From 579a737d8c1440ea43159a32d8666db9f497fe02 Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 11 Feb 2025 20:11:42 +0000 Subject: [PATCH] Build branch runner_multiple_input_directories with version runner_multiple_input_directories (fc48924) Build pipeline: viash-hub.htrnaseq.runner-multiple-input-directories-xrw45 Source commit: https://github.com/viash-hub/htrnaseq/commit/fc48924aa82d885ede794fd8e19a3514206bbd2d Source message: Fix FASTQ paths --- src/workflows/runner/main.nf | 2 +- src/workflows/well_demultiplex/main.nf | 6 ++++-- target/executable/eset/create_eset/.config.vsh.yaml | 2 +- target/executable/eset/create_eset/create_eset | 4 ++-- target/executable/eset/create_fdata/.config.vsh.yaml | 2 +- target/executable/eset/create_fdata/create_fdata | 4 ++-- target/executable/eset/create_pdata/.config.vsh.yaml | 2 +- target/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/check_cutadapt_output | 4 ++-- target/executable/io/publish_fastqs/.config.vsh.yaml | 2 +- target/executable/io/publish_fastqs/publish_fastqs | 4 ++-- target/executable/io/publish_results/.config.vsh.yaml | 2 +- target/executable/io/publish_results/publish_results | 4 ++-- target/executable/parallel_map/.config.vsh.yaml | 2 +- target/executable/parallel_map/parallel_map | 4 ++-- target/executable/report/create_report/.config.vsh.yaml | 2 +- target/executable/report/create_report/create_report | 4 ++-- .../executable/stats/combine_star_logs/.config.vsh.yaml | 2 +- .../executable/stats/combine_star_logs/combine_star_logs | 4 ++-- .../stats/generate_pool_statistics/.config.vsh.yaml | 2 +- .../generate_pool_statistics/generate_pool_statistics | 4 ++-- .../stats/generate_well_statistics/.config.vsh.yaml | 2 +- .../generate_well_statistics/generate_well_statistics | 4 ++-- target/nextflow/eset/create_eset/.config.vsh.yaml | 2 +- target/nextflow/eset/create_eset/main.nf | 2 +- target/nextflow/eset/create_fdata/.config.vsh.yaml | 2 +- target/nextflow/eset/create_fdata/main.nf | 2 +- target/nextflow/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 +- .../well_demultiplexing/check_cutadapt_output/main.nf | 2 +- target/nextflow/io/publish_fastqs/.config.vsh.yaml | 2 +- target/nextflow/io/publish_fastqs/main.nf | 2 +- target/nextflow/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 +- target/nextflow/report/create_report/.config.vsh.yaml | 2 +- target/nextflow/report/create_report/main.nf | 2 +- target/nextflow/stats/combine_star_logs/.config.vsh.yaml | 2 +- target/nextflow/stats/combine_star_logs/main.nf | 2 +- .../stats/generate_pool_statistics/.config.vsh.yaml | 2 +- target/nextflow/stats/generate_pool_statistics/main.nf | 2 +- .../stats/generate_well_statistics/.config.vsh.yaml | 2 +- target/nextflow/stats/generate_well_statistics/main.nf | 2 +- target/nextflow/utils/listInputDir/.config.vsh.yaml | 2 +- target/nextflow/utils/listInputDir/main.nf | 2 +- target/nextflow/workflows/htrnaseq/.config.vsh.yaml | 2 +- target/nextflow/workflows/htrnaseq/main.nf | 2 +- target/nextflow/workflows/runner/.config.vsh.yaml | 2 +- target/nextflow/workflows/runner/main.nf | 4 ++-- .../nextflow/workflows/well_demultiplex/.config.vsh.yaml | 2 +- target/nextflow/workflows/well_demultiplex/main.nf | 8 +++++--- target/nextflow/workflows/well_metadata/.config.vsh.yaml | 2 +- target/nextflow/workflows/well_metadata/main.nf | 2 +- 60 files changed, 80 insertions(+), 76 deletions(-) diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index f086adaa..ed97f92e 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -14,7 +14,7 @@ workflow run_wf { | 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] + def state_item = state + ["input": input_dir, "index": id_index, "run_id": id] return ["${id}_${id_index}".toString(), state_item] } return new_state diff --git a/src/workflows/well_demultiplex/main.nf b/src/workflows/well_demultiplex/main.nf index 31a94c9c..8034ed8f 100644 --- a/src/workflows/well_demultiplex/main.nf +++ b/src/workflows/well_demultiplex/main.nf @@ -187,7 +187,8 @@ workflow run_wf { [ input: state.output_r1, gzip_output: false, - output: "${state.pool}/${state.barcode_id}_R1.fastq" + // Remark: the fastq path part may seem superfluous but is necessary for publising later + output: "fastq/${state.pool}/${state.barcode_id}_R1.fastq" ] }, toState: { id, result, state -> @@ -203,7 +204,8 @@ workflow run_wf { [ input: state.output_r2, gzip_output: false, - output: "${state.pool}/${state.barcode_id}_R2.fastq", + // Remark: the fastq path part may seem superfluous but is necessary for publising later + output: "fastq/${state.pool}/${state.barcode_id}_R2.fastq", ] }, toState: { id, result, state -> diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 014d1b43..5045dc3f 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 27435f13..dee3ff9d 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="2025-02-11T15:24:07Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 0c7ab032..1fb7b459 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 21d97031..7f87a4f2 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="2025-02-11T15:24:08Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 e5eb9348..268d37cc 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 ff880390..cd9bf21e 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="2025-02-11T15:24:07Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 46073ba8..34a478ab 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 8d96f81e..d3be1de8 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="2025-02-11T15:24:07Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 51c2df4f..c0134b30 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 398c3fae..778a624b 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="2025-02-11T15:24:07Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 55e524d2..adb49e52 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 b4f92383..34b4f042 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="2025-02-11T15:24:05Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 30cabb8c..10fc5a7f 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 7eaaaa5c..8c8f408f 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="2025-02-11T15:24:06Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:21Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 c373459c..f794cb3a 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 3fcf5792..bd6f775f 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="2025-02-11T15:24:08Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:23Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 e77a951c..035b7cf0 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 82111701..6dfde610 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="2025-02-11T15:24:08Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:23Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 478bc70b..aba3ab93 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 2570048c..43933acc 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="2025-02-11T15:24:05Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:20Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 67236d78..d4c0306b 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 599ce1d7..f568736c 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="2025-02-11T15:24:06Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:21Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 2b00e5f3..6a4fbf2e 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 7f7cab8f..479cacbd 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="2025-02-11T15:24:07Z" +LABEL org.opencontainers.image.created="2025-02-11T19:25:21Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e" +LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 c8a174b9..c10dd066 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 85e367e5..5669c0f2 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 fbdbe00c..1b44a16e 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 0ff56b68..5ca9988e 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 df4d2769..b3903359 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 86019bcf..9eb97e40 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 4778dd5f..c68a2bef 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 42228605..96806858 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 db9b397d..05c40d04 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 12287c2e..0ef26f82 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 cf366b5d..79ecbb88 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 db84f8cc..f7bc311b 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 af47a13f..2cb33019 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 30d8a7f6..cd73ef6f 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 0f0495ce..bca0f44f 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 3c4cd853..7ce8d0c1 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 b6be5166..c85b334b 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 7e521276..ccb124b1 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 8e43ec15..8006aefe 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 909808fb..dea389c3 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 84d3c1d6..ecdb3d48 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 b6015e84..03940ddf 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 5995c13f..57b60ba9 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 f29406b1..1de04cfe 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 ff3307e6..0cddb241 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 6277a99c..b847a48a 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 90a6d957..6da4880b 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 d9b2eeae..4afd5475 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "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 81be2a6e..e7f032e1 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 0913ac32..e714144e 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3124,7 +3124,7 @@ workflow run_wf { | 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] + def state_item = state + ["input": input_dir, "index": id_index, "run_id": id] return ["${id}_${id_index}".toString(), state_item] } return new_state diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 4a056d09..584a886e 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -211,7 +211,7 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt" diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index fd99b636..aaf1b2c8 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -3084,7 +3084,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.0", - "git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3322,7 +3322,8 @@ workflow run_wf { [ input: state.output_r1, gzip_output: false, - output: "${state.pool}/${state.barcode_id}_R1.fastq" + // Remark: the fastq path part may seem superfluous but is necessary for publising later + output: "fastq/${state.pool}/${state.barcode_id}_R1.fastq" ] }, toState: { id, result, state -> @@ -3338,7 +3339,8 @@ workflow run_wf { [ input: state.output_r2, gzip_output: false, - output: "${state.pool}/${state.barcode_id}_R2.fastq", + // Remark: the fastq path part may seem superfluous but is necessary for publising later + output: "fastq/${state.pool}/${state.barcode_id}_R2.fastq", ] }, toState: { id, result, state -> diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml index 4b65f587..dc9b55ec 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e" + git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d" 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 57535f89..ade506e0 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" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e", + "git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : {