From 2121a3ac1c14f87b4f3ea4345b3597048acc910a Mon Sep 17 00:00:00 2001 From: CI Date: Wed, 11 Dec 2024 15:44:12 +0000 Subject: [PATCH] Build branch main with version main (5c096fc) Build pipeline: viash-hub.demultiplex.main-svj8q Source commit: https://github.com/viash-hub/demultiplex/commit/5c096fce4015435019d81e2cc524a478f4034adc Source message: Fixes for v0.3.0 (#27) Co-authored-by: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com> --- CHANGELOG.md | 6 ++++ src/demultiplex/main.nf | 9 +++-- src/runner/config.vsh.yaml | 18 ++++++++++ src/runner/main.nf | 4 ++- .../interop_summary_to_csv/.config.vsh.yaml | 6 ++-- .../interop_summary_to_csv | 4 +-- target/executable/io/publish/.config.vsh.yaml | 6 ++-- target/executable/io/publish/publish | 4 +-- target/executable/io/untar/.config.vsh.yaml | 6 ++-- target/executable/io/untar/untar | 4 +-- .../dataflow/combine_samples/.config.vsh.yaml | 6 ++-- .../nextflow/dataflow/combine_samples/main.nf | 6 ++-- .../.config.vsh.yaml | 6 ++-- .../gather_fastqs_and_validate/main.nf | 6 ++-- target/nextflow/demultiplex/.config.vsh.yaml | 6 ++-- target/nextflow/demultiplex/main.nf | 15 +++++--- .../interop_summary_to_csv/.config.vsh.yaml | 6 ++-- .../io/interop_summary_to_csv/main.nf | 6 ++-- target/nextflow/io/publish/.config.vsh.yaml | 6 ++-- target/nextflow/io/publish/main.nf | 6 ++-- target/nextflow/io/untar/.config.vsh.yaml | 6 ++-- target/nextflow/io/untar/main.nf | 6 ++-- target/nextflow/runner/.config.vsh.yaml | 32 +++++++++++++++-- target/nextflow/runner/main.nf | 34 ++++++++++++++++--- target/nextflow/runner/nextflow_schema.json | 22 ++++++++++++ 25 files changed, 173 insertions(+), 63 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4f3c62a..9aa01b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,9 +1,15 @@ # demultiplex v0.3.1 +# Minor updates + +* Add `--run_information` and `--demultiplexer` arguments to `runner` workflow (PR #27). + # Bug fixes * Fix detection of sample IDs from Illumina V2 sample sheets (PR #28). +* Provide a clear error message when `--run_information` is provided but not `--demultiplexer` (PR #27). + # demultiplex v0.3.0 ## Major updates diff --git a/src/demultiplex/main.nf b/src/demultiplex/main.nf index 4f2f7fb..470fbd8 100644 --- a/src/demultiplex/main.nf +++ b/src/demultiplex/main.nf @@ -25,6 +25,11 @@ workflow run_wf { | map {id, state -> def newState = [:] println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}") + // No auto-detection of run information file (it is user provided), + // in this case the demultiplexer should also be specified. + assert (!state.run_information || state.demultiplexer): "When setting --run_information, " + + "you must also provide a demultiplexer" + if (!state.run_information) { println("Run information was not specified, auto-detecting...") // The supported_platforms hashmap must be a 1-on-1 mapping @@ -62,7 +67,7 @@ workflow run_wf { "found in input directory." // When autodetecting, the demultiplexer must be set if the run information was found - assert demultiplexer, "State error: the demultiplexer should have been autodetected. " + + assert demultiplexer: "State error: the demultiplexer should have been autodetected. " + "Please report this as a bug." // When autodetecting, the found demultiplexer must match @@ -82,7 +87,7 @@ workflow run_wf { "run_information": run_information, "demultiplexer": demultiplexer, ] - } + } // end auto-detection logic if (newState.demultiplexer in ["bclconvert"]) { // Do not add InterOp to state because we generate the summary csv's in the next diff --git a/src/runner/config.vsh.yaml b/src/runner/config.vsh.yaml index 53ca7db..50e4a1c 100644 --- a/src/runner/config.vsh.yaml +++ b/src/runner/config.vsh.yaml @@ -7,6 +7,24 @@ argument_groups: description: Base directory of the form `s3://Sequencing///` type: file required: true + - name: --run_information + description: | + CSV file containing sample information, which will be used as + input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina) + or 'RunManifest.csv' (Element Biosciences). If not specified, + will try to autodetect the sample sheet in the input directory. + Requires --demultiplexer to be set. + type: file + required: false + - name: "--demultiplexer" + type: string + required: false + choices: ["bases2fastq", "bclconvert"] + description: | + Demultiplexer to use, choice depends on the provider + of the instrument that was used to generate the data. + When not using --sample_sheet, specifying this argument is not + required. - name: Annotation flags arguments: - name: --add_date_time diff --git a/src/runner/main.nf b/src/runner/main.nf index 404f40d..5a92905 100644 --- a/src/runner/main.nf +++ b/src/runner/main.nf @@ -12,9 +12,11 @@ workflow run_wf { | demultiplex.run( fromState: [ "input": "input", + "run_information": "run_information", + "demultiplexer": "demultiplexer", "output": "fastq", "output_falco": "qc/fastqc", - "output_multiqc": "qc/multiqc_report.html", + "output_multiqc": "qc/multiqc_report.html" ], toState: { id, result, state -> state + result 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 de268e7..f71767b 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -141,9 +141,9 @@ 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: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" package_config: name: "demultiplex" version: "main" 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 fa0993e..739e856 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="2024-12-11T14:07:52Z" +LABEL org.opencontainers.image.created="2024-12-11T15:28:43Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47" +LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index 1eec766..e5041e8 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -170,9 +170,9 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.0" - git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index 9e17ac6..76bfba9 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -482,9 +482,9 @@ 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="2024-12-11T14:07:53Z" +LABEL org.opencontainers.image.created="2024-12-11T15:28:44Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47" +LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc" 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 0cd16a5..3d9c84d 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -148,9 +148,9 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.0" - git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index c881d19..600b94c 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="2024-12-11T14:07:53Z" +LABEL org.opencontainers.image.created="2024-12-11T15:28:44Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47" +LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc" 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 451865c..f04f040 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -139,9 +139,9 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.0" - git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index c83d1f8..4f833f9 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -2972,9 +2972,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.0", - "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47", - "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-9-gd3a9c9b" + "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", + "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-10-g5c096fc" }, "package_config" : { "name" : "demultiplex", 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 33f2bc7..c553c7a 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -133,9 +133,9 @@ 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: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index b6c9b2d..33006d5 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -2965,9 +2965,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.0", - "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47", - "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-9-gd3a9c9b" + "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", + "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-10-g5c096fc" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 4e94758..fa692fe 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -220,9 +220,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" dependencies: - "target/nextflow/io/untar" - "target/nextflow/dataflow/gather_fastqs_and_validate" diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index 4b06f5f..9f2c6d5 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -3088,9 +3088,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.0", - "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47", - "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-9-gd3a9c9b" + "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", + "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-10-g5c096fc" }, "package_config" : { "name" : "demultiplex", @@ -3169,6 +3169,11 @@ workflow run_wf { | map {id, state -> def newState = [:] println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}") + // No auto-detection of run information file (it is user provided), + // in this case the demultiplexer should also be specified. + assert (!state.run_information || state.demultiplexer): "When setting --run_information, " + + "you must also provide a demultiplexer" + if (!state.run_information) { println("Run information was not specified, auto-detecting...") // The supported_platforms hashmap must be a 1-on-1 mapping @@ -3206,7 +3211,7 @@ workflow run_wf { "found in input directory." // When autodetecting, the demultiplexer must be set if the run information was found - assert demultiplexer, "State error: the demultiplexer should have been autodetected. " + + assert demultiplexer: "State error: the demultiplexer should have been autodetected. " + "Please report this as a bug." // When autodetecting, the found demultiplexer must match @@ -3226,7 +3231,7 @@ workflow run_wf { "run_information": run_information, "demultiplexer": demultiplexer, ] - } + } // end auto-detection logic if (newState.demultiplexer in ["bclconvert"]) { // Do not add InterOp to state because we generate the summary csv's in the next 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 4997a2c..7666617 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -141,9 +141,9 @@ 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: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index f5db72f..d667e1b 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -2977,9 +2977,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.0", - "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47", - "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-9-gd3a9c9b" + "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", + "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-10-g5c096fc" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index c5897f3..41711d9 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -170,9 +170,9 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.0" - git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index d56ddd6..3fba507 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -3012,9 +3012,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.0", - "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47", - "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-9-gd3a9c9b" + "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", + "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-10-g5c096fc" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 3912e44..0698743 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -148,9 +148,9 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.0" - git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index 881079e..4338c16 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -2989,9 +2989,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.0", - "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47", - "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-9-gd3a9c9b" + "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", + "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-10-g5c096fc" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index de43ce9..12124e1 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -13,6 +13,32 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "file" + name: "--run_information" + description: "CSV file containing sample information, which will be used as \n\ + input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\n\ + or 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect\ + \ the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--demultiplexer" + description: "Demultiplexer to use, choice depends on the provider\nof the instrument\ + \ that was used to generate the data.\nWhen not using --sample_sheet, specifying\ + \ this argument is not\nrequired.\n" + info: null + required: false + choices: + - "bases2fastq" + - "bclconvert" + direction: "input" + multiple: false + multiple_sep: ";" - name: "Annotation flags" arguments: - type: "boolean_true" @@ -156,9 +182,9 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.0" - git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47" - git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-9-gd3a9c9b" + git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" + git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-10-g5c096fc" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index 324d6cc..478b058 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -2820,6 +2820,30 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--run_information", + "description" : "CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\nor 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--demultiplexer", + "description" : "Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n", + "required" : false, + "choices" : [ + "bases2fastq", + "bclconvert" + ], + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" } ] }, @@ -3003,9 +3027,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.0", - "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47", - "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-9-gd3a9c9b" + "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", + "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-10-g5c096fc" }, "package_config" : { "name" : "demultiplex", @@ -3065,9 +3089,11 @@ workflow run_wf { | demultiplex.run( fromState: [ "input": "input", + "run_information": "run_information", + "demultiplexer": "demultiplexer", "output": "fastq", "output_falco": "qc/fastqc", - "output_multiqc": "qc/multiqc_report.html", + "output_multiqc": "qc/multiqc_report.html" ], toState: { id, result, state -> state + result diff --git a/target/nextflow/runner/nextflow_schema.json b/target/nextflow/runner/nextflow_schema.json index 33b0f29..47af365 100644 --- a/target/nextflow/runner/nextflow_schema.json +++ b/target/nextflow/runner/nextflow_schema.json @@ -23,6 +23,28 @@ } + , + "run_information": { + "type": + "string", + "description": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer", + "help_text": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called \u0027SampleSheet.csv\u0027 (Illumina)\nor \u0027RunManifest.csv\u0027 (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n" + + } + + + , + "demultiplexer": { + "type": + "string", + "description": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data", + "help_text": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n", + "enum": ["bases2fastq", "bclconvert"] + + + } + + } },