From caa6cec4e2fba4f32606f89fde3db5571cc31b67 Mon Sep 17 00:00:00 2001 From: CI Date: Thu, 13 Feb 2025 12:35:46 +0000 Subject: [PATCH] Build branch runner_multiple_input_directories with version runner_multiple_input_directories (ed94807) Build pipeline: viash-hub.htrnaseq.runner-multiple-input-directories-z22c4 Source commit: https://github.com/viash-hub/htrnaseq/commit/ed9480768e77078704939482fe909186c92b0b59 Source message: Fix lanes --- src/utils/listInputDir/config.vsh.yaml | 4 ++ src/utils/listInputDir/main.nf | 35 ++++++++------ src/workflows/runner/main.nf | 1 + .../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 | 10 +++- target/nextflow/utils/listInputDir/main.nf | 46 +++++++++++++------ .../utils/listInputDir/nextflow_schema.json | 10 ++++ .../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 | 3 +- .../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 +- 62 files changed, 145 insertions(+), 98 deletions(-) diff --git a/src/utils/listInputDir/config.vsh.yaml b/src/utils/listInputDir/config.vsh.yaml index 0ef8af9f..30622137 100644 --- a/src/utils/listInputDir/config.vsh.yaml +++ b/src/utils/listInputDir/config.vsh.yaml @@ -24,6 +24,10 @@ arguments: type: string description: Sample nr direction: output + - name: "--sample_id" + type: string + description: Sample name + direction: output resources: - type: nextflow_script diff --git a/src/utils/listInputDir/main.nf b/src/utils/listInputDir/main.nf index 4ba942e6..3b9d7669 100644 --- a/src/utils/listInputDir/main.nf +++ b/src/utils/listInputDir/main.nf @@ -18,7 +18,7 @@ workflow run_wf { println("Extracting information from fastq/fasta filenames") def processed_fastqs = allFastqs.collect { f -> - def regex = ~/^(\w+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/ + def regex = ~/^(\w+)_S(\d+)_(L(\d+))_?R(\d)_(\d+)\.fast[qa](\.gz)?$/ def validFastq = f.name ==~ regex assert validFastq: "${f} does not match the regex ${regex}" @@ -36,20 +36,27 @@ workflow run_wf { println("Group paired fastq/fasta files") def grouped = processed_fastqs - .groupBy({it.sample_id}) - .collect{ k, vs -> - def r1 = vs.find{it.read == "1"} - def r2 = vs.find{it.read == "2"} - def newState = [ - r1_output: r1.fastq, - r2_output: r2.fastq - ] - def updtState = newState + vs[0].findAll{ it.key in ["sample", "lane"] } - return [k, updtState] - } + .groupBy({it.sample_id}, {it.lane}) + .collectMany{ sample_id, states_per_lane -> + def result = states_per_lane.collect{lane, lane_states -> + assert lane_states.size() == 2, "Expected to find two fastq files per lane! " + + "Found ${lane_states.size()}. State: ${states_per_lane}" + def r1_state = lane_states.find({it.read == "1"}) + def r2_state = lane_states.find({it.read == "2"}) + def fastq_state = [ + "r1_output": r1_state.fastq, + "r2_output": r2_state.fastq + ] + def new_state = fastq_state + + r1_state.findAll{it.key in ["sample_id", "sample", "lane"]} + + ["_meta": ["join_id": id]] + return ["${sample_id}_${lane}".toString(), new_state] + } + return result + + } + return grouped - grouped - .collect{ [ it[0], it[1] + [ _meta: [ join_id: id ] ] ] } } emit: out_ diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index ed97f92e..d102dbdf 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -35,6 +35,7 @@ workflow run_wf { // 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. + | map {id, state -> [state.sample_id, state]} | groupTuple(by: 0, sort: { state1, state2 -> if (state1.index == state2.index) { return state1.lane <=> state2.lane diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 4ea4f710..d30cac84 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 fb79bc17..53269ed4 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="2025-02-13T08:19:03Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 79ce7d15..20833e6e 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 0e3a532a..3e9ce413 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="2025-02-13T08:19:03Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 f3da160e..105dd5e0 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 95e9024c..16fb00a1 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="2025-02-13T08:19:03Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 1895bd91..46e1b3bd 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 54cdb40c..5cc43ecc 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="2025-02-13T08:19:03Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 34bfe044..ecfc8954 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 a85876e1..31d95c99 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="2025-02-13T08:19:03Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 d63a8706..045748eb 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 f799da13..25c605fb 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="2025-02-13T08:19:01Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:09Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 a7789acf..e72250bd 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 35c1c78d..10e25942 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="2025-02-13T08:19:02Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:09Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 97335e3f..5582c964 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 38800477..4c86e18a 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="2025-02-13T08:19:04Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 60e694d0..28d29794 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 a21227f4..f17b1ee7 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="2025-02-13T08:19:04Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 62e2b21f..2be2c7ce 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 aab772ef..dd76d8c4 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="2025-02-13T08:19:01Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:09Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 bcf624c4..c9abf6c6 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 678e9ad1..e8c23353 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="2025-02-13T08:19:02Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:09Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 39939060..13581e69 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 5ceebadc..5d89bece 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="2025-02-13T08:19:02Z" +LABEL org.opencontainers.image.created="2025-02-13T11:46:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" +LABEL org.opencontainers.image.revision="ed9480768e77078704939482fe909186c92b0b59" 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 6d05b279..41822a0c 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 47a4fccf..dfdb490d 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 b936dcaa..4f08f4b1 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 fca3a382..b7d3e1a6 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 81763825..5f4e0cac 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 3b5d02dd..cbf10f8a 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 ef8f43b9..5f05be59 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 9a74c58e..3fea45b0 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 7d9bdcfc..898cff53 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 90840411..e3595683 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 99d2c2e4..6785978e 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 7bded402..0ef2fa7d 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 21f5981b..d4af22f6 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 2723a907..e318379d 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 20a5efe3..a1231167 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 e775f932..9357d724 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 b65153e0..0969252a 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 00d9c3c4..e0e07c9d 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 32c7cb9d..c07dfba7 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 2463eb2e..16d18036 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 7cd1bed1..083b54b5 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 cc8efa32..54436bf8 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 0b09e1c3..c5145cbd 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 cd077d37..f0983741 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 94b0e815..ce7fd618 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -54,6 +54,14 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "string" + name: "--sample_id" + description: "Sample name" + info: null + required: false + direction: "output" + multiple: false + multiple_sep: ";" resources: - type: "nextflow_script" path: "main.nf" @@ -147,7 +155,7 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.0" - git_commit: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 740e7571..9c5dca4e 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -2867,6 +2867,15 @@ meta = [ "direction" : "output", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--sample_id", + "description" : "Sample name", + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" } ] } @@ -2983,7 +2992,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.0", - "git_commit" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3050,7 +3059,7 @@ workflow run_wf { println("Extracting information from fastq/fasta filenames") def processed_fastqs = allFastqs.collect { f -> - def regex = ~/^(\w+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/ + def regex = ~/^(\w+)_S(\d+)_(L(\d+))_?R(\d)_(\d+)\.fast[qa](\.gz)?$/ def validFastq = f.name ==~ regex assert validFastq: "${f} does not match the regex ${regex}" @@ -3068,20 +3077,27 @@ workflow run_wf { println("Group paired fastq/fasta files") def grouped = processed_fastqs - .groupBy({it.sample_id}) - .collect{ k, vs -> - def r1 = vs.find{it.read == "1"} - def r2 = vs.find{it.read == "2"} - def newState = [ - r1_output: r1.fastq, - r2_output: r2.fastq - ] - def updtState = newState + vs[0].findAll{ it.key in ["sample", "lane"] } - return [k, updtState] - } + .groupBy({it.sample_id}, {it.lane}) + .collectMany{ sample_id, states_per_lane -> + def result = states_per_lane.collect{lane, lane_states -> + assert lane_states.size() == 2, "Expected to find two fastq files per lane! " + + "Found ${lane_states.size()}. State: ${states_per_lane}" + def r1_state = lane_states.find({it.read == "1"}) + def r2_state = lane_states.find({it.read == "2"}) + def fastq_state = [ + "r1_output": r1_state.fastq, + "r2_output": r2_state.fastq + ] + def new_state = fastq_state + + r1_state.findAll{it.key in ["sample_id", "sample", "lane"]} + + ["_meta": ["join_id": id]] + return ["${sample_id}_${lane}".toString(), new_state] + } + return result + + } + return grouped - grouped - .collect{ [ it[0], it[1] + [ _meta: [ join_id: id ] ] ] } } emit: out_ diff --git a/target/nextflow/utils/listInputDir/nextflow_schema.json b/target/nextflow/utils/listInputDir/nextflow_schema.json index 19c117f4..1eb4602e 100644 --- a/target/nextflow/utils/listInputDir/nextflow_schema.json +++ b/target/nextflow/utils/listInputDir/nextflow_schema.json @@ -65,6 +65,16 @@ } + , + "sample_id": { + "type": + "string", + "description": "Type: `string`. Sample name", + "help_text": "Type: `string`. Sample name" + + } + + } }, diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index b1ee8dc9..6465bfc9 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 b16ad88a..8aa1ac6a 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 de40d0f1..506f8da1 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 aa1cdb36..0f19bd59 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3145,6 +3145,7 @@ workflow run_wf { // 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. + | map {id, state -> [state.sample_id, state]} | groupTuple(by: 0, sort: { state1, state2 -> if (state1.index == state2.index) { return state1.lane <=> state2.lane diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index a437f75a..f2f15330 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 c35eddac..ffcfed50 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "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 1c203188..44a79cf1 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: "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad" + git_commit: "ed9480768e77078704939482fe909186c92b0b59" 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 849e8782..75a875ff 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" : "7e277fcb9b7cf69a96bbcc1212e31afbf30055ad", + "git_commit" : "ed9480768e77078704939482fe909186c92b0b59", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : {