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report", + "help_text": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report.\n" } @@ -80,8 +80,8 @@ "include_modules": { "type": "string", - "description": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Use only these module", - "help_text": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Use only these module" + "description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module", + "help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module" } @@ -90,8 +90,8 @@ "exclude_modules": { "type": "string", - "description": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Do not use only these modules", - "help_text": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Do not use only these modules" + "description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules", + "help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules" } @@ -100,8 +100,8 @@ "ignore_analysis": { "type": "string", - "description": "Type: List of `string`, example: `run_one/*,run_two/*`, multiple_sep: `\",\"`. ", - "help_text": "Type: List of `string`, example: `run_one/*,run_two/*`, multiple_sep: `\",\"`. " + "description": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. ", + "help_text": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. " } @@ -110,8 +110,8 @@ "ignore_samples": { "type": "string", - "description": "Type: List of `string`, example: `sample_1*,sample_3*`, multiple_sep: `\",\"`. ", - "help_text": "Type: List of `string`, example: `sample_1*,sample_3*`, multiple_sep: `\",\"`. " + "description": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. ", + "help_text": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. " } 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 5fb1fd8..ce2ca58 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -141,7 +141,7 @@ build_info: output: "target/executable/io/interop_summary_to_csv" executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv" viash_version: "0.9.0" - git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" + git_commit: "399e46901d6ce882a7430842b0d74774736439e2" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" 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 eca9597..28a5615 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 @@ -470,9 +470,9 @@ 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="2024-09-12T12:25:58Z" +LABEL org.opencontainers.image.created="2024-09-13T09:38:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" +LABEL org.opencontainers.image.revision="399e46901d6ce882a7430842b0d74774736439e2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index ddb29d5..f4f0126 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -148,7 +148,7 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.0" - git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" + git_commit: "399e46901d6ce882a7430842b0d74774736439e2" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 6d87b4d..1e3ddf0 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -476,9 +476,9 @@ 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="2024-09-12T12:25:58Z" +LABEL org.opencontainers.image.created="2024-09-13T09:38:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" +LABEL org.opencontainers.image.revision="399e46901d6ce882a7430842b0d74774736439e2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index 3ad0286..758c83f 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -139,7 +139,7 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.0" - git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" + git_commit: "399e46901d6ce882a7430842b0d74774736439e2" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index 61d5b04..8f8587e 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -2972,7 +2972,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.0", - "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f", + "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { 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 5a3bfb8..0607dd2 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -133,7 +133,7 @@ build_info: output: "target/nextflow/dataflow/gather_fastqs_and_validate" executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf" viash_version: "0.9.0" - git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" + git_commit: "399e46901d6ce882a7430842b0d74774736439e2" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index 77a41a6..7bae842 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -2965,7 +2965,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.0", - "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f", + "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 68f0e6b..11a91f1 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -93,22 +93,22 @@ dependencies: repository: type: "vsh" repo: "biobox" - tag: "v0.1.0" + tag: "v0.2.0" - name: "falco" repository: type: "vsh" repo: "biobox" - tag: "v0.1.0" + tag: "v0.2.0" - name: "multiqc" repository: type: "vsh" repo: "biobox" - tag: "v0.1.0" + tag: "v0.2.0" repositories: - type: "vsh" name: "bb" repo: "biobox" - tag: "v0.1.0" + tag: "v0.2.0" license: "MIT" links: repository: "https://github.com/viash-hub/demultiplex" @@ -186,16 +186,16 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" + git_commit: "399e46901d6ce882a7430842b0d74774736439e2" 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/v0.1.0/nextflow/bcl_convert" - - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco" - - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc" + - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert" + - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco" + - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index cc040a7..6c01e56 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -2932,7 +2932,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "biobox", - "tag" : "v0.1.0" + "tag" : "v0.2.0" } }, { @@ -2940,7 +2940,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "biobox", - "tag" : "v0.1.0" + "tag" : "v0.2.0" } }, { @@ -2948,7 +2948,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "biobox", - "tag" : "v0.1.0" + "tag" : "v0.2.0" } } ], @@ -2957,7 +2957,7 @@ meta = [ "type" : "vsh", "name" : "bb", "repo" : "biobox", - "tag" : "v0.1.0" + "tag" : "v0.2.0" } ], "license" : "MIT", @@ -3049,7 +3049,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.0", - "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f", + "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { @@ -3095,9 +3095,9 @@ 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 "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/main.nf" -include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/main.nf" -include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/main.nf" +include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf" +include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf" +include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf" // inner workflow // user-provided Nextflow code 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 cd79f02..c8d89a6 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -141,7 +141,7 @@ build_info: output: "target/nextflow/io/interop_summary_to_csv" executable: "target/nextflow/io/interop_summary_to_csv/main.nf" viash_version: "0.9.0" - git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" + git_commit: "399e46901d6ce882a7430842b0d74774736439e2" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index 0b19195..3a25ff1 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -2977,7 +2977,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.0", - "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f", + "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 41a2120..def01b8 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -148,7 +148,7 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.0" - git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f" + git_commit: "399e46901d6ce882a7430842b0d74774736439e2" git_remote: "https://github.com/viash-hub/demultiplex" package_config: name: "demultiplex" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index ec7034c..9447ad2 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -2989,7 +2989,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.0", - "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f", + "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2", "git_remote" : "https://github.com/viash-hub/demultiplex" }, "package_config" : { diff --git a/test_resources b/test_resources deleted file mode 120000 index 6970768..0000000 --- a/test_resources +++ /dev/null @@ -1 +0,0 @@ -/work/viash_hub_resources/viash-hub/demultiplex/ebb861b02ab66db004c32fa46573bb1e/200624_A00834_0183_BHMTFYDRXX.tar.gz \ No newline at end of file