From b201cc90458c8e9a8d334045e07a0ece1ebe338b Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 11 Feb 2025 16:11:49 +0000 Subject: [PATCH] Build branch runner_multiple_input_directories with version runner_multiple_input_directories (b8bad58) Build pipeline: viash-hub.htrnaseq.runner-multiple-input-directories-9zjcp Source commit: https://github.com/viash-hub/htrnaseq/commit/b8bad5851d5d9c579d95ec2c382626a350d00d9e Source message: Fix sorting --- CHANGELOG.md | 2 +- src/workflows/runner/main.nf | 24 ++++++++++------- .../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 | 2 +- target/nextflow/utils/listInputDir/main.nf | 2 +- .../workflows/htrnaseq/.config.vsh.yaml | 2 +- target/nextflow/workflows/htrnaseq/main.nf | 2 +- .../workflows/runner/.config.vsh.yaml | 2 +- target/nextflow/workflows/runner/main.nf | 26 +++++++++++-------- .../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 +- 60 files changed, 99 insertions(+), 91 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c019ee42..3d133c33 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,7 @@ simplify running these steps as seperate steps (PR #37). ## New functionality * Multiple input directories can not be provided. The input reads from these from these directories - will be joined per barcode before mapping. This is usefull when data has been generated using + will be joined per barcode before mapping. This is useful when data has been generated using multiple sequencing runs in order to increase sequencing depth (PR #38). # htrnaseq v0.3.0 diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index 992c7b78..f086adaa 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -9,12 +9,12 @@ workflow run_wf { main: output_ch = input_ch - // Multiple runs can be provided, and the reads for these runs will + // Multiple runs can be provided, and the reads for these runs will // be concatenated. Here, we gather the FASTQ files from each input directory first. | flatMap {id, state -> // Create an input event per input directory def new_state = state.input.withIndex().collect{input_dir, id_index -> - def state_item = state + ["input": input_dir, "index": id_index, "run_id": id] + def state_item = state + ["input": input_dir, "index": id_index] return ["${id}_${id_index}".toString(), state_item] } return new_state @@ -28,14 +28,18 @@ workflow run_wf { clean_state + result } ) - // Set the pool as ID in order to group the FASTQ files - // back on level. By using the run_id, lanes are also - // automatically gathered. - | map {id, state -> - def new_event = [state.run_id, state] - } - | groupTuple(by: 0, sort: { state -> - state.index <=> state.index + // ListInputDir puts the sample_id as the event ID (slot 0 from the tuple). + // The sample_id was inferred from the start of the file name, + // and it can be used to group the FASTQ files, because an input folder + // can contain input files from multiple samples (pools). Additionally, + // there might be multiple FASTQs for a single sample that correspond to the + // lanes. So the fastq files must be gathered across lanes and input folders + // in order to create an input lists for R1 and R2. + | groupTuple(by: 0, sort: { state1, state2 -> + if (state1.index == state2.index) { + return state1.lane <=> state2.lane + } + return state1.index <=> state2.index }) | map {id, states -> def new_r1 = states.collect{it.r1_output} diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 1de9e473..014d1b43 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 59db64ba..27435f13 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="2025-02-11T12:11:26Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:07Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index efcef2db..0c7ab032 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 8b1de01c..21d97031 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="2025-02-11T12:11:26Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:08Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index f1e9745e..e5eb9348 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 0f1d6806..ff880390 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="2025-02-11T12:11:26Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:07Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" 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 8f3af062..46073ba8 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 0ae2064d..8d96f81e 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="2025-02-11T12:11:26Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:07Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" 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 ce58defc..51c2df4f 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 f4638ba8..398c3fae 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="2025-02-11T12:11:26Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:07Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index 84541f32..55e524d2 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 919f4021..b4f92383 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="2025-02-11T12:11:25Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index d9558633..30cabb8c 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 ac4f720b..7eaaaa5c 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="2025-02-11T12:11:25Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:06Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 933f2bdb..c373459c 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 c2311dae..3fcf5792 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="2025-02-11T12:11:27Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:08Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index d6b5aab4..e77a951c 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 8d175325..82111701 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="2025-02-11T12:11:27Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:08Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index 948cf5be..478bc70b 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 7d47e613..2570048c 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="2025-02-11T12:11:25Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index 98f4752a..67236d78 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 330b3dbb..599ce1d7 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="2025-02-11T12:11:25Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:06Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index 9cf8d17b..2b00e5f3 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 1735d780..7f7cab8f 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="2025-02-11T12:11:26Z" +LABEL org.opencontainers.image.created="2025-02-11T15:24:07Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="a2b2f9591746172428cbc0cf7e11d3db7595c5ac" +LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" LABEL org.opencontainers.image.version="runner_multiple_input_directories" VIASHDOCKER diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index d6b54220..c8a174b9 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 f7638b7b..85e367e5 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 c9dacbd8..fbdbe00c 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 218a431b..0ff56b68 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 802de15e..df4d2769 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 0c226f2f..86019bcf 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 ce2c4a19..4778dd5f 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 5f4fe5b4..42228605 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 a4acb9de..db9b397d 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 6d6d1187..12287c2e 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 0fd30f62..cf366b5d 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 172b7fa6..db84f8cc 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 a7e7583a..af47a13f 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 36799e52..30d8a7f6 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 e2be9c2d..0f0495ce 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 87eae268..3c4cd853 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 08993b1c..b6be5166 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 3f78a236..7e521276 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 00537610..8e43ec15 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 b3291105..909808fb 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 457663ec..84d3c1d6 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 377e00e5..b6015e84 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 d1ab1d43..5995c13f 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 51909884..f29406b1 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 64f35c57..ff3307e6 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -147,7 +147,7 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.0" - git_commit: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 a3eef5d2..6277a99c 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -2983,7 +2983,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.0", - "git_commit" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index a0cc4af9..90a6d957 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 99400a8a..d9b2eeae 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 e237e7f9..81be2a6e 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -197,7 +197,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.0" - git_commit: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 8b5fec90..0913ac32 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -3057,7 +3057,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.0", - "git_commit" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3119,12 +3119,12 @@ workflow run_wf { main: output_ch = input_ch - // Multiple runs can be provided, and the reads for these runs will + // Multiple runs can be provided, and the reads for these runs will // be concatenated. Here, we gather the FASTQ files from each input directory first. | flatMap {id, state -> // Create an input event per input directory def new_state = state.input.withIndex().collect{input_dir, id_index -> - def state_item = state + ["input": input_dir, "index": id_index, "run_id": id] + def state_item = state + ["input": input_dir, "index": id_index] return ["${id}_${id_index}".toString(), state_item] } return new_state @@ -3138,14 +3138,18 @@ workflow run_wf { clean_state + result } ) - // Set the pool as ID in order to group the FASTQ files - // back on level. By using the run_id, lanes are also - // automatically gathered. - | map {id, state -> - def new_event = [state.run_id, state] - } - | groupTuple(by: 0, sort: { state -> - state.index <=> state.index + // ListInputDir puts the sample_id as the event ID (slot 0 from the tuple). + // The sample_id was inferred from the start of the file name, + // and it can be used to group the FASTQ files, because an input folder + // can contain input files from multiple samples (pools). Additionally, + // there might be multiple FASTQs for a single sample that correspond to the + // lanes. So the fastq files must be gathered across lanes and input folders + // in order to create an input lists for R1 and R2. + | groupTuple(by: 0, sort: { state1, state2 -> + if (state1.index == state2.index) { + return state1.lane <=> state2.lane + } + return state1.index <=> state2.index }) | map {id, states -> def new_r1 = states.collect{it.r1_output} diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 50e766cf..4a056d09 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 276d2e66..fd99b636 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "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 2facfc9c..4b65f587 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: "a2b2f9591746172428cbc0cf7e11d3db7595c5ac" + git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" 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 4bfaec59..57535f89 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" : "a2b2f9591746172428cbc0cf7e11d3db7595c5ac", + "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : {