From 96e74933b47fcf3315975a857ff266772f33926e Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 14 Feb 2025 11:38:08 +0000 Subject: [PATCH] Build branch main with version main (55b0251) Build pipeline: viash-hub.htrnaseq.main-ddh59 Source commit: https://github.com/viash-hub/htrnaseq/commit/55b025124d174ff062636130a44b7165be74d3da Source message: Add ignore parameter (#39) --- CHANGELOG.md | 7 +++++ src/utils/listInputDir/config.vsh.yaml | 5 ++++ src/utils/listInputDir/main.nf | 15 ++++++---- src/workflows/runner/config.vsh.yaml | 5 ++++ src/workflows/runner/main.nf | 5 +++- .../eset/create_eset/.config.vsh.yaml | 2 +- .../executable/eset/create_eset/create_eset | 4 +-- .../eset/create_fdata/.config.vsh.yaml | 2 +- .../executable/eset/create_fdata/create_fdata | 4 +-- .../eset/create_pdata/.config.vsh.yaml | 2 +- .../executable/eset/create_pdata/create_pdata | 4 +-- .../htrnaseq/check_eset/.config.vsh.yaml | 2 +- .../htrnaseq/check_eset/check_eset | 4 +-- .../check_cutadapt_output/.config.vsh.yaml | 2 +- .../check_cutadapt_output | 4 +-- .../io/publish_fastqs/.config.vsh.yaml | 2 +- .../io/publish_fastqs/publish_fastqs | 4 +-- .../io/publish_results/.config.vsh.yaml | 2 +- .../io/publish_results/publish_results | 4 +-- .../executable/parallel_map/.config.vsh.yaml | 2 +- target/executable/parallel_map/parallel_map | 4 +-- .../report/create_report/.config.vsh.yaml | 2 +- .../report/create_report/create_report | 4 +-- .../stats/combine_star_logs/.config.vsh.yaml | 2 +- .../stats/combine_star_logs/combine_star_logs | 4 +-- .../generate_pool_statistics/.config.vsh.yaml | 2 +- .../generate_pool_statistics | 4 +-- .../generate_well_statistics/.config.vsh.yaml | 2 +- .../generate_well_statistics | 4 +-- .../eset/create_eset/.config.vsh.yaml | 2 +- target/nextflow/eset/create_eset/main.nf | 2 +- .../eset/create_fdata/.config.vsh.yaml | 2 +- target/nextflow/eset/create_fdata/main.nf | 2 +- .../eset/create_pdata/.config.vsh.yaml | 2 +- target/nextflow/eset/create_pdata/main.nf | 2 +- .../htrnaseq/check_eset/.config.vsh.yaml | 2 +- .../htrnaseq/check_eset/main.nf | 2 +- .../check_cutadapt_output/.config.vsh.yaml | 2 +- .../check_cutadapt_output/main.nf | 2 +- .../io/publish_fastqs/.config.vsh.yaml | 2 +- target/nextflow/io/publish_fastqs/main.nf | 2 +- .../io/publish_results/.config.vsh.yaml | 2 +- target/nextflow/io/publish_results/main.nf | 2 +- target/nextflow/parallel_map/.config.vsh.yaml | 2 +- target/nextflow/parallel_map/main.nf | 2 +- .../report/create_report/.config.vsh.yaml | 2 +- target/nextflow/report/create_report/main.nf | 2 +- .../stats/combine_star_logs/.config.vsh.yaml | 2 +- .../nextflow/stats/combine_star_logs/main.nf | 2 +- .../generate_pool_statistics/.config.vsh.yaml | 2 +- .../stats/generate_pool_statistics/main.nf | 2 +- .../generate_well_statistics/.config.vsh.yaml | 2 +- .../stats/generate_well_statistics/main.nf | 2 +- .../utils/listInputDir/.config.vsh.yaml | 12 +++++++- target/nextflow/utils/listInputDir/main.nf | 29 +++++++++++++++---- .../utils/listInputDir/nextflow_schema.json | 11 +++++++ .../workflows/htrnaseq/.config.vsh.yaml | 2 +- target/nextflow/workflows/htrnaseq/main.nf | 2 +- .../workflows/runner/.config.vsh.yaml | 12 +++++++- target/nextflow/workflows/runner/main.nf | 19 ++++++++++-- .../workflows/runner/nextflow_schema.json | 11 +++++++ .../well_demultiplex/.config.vsh.yaml | 2 +- .../workflows/well_demultiplex/main.nf | 2 +- .../workflows/well_metadata/.config.vsh.yaml | 2 +- .../nextflow/workflows/well_metadata/main.nf | 2 +- 65 files changed, 181 insertions(+), 82 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d133c33..58bbd91e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,10 @@ +# htrnaseq v0.5.0 + +## New functionality + +* Added `ignore` parameter was added to the runner workflow in order to pass over certain input files + from the input directory (PR #39). + # htrnaseq v0.4.0 ## Breaking changes diff --git a/src/utils/listInputDir/config.vsh.yaml b/src/utils/listInputDir/config.vsh.yaml index 30622137..98f290d1 100644 --- a/src/utils/listInputDir/config.vsh.yaml +++ b/src/utils/listInputDir/config.vsh.yaml @@ -8,6 +8,11 @@ arguments: description: Path to the directory containing fastq files required: true example: fastq_dir + - name: --ignore + description: "Pool names to ignore." + type: string + multiple: true + default: ["Undetermined"] - name: "--r1_output" type: file description: Path to read 1 fastq/fasta file diff --git a/src/utils/listInputDir/main.nf b/src/utils/listInputDir/main.nf index 76f5cca8..03c97fc3 100644 --- a/src/utils/listInputDir/main.nf +++ b/src/utils/listInputDir/main.nf @@ -27,17 +27,22 @@ workflow run_wf { def lane = parsedFastq[0][3] // Remove the trailing '_' def lane_remove_trailing = lane == null ? "" : lane.replaceAll('_$', "") + def sample_id = parsedFastq[0][1] + if (sample_id in state.ignore) { + return null + } return [ - fastq: f, - sample_id: parsedFastq[0][1], - sample: parsedFastq[0][2], - lane: lane_remove_trailing, - read: parsedFastq[0][5], + "fastq": f, + "sample_id": sample_id, + "sample": parsedFastq[0][2], + "lane": lane_remove_trailing, + "read": parsedFastq[0][5], ] } println("Group paired fastq/fasta files") def grouped = processed_fastqs + .findAll{it != null} .groupBy({it.sample_id}, {it.lane}) .collectMany{ sample_id, states_per_lane -> def result = states_per_lane.collect{lane, lane_states -> diff --git a/src/workflows/runner/config.vsh.yaml b/src/workflows/runner/config.vsh.yaml index bcfd069f..6bdd5a05 100644 --- a/src/workflows/runner/config.vsh.yaml +++ b/src/workflows/runner/config.vsh.yaml @@ -18,6 +18,11 @@ argument_groups: - name: --annotation type: file required: true + - name: --ignore + description: "Pool names to ignore." + type: string + multiple: true + default: ["Undetermined"] - name: Metadata arguments arguments: - name: --id diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index d102dbdf..27764447 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -22,7 +22,10 @@ workflow run_wf { // List the FASTQ files per input directory // Be careful: an event per lane is created! | listInputDir.run( - fromState: [ input: "input" ], + fromState: [ + "input": "input", + "ignore": "ignore", + ], toState: { id, state, result -> def clean_state = state.findAll{ it.key != "input" } clean_state + result diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 8e5c6130..24a92477 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -198,7 +198,7 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index 48a80297..55124803 100755 --- a/target/executable/eset/create_eset/create_eset +++ b/target/executable/eset/create_eset/create_eset @@ -477,9 +477,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_eset" -LABEL org.opencontainers.image.created="2025-02-13T15:18:38Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:19Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index 55ee52be..0ca92b6c 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -177,7 +177,7 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index 892a744b..f7a2f619 100755 --- a/target/executable/eset/create_fdata/create_fdata +++ b/target/executable/eset/create_fdata/create_fdata @@ -478,9 +478,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata" -LABEL org.opencontainers.image.created="2025-02-13T15:18:38Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 08480e0c..65b07a90 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -191,7 +191,7 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index c3dc1027..73d782e3 100755 --- a/target/executable/eset/create_pdata/create_pdata +++ b/target/executable/eset/create_pdata/create_pdata @@ -488,9 +488,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata" -LABEL org.opencontainers.image.created="2025-02-13T15:18:38Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:19Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index e0566b22..9c5b5f3f 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -148,7 +148,7 @@ build_info: output: "target/executable/integration_test_components/htrnaseq/check_eset" executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset index 5defbec5..c64be389 100755 --- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset +++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset @@ -470,9 +470,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset" -LABEL org.opencontainers.image.created="2025-02-13T15:18:38Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:19Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index a9edcbfa..e3617d96 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -158,7 +158,7 @@ build_info: output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output index 22e968b8..35ab211d 100755 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output @@ -476,9 +476,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output" -LABEL org.opencontainers.image.created="2025-02-13T15:18:38Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:19Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index d3b2f3bc..3c019cc2 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -143,7 +143,7 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index 3b412687..e3508f72 100755 --- a/target/executable/io/publish_fastqs/publish_fastqs +++ b/target/executable/io/publish_fastqs/publish_fastqs @@ -470,9 +470,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs" -LABEL org.opencontainers.image.created="2025-02-13T15:18:36Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:18Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index e0b63350..6d701359 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index 7858fb66..cb7e8fbc 100755 --- a/target/executable/io/publish_results/publish_results +++ b/target/executable/io/publish_results/publish_results @@ -484,9 +484,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_results" -LABEL org.opencontainers.image.created="2025-02-13T15:18:37Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:18Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 869ffd9a..44b0164c 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -279,7 +279,7 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index 7b107099..1058bd6b 100755 --- a/target/executable/parallel_map/parallel_map +++ b/target/executable/parallel_map/parallel_map @@ -540,9 +540,9 @@ ENV STAR_BINARY=STAR COPY STAR /usr/local/bin/$STAR_BINARY LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component parallel_map" -LABEL org.opencontainers.image.created="2025-02-13T15:18:39Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index e07a962d..f4890f8a 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -201,7 +201,7 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index 8342fc35..d8ba0f88 100755 --- a/target/executable/report/create_report/create_report +++ b/target/executable/report/create_report/create_report @@ -476,9 +476,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component report create_report" -LABEL org.opencontainers.image.created="2025-02-13T15:18:39Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index 4ab1f526..779c23af 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -198,7 +198,7 @@ build_info: output: "target/executable/stats/combine_star_logs" executable: "target/executable/stats/combine_star_logs/combine_star_logs" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index 38053b93..c6e27d95 100755 --- a/target/executable/stats/combine_star_logs/combine_star_logs +++ b/target/executable/stats/combine_star_logs/combine_star_logs @@ -490,9 +490,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs" -LABEL org.opencontainers.image.created="2025-02-13T15:18:36Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:18Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index d7c38c09..cdad703f 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -182,7 +182,7 @@ build_info: output: "target/executable/stats/generate_pool_statistics" executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index 899ef40c..a2e782ec 100755 --- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics +++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics @@ -483,9 +483,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics" -LABEL org.opencontainers.image.created="2025-02-13T15:18:37Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:18Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index 42916181..7549f24e 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -262,7 +262,7 @@ build_info: output: "target/executable/stats/generate_well_statistics" executable: "target/executable/stats/generate_well_statistics/generate_well_statistics" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index 48ef38d6..15a7c28d 100755 --- a/target/executable/stats/generate_well_statistics/generate_well_statistics +++ b/target/executable/stats/generate_well_statistics/generate_well_statistics @@ -520,9 +520,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics" -LABEL org.opencontainers.image.created="2025-02-13T15:18:37Z" +LABEL org.opencontainers.image.created="2025-02-14T10:51:19Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="900f5ed35659137aa5c62d183232e0f33de97873" +LABEL org.opencontainers.image.revision="55b025124d174ff062636130a44b7165be74d3da" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index 7851bfc3..b5649985 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -198,7 +198,7 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index e8d3c0ff..fba89997 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -3072,7 +3072,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml index 331ac035..9d2e1051 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -177,7 +177,7 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index 43b2076f..df8a0bc6 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -3044,7 +3044,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml index d5a4d07d..c34ddb6b 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -191,7 +191,7 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index db9314ed..769118b9 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -3058,7 +3058,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index 1d138655..c31215c4 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -148,7 +148,7 @@ build_info: output: "target/nextflow/integration_test_components/htrnaseq/check_eset" executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf index b0388f30..8c44b368 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -2997,7 +2997,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 7089e7ee..eca71e39 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -158,7 +158,7 @@ build_info: output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf index b6d73d6a..fa76a906 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf @@ -3009,7 +3009,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml index 4773e874..9d34f737 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -143,7 +143,7 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index 0f870bd8..9f568ef1 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -2983,7 +2983,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml index 98dab746..8a102681 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index 27fb15f9..f0e03dc1 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -3032,7 +3032,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index 8f979f99..45b06c3b 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -279,7 +279,7 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index 321f0469..53840e28 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -3144,7 +3144,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml index 38add69a..edf9eb6d 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -201,7 +201,7 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index f94268fc..5b11a404 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -3077,7 +3077,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml index aa846b10..26dab0ef 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -198,7 +198,7 @@ build_info: output: "target/nextflow/stats/combine_star_logs" executable: "target/nextflow/stats/combine_star_logs/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index db27e71c..512c77c6 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -3060,7 +3060,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml index 950730e5..aed62376 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -182,7 +182,7 @@ build_info: output: "target/nextflow/stats/generate_pool_statistics" executable: "target/nextflow/stats/generate_pool_statistics/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index 010f4a3c..114fd95e 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -3044,7 +3044,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml index dc52aa86..8d8cd9dd 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -262,7 +262,7 @@ build_info: output: "target/nextflow/stats/generate_well_statistics" executable: "target/nextflow/stats/generate_well_statistics/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index 99ff9dff..5535b60c 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -3135,7 +3135,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml index c282379d..6293c99c 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -18,6 +18,16 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "string" + name: "--ignore" + description: "Pool names to ignore." + info: null + default: + - "Undetermined" + required: false + direction: "input" + multiple: true + multiple_sep: ";" - type: "file" name: "--r1_output" description: "Path to read 1 fastq/fasta file" @@ -155,7 +165,7 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf index 0e97cc11..1f97ee50 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -2828,6 +2828,18 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "string", + "name" : "--ignore", + "description" : "Pool names to ignore.", + "default" : [ + "Undetermined" + ], + "required" : false, + "direction" : "input", + "multiple" : true, + "multiple_sep" : ";" + }, { "type" : "file", "name" : "--r1_output", @@ -2992,7 +3004,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3068,17 +3080,22 @@ workflow run_wf { def lane = parsedFastq[0][3] // Remove the trailing '_' def lane_remove_trailing = lane == null ? "" : lane.replaceAll('_$', "") + def sample_id = parsedFastq[0][1] + if (sample_id in state.ignore) { + return null + } return [ - fastq: f, - sample_id: parsedFastq[0][1], - sample: parsedFastq[0][2], - lane: lane_remove_trailing, - read: parsedFastq[0][5], + "fastq": f, + "sample_id": sample_id, + "sample": parsedFastq[0][2], + "lane": lane_remove_trailing, + "read": parsedFastq[0][5], ] } println("Group paired fastq/fasta files") def grouped = processed_fastqs + .findAll{it != null} .groupBy({it.sample_id}, {it.lane}) .collectMany{ sample_id, states_per_lane -> def result = states_per_lane.collect{lane, lane_states -> diff --git a/target/nextflow/utils/listInputDir/nextflow_schema.json b/target/nextflow/utils/listInputDir/nextflow_schema.json index 1eb4602e..0e90a1d0 100644 --- a/target/nextflow/utils/listInputDir/nextflow_schema.json +++ b/target/nextflow/utils/listInputDir/nextflow_schema.json @@ -23,6 +23,17 @@ } + , + "ignore": { + "type": + "string", + "description": "Type: List of `string`, default: `Undetermined`, multiple_sep: `\";\"`. Pool names to ignore", + "help_text": "Type: List of `string`, default: `Undetermined`, multiple_sep: `\";\"`. Pool names to ignore." + , + "default":"Undetermined" + } + + , "r1_output": { "type": diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index b9e68672..6448bdc1 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -319,7 +319,7 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/stats/combine_star_logs" diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index 627cd336..f29ebeec 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -3223,7 +3223,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index 1a46b3d8..48b42e93 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -41,6 +41,16 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "string" + name: "--ignore" + description: "Pool names to ignore." + info: null + default: + - "Undetermined" + required: false + direction: "input" + multiple: true + multiple_sep: ";" - name: "Metadata arguments" arguments: - type: "string" @@ -197,7 +207,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/utils/listInputDir" diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index a72b536d..fcad17a7 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -2851,6 +2851,18 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--ignore", + "description" : "Pool names to ignore.", + "default" : [ + "Undetermined" + ], + "required" : false, + "direction" : "input", + "multiple" : true, + "multiple_sep" : ";" } ] }, @@ -3057,7 +3069,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3132,7 +3144,10 @@ workflow run_wf { // List the FASTQ files per input directory // Be careful: an event per lane is created! | listInputDir.run( - fromState: [ input: "input" ], + fromState: [ + "input": "input", + "ignore": "ignore", + ], toState: { id, state, result -> def clean_state = state.findAll{ it.key != "input" } clean_state + result diff --git a/target/nextflow/workflows/runner/nextflow_schema.json b/target/nextflow/workflows/runner/nextflow_schema.json index 749c4b2c..cfa52cfc 100644 --- a/target/nextflow/workflows/runner/nextflow_schema.json +++ b/target/nextflow/workflows/runner/nextflow_schema.json @@ -53,6 +53,17 @@ } + , + "ignore": { + "type": + "string", + "description": "Type: List of `string`, default: `Undetermined`, multiple_sep: `\";\"`. Pool names to ignore", + "help_text": "Type: List of `string`, default: `Undetermined`, multiple_sep: `\";\"`. Pool names to ignore." + , + "default":"Undetermined" + } + + } }, diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 11461518..c3aca665 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -211,7 +211,7 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt" diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index e9b45306..04c8bdc2 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -3084,7 +3084,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml index 323ddb9d..c39c7dd1 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -209,7 +209,7 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.0" - git_commit: "900f5ed35659137aa5c62d183232e0f33de97873" + git_commit: "55b025124d174ff062636130a44b7165be74d3da" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index 21b6c3b6..0ff28a2f 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -3064,7 +3064,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.0", - "git_commit" : "900f5ed35659137aa5c62d183232e0f33de97873", + "git_commit" : "55b025124d174ff062636130a44b7165be74d3da", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : {