From 3e82b40207e71987a1e9e8cf948245c6470aea6f Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 14 Jan 2025 11:49:04 +0000 Subject: [PATCH] Build branch copycomplete_check with version copycomplete_check (e5828d4) Build pipeline: viash-hub.demultiplex.copycomplete-check-txgn4 Source commit: https://github.com/viash-hub/demultiplex/commit/e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc Source message: Also add argument to runner --- src/runner/config.vsh.yaml | 8 +++++- src/runner/main.nf | 1 + .../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 | 6 ++--- .../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 | 14 ++++++++--- target/nextflow/runner/main.nf | 18 ++++++++++--- target/nextflow/runner/nextflow_schema.json | 25 +++++++++++++++++++ 23 files changed, 110 insertions(+), 58 deletions(-) diff --git a/src/runner/config.vsh.yaml b/src/runner/config.vsh.yaml index 020be85..5359d54 100644 --- a/src/runner/config.vsh.yaml +++ b/src/runner/config.vsh.yaml @@ -49,7 +49,13 @@ argument_groups: type: file direction: output default: "qc/multiqc_report.html" - + - name: "Other arguments" + arguments: + - name: --skip_copycomplete_check + type: boolean_true + description: | + Disable the check for the presence of a "CopyComplete.txt" file in input + directory in case of Illumina data. resources: - type: nextflow_script path: main.nf diff --git a/src/runner/main.nf b/src/runner/main.nf index c705a09..87d21f7 100644 --- a/src/runner/main.nf +++ b/src/runner/main.nf @@ -24,6 +24,7 @@ workflow run_wf { "input": state.input, "run_information": state.run_information, "demultiplexer": state.demultiplexer, + "skip_copycomplete_check": state.skip_copycomplete_check, "output": "fastq", "output_falco": "qc/fastqc", "output_multiqc": "qc/multiqc_report.html", 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 a1bcc62..41a92d1 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -146,9 +146,9 @@ 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: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" package_config: name: "demultiplex" version: "copycomplete_check" 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 4169afb..bcb3eae 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="2025-01-10T14:59:08Z" +LABEL org.opencontainers.image.created="2025-01-14T11:35:41Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="4d8c825fdf075218611913f59ab92fd85043b499" +LABEL org.opencontainers.image.revision="e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" LABEL org.opencontainers.image.version="copycomplete_check" VIASHDOCKER diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index a3837af..019c314 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -196,9 +196,9 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.0" - git_commit: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" package_config: name: "demultiplex" version: "copycomplete_check" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index b7b6486..7dc32e0 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -490,9 +490,9 @@ 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="2025-01-10T14:59:08Z" +LABEL org.opencontainers.image.created="2025-01-14T11:35:41Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="4d8c825fdf075218611913f59ab92fd85043b499" +LABEL org.opencontainers.image.revision="e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" LABEL org.opencontainers.image.version="copycomplete_check" VIASHDOCKER diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index cf61171..a0cf716 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -153,9 +153,9 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.0" - git_commit: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" package_config: name: "demultiplex" version: "copycomplete_check" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 6226438..363fbe5 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="2025-01-10T14:59:08Z" +LABEL org.opencontainers.image.created="2025-01-14T11:35:42Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="4d8c825fdf075218611913f59ab92fd85043b499" +LABEL org.opencontainers.image.revision="e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" LABEL org.opencontainers.image.version="copycomplete_check" VIASHDOCKER diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index fc99c3d..373ae5a 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -144,9 +144,9 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.0" - git_commit: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" package_config: name: "demultiplex" version: "copycomplete_check" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index 3cfe775..42d7e33 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -2980,9 +2980,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.0", - "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499", - "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-16-g4d8c825" + "git_commit" : "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc", + "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-17-ge5828d4" }, "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 673509b..67ae1f3 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -138,9 +138,9 @@ 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: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" package_config: name: "demultiplex" version: "copycomplete_check" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index 57a01a0..c09792e 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -2973,9 +2973,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.0", - "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499", - "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-16-g4d8c825" + "git_commit" : "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc", + "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-17-ge5828d4" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 314785f..1734a0d 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -244,9 +244,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" 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 755a281..6b4c534 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -3120,9 +3120,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.0", - "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499", - "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-16-g4d8c825" + "git_commit" : "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc", + "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-17-ge5828d4" }, "package_config" : { "name" : "demultiplex", 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 ec03767..06227ba 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -146,9 +146,9 @@ 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: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" package_config: name: "demultiplex" version: "copycomplete_check" diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index aa4fd1b..81fd2cb 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -2985,9 +2985,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.0", - "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499", - "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-16-g4d8c825" + "git_commit" : "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc", + "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-17-ge5828d4" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index 688b22e..1a608b8 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -196,9 +196,9 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.0" - git_commit: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" package_config: name: "demultiplex" version: "copycomplete_check" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index 56b73ca..5a76bac 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -3044,9 +3044,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.0", - "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499", - "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-16-g4d8c825" + "git_commit" : "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc", + "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-17-ge5828d4" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 23cf9d8..1e37181 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -153,9 +153,9 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.0" - git_commit: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" package_config: name: "demultiplex" version: "copycomplete_check" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index bed9e44..95d5b31 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -2997,9 +2997,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.0", - "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499", - "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-16-g4d8c825" + "git_commit" : "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc", + "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-17-ge5828d4" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index e73819e..a7451ac 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -84,6 +84,14 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" +- name: "Other arguments" + arguments: + - type: "boolean_true" + name: "--skip_copycomplete_check" + description: "Disable the check for the presence of a \"CopyComplete.txt\" file\ + \ in input\ndirectory in case of Illumina data.\n" + info: null + direction: "input" resources: - type: "nextflow_script" path: "main.nf" @@ -184,9 +192,9 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.0" - git_commit: "4d8c825fdf075218611913f59ab92fd85043b499" - git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-16-g4d8c825" + git_commit: "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc" + git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-17-ge5828d4" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index 6062c60..e8488ed 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -2901,6 +2901,17 @@ meta = [ "multiple_sep" : ";" } ] + }, + { + "name" : "Other arguments", + "arguments" : [ + { + "type" : "boolean_true", + "name" : "--skip_copycomplete_check", + "description" : "Disable the check for the presence of a \\"CopyComplete.txt\\" file in input\ndirectory in case of Illumina data.\n", + "direction" : "input" + } + ] } ], "resources" : [ @@ -3029,9 +3040,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.0", - "git_commit" : "4d8c825fdf075218611913f59ab92fd85043b499", - "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-16-g4d8c825" + "git_commit" : "e5828d4ad9ef3784f1f5bc3133f227ff9e28d2dc", + "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-17-ge5828d4" }, "package_config" : { "name" : "demultiplex", @@ -3103,6 +3114,7 @@ workflow run_wf { "input": state.input, "run_information": state.run_information, "demultiplexer": state.demultiplexer, + "skip_copycomplete_check": state.skip_copycomplete_check, "output": "fastq", "output_falco": "qc/fastqc", "output_multiqc": "qc/multiqc_report.html", diff --git a/target/nextflow/runner/nextflow_schema.json b/target/nextflow/runner/nextflow_schema.json index 7153e21..a7bb138 100644 --- a/target/nextflow/runner/nextflow_schema.json +++ b/target/nextflow/runner/nextflow_schema.json @@ -109,6 +109,27 @@ } +} +}, + + + "other arguments" : { + "title": "Other arguments", + "type": "object", + "description": "No description", + "properties": { + + + "skip_copycomplete_check": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete", + "help_text": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete.txt\" file in input\ndirectory in case of Illumina data.\n" + , + "default":false + } + + } }, @@ -157,6 +178,10 @@ "$ref": "#/definitions/output arguments" }, + { + "$ref": "#/definitions/other arguments" + }, + { "$ref": "#/definitions/nextflow input-output arguments" }