From d67e37efb99e1ca4813b8f1e1f9aa6e5ce6e2076 Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 6 May 2025 09:04:20 +0000 Subject: [PATCH] Build branch save-params with version save-params (afdc3f4) Build pipeline: viash-hub.htrnaseq.save-params-h7kx4 Source commit: https://github.com/viash-hub/htrnaseq/commit/afdc3f4ed8c09d39a40ba036f794b7061a689bd6 Source message: keep id in component --- src/utils/save_params/script.py | 9 --------- target/executable/eset/create_eset/.config.vsh.yaml | 2 +- target/executable/eset/create_eset/create_eset | 4 ++-- .../executable/eset/create_fdata/.config.vsh.yaml | 2 +- target/executable/eset/create_fdata/create_fdata | 4 ++-- .../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 ++-- .../executable/io/publish_fastqs/.config.vsh.yaml | 2 +- target/executable/io/publish_fastqs/publish_fastqs | 4 ++-- .../executable/io/publish_results/.config.vsh.yaml | 2 +- .../executable/io/publish_results/publish_results | 4 ++-- target/executable/parallel_map/.config.vsh.yaml | 2 +- target/executable/parallel_map/parallel_map | 4 ++-- .../report/create_report/.config.vsh.yaml | 2 +- .../executable/report/create_report/create_report | 4 ++-- .../stats/combine_star_logs/.config.vsh.yaml | 2 +- .../stats/combine_star_logs/combine_star_logs | 4 ++-- .../stats/generate_pool_statistics/.config.vsh.yaml | 2 +- .../generate_pool_statistics | 4 ++-- .../stats/generate_well_statistics/.config.vsh.yaml | 2 +- .../generate_well_statistics | 4 ++-- .../executable/utils/save_params/.config.vsh.yaml | 2 +- target/executable/utils/save_params/save_params | 13 ++----------- 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 +- .../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 +- .../nextflow/report/create_report/.config.vsh.yaml | 2 +- target/nextflow/report/create_report/main.nf | 2 +- .../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 +- .../nextflow/stats/generate_pool_statistics/main.nf | 2 +- .../stats/generate_well_statistics/.config.vsh.yaml | 2 +- .../nextflow/stats/generate_well_statistics/main.nf | 2 +- target/nextflow/utils/concatRuns/.config.vsh.yaml | 2 +- target/nextflow/utils/concatRuns/main.nf | 2 +- target/nextflow/utils/listInputDir/.config.vsh.yaml | 2 +- target/nextflow/utils/listInputDir/main.nf | 2 +- target/nextflow/utils/save_params/.config.vsh.yaml | 2 +- target/nextflow/utils/save_params/main.nf | 11 +---------- 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 | 2 +- .../workflows/well_demultiplex/.config.vsh.yaml | 2 +- target/nextflow/workflows/well_demultiplex/main.nf | 2 +- .../workflows/well_metadata/.config.vsh.yaml | 2 +- target/nextflow/workflows/well_metadata/main.nf | 2 +- 65 files changed, 77 insertions(+), 104 deletions(-) diff --git a/src/utils/save_params/script.py b/src/utils/save_params/script.py index c7652c94..1ea3aa97 100644 --- a/src/utils/save_params/script.py +++ b/src/utils/save_params/script.py @@ -21,18 +21,9 @@ def decode_params_yaml(encoded_yaml): return yaml_data -# def replace_id(value, sample_id): -# if isinstance(value, str): -# return value.replace('$id', sample_id) -# elif isinstance(value, list): -# return [replace_id(item, sample_id) for item in value] -# return value - print(par['params_yaml']) params = decode_params_yaml(par['params_yaml']) -# for key, value in params.items(): -# params[key] = replace_id(value, par["id"]) with open(par["output"], 'w') as f: yaml.dump(params, f, default_flow_style=False, Dumper=Dumper) diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 1ee263d6..65f86d6e 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -203,7 +203,7 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 34544d46..e9182ed4 100755 --- a/target/executable/eset/create_eset/create_eset +++ b/target/executable/eset/create_eset/create_eset @@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR 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="2025-05-02T07:23:37Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index f53d750b..00749a2a 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -180,7 +180,7 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 2fe9174e..4c761e60 100755 --- a/target/executable/eset/create_fdata/create_fdata +++ b/target/executable/eset/create_fdata/create_fdata @@ -458,9 +458,9 @@ 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="2025-05-02T07:23:36Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 2d19446c..ed8a36b1 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -194,7 +194,7 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 0b539ac0..ca673708 100755 --- a/target/executable/eset/create_pdata/create_pdata +++ b/target/executable/eset/create_pdata/create_pdata @@ -458,9 +458,9 @@ 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="2025-05-02T07:23:37Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" 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 5918c767..2e27b46e 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 @@ -152,7 +152,7 @@ build_info: output: "target/executable/integration_test_components/htrnaseq/check_eset" executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 590f0c93..1db23a77 100755 --- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset +++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset @@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR 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="2025-05-02T07:23:35Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:04Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" 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 1d933335..2fc5fc75 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 @@ -161,7 +161,7 @@ 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: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 6cfff35a..19b32947 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 @@ -457,9 +457,9 @@ 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="2025-05-02T07:23:37Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index e422d403..924a5a78 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -136,7 +136,7 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 1739056a..cba3d277 100755 --- a/target/executable/io/publish_fastqs/publish_fastqs +++ b/target/executable/io/publish_fastqs/publish_fastqs @@ -450,9 +450,9 @@ 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="2025-05-02T07:23:36Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index 3f74a813..4dd4130b 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -190,7 +190,7 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 9100abe2..15b31a7a 100755 --- a/target/executable/io/publish_results/publish_results +++ b/target/executable/io/publish_results/publish_results @@ -450,9 +450,9 @@ 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="2025-05-02T07:23:36Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 858234c7..09fd1f9f 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -282,7 +282,7 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 382a199f..a2e3cdf6 100755 --- a/target/executable/parallel_map/parallel_map +++ b/target/executable/parallel_map/parallel_map @@ -461,9 +461,9 @@ 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="2025-05-02T07:23:37Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index d565f28a..da469619 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -206,7 +206,7 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 5d695a02..c3962d0d 100755 --- a/target/executable/report/create_report/create_report +++ b/target/executable/report/create_report/create_report @@ -462,9 +462,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR 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="2025-05-02T07:23:37Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index 93daba7d..2aa71b23 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -201,7 +201,7 @@ build_info: output: "target/executable/stats/combine_star_logs" executable: "target/executable/stats/combine_star_logs/combine_star_logs" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 b41536f7..f044f412 100755 --- a/target/executable/stats/combine_star_logs/combine_star_logs +++ b/target/executable/stats/combine_star_logs/combine_star_logs @@ -457,9 +457,9 @@ 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="2025-05-02T07:23:35Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:04Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index 3193d181..025f015f 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -185,7 +185,7 @@ build_info: output: "target/executable/stats/generate_pool_statistics" executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 05273b2c..c14f5690 100755 --- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics +++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics @@ -458,9 +458,9 @@ 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="2025-05-02T07:23:36Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index fdd0376b..80baf3d1 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -267,7 +267,7 @@ build_info: output: "target/executable/stats/generate_well_statistics" executable: "target/executable/stats/generate_well_statistics/generate_well_statistics" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 8a23cd4c..aaae55df 100755 --- a/target/executable/stats/generate_well_statistics/generate_well_statistics +++ b/target/executable/stats/generate_well_statistics/generate_well_statistics @@ -461,9 +461,9 @@ 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="2025-05-02T07:23:36Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml index 1fa84bdb..6bd66885 100644 --- a/target/executable/utils/save_params/.config.vsh.yaml +++ b/target/executable/utils/save_params/.config.vsh.yaml @@ -146,7 +146,7 @@ build_info: output: "target/executable/utils/save_params" executable: "target/executable/utils/save_params/save_params" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/utils/save_params/save_params b/target/executable/utils/save_params/save_params index 6c794078..c27f4bd1 100755 --- a/target/executable/utils/save_params/save_params +++ b/target/executable/utils/save_params/save_params @@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "pyyaml" LABEL org.opencontainers.image.description="Companion container for running component utils save_params" -LABEL org.opencontainers.image.created="2025-05-02T07:23:38Z" +LABEL org.opencontainers.image.created="2025-05-06T08:16:06Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="b9a380acae42705fc901f8d9e73e698ef55f4b65" +LABEL org.opencontainers.image.revision="afdc3f4ed8c09d39a40ba036f794b7061a689bd6" LABEL org.opencontainers.image.version="save-params" VIASHDOCKER @@ -1085,18 +1085,9 @@ def decode_params_yaml(encoded_yaml): return yaml_data -# def replace_id(value, sample_id): -# if isinstance(value, str): -# return value.replace('\$id', sample_id) -# elif isinstance(value, list): -# return [replace_id(item, sample_id) for item in value] -# return value - print(par['params_yaml']) params = decode_params_yaml(par['params_yaml']) -# for key, value in params.items(): -# params[key] = replace_id(value, par["id"]) with open(par["output"], 'w') as f: yaml.dump(params, f, default_flow_style=False, Dumper=Dumper) diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index 381caf39..35fa28f4 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -203,7 +203,7 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 43a3d8b5..7a258e80 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -3309,7 +3309,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 e1b100e0..fa988eb8 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -180,7 +180,7 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 f68db962..b7a73c19 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -3279,7 +3279,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 c2af98c2..6944cf9b 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -194,7 +194,7 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 2099a60e..a00f8f98 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -3293,7 +3293,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 a0f434db..0cfc3d43 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 @@ -152,7 +152,7 @@ build_info: output: "target/nextflow/integration_test_components/htrnaseq/check_eset" executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 3a9145f1..1917f0bb 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -3233,7 +3233,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 1658fa16..7d998152 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 @@ -161,7 +161,7 @@ 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: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 a56855d2..086c5e95 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 @@ -3244,7 +3244,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 d4f995ff..f3c40743 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -136,7 +136,7 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 410f2606..ae442998 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -3207,7 +3207,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 4c4ced12..529a168e 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -190,7 +190,7 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 8bd68e9b..ac83b985 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -3267,7 +3267,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 0d4e7f6a..519ac5c1 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -282,7 +282,7 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 2a86d124..a9fec52d 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -3379,7 +3379,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 21912c26..b3de8b95 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -206,7 +206,7 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 057a2055..726a49ba 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -3314,7 +3314,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 9ce71bae..bd208a1e 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -201,7 +201,7 @@ build_info: output: "target/nextflow/stats/combine_star_logs" executable: "target/nextflow/stats/combine_star_logs/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 6bbd9c02..adb1d385 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -3295,7 +3295,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 76fc54d1..6fc8dade 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -185,7 +185,7 @@ build_info: output: "target/nextflow/stats/generate_pool_statistics" executable: "target/nextflow/stats/generate_pool_statistics/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 f84a7590..fbf1efde 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -3279,7 +3279,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 ff4d3600..174a08ea 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -267,7 +267,7 @@ build_info: output: "target/nextflow/stats/generate_well_statistics" executable: "target/nextflow/stats/generate_well_statistics/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 83891fd4..8002dfd1 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -3374,7 +3374,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml index 304e6719..70c04dc0 100644 --- a/target/nextflow/utils/concatRuns/.config.vsh.yaml +++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml @@ -157,7 +157,7 @@ build_info: output: "target/nextflow/utils/concatRuns" executable: "target/nextflow/utils/concatRuns/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text" diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf index 29b7a96c..390b9d3c 100644 --- a/target/nextflow/utils/concatRuns/main.nf +++ b/target/nextflow/utils/concatRuns/main.nf @@ -3229,7 +3229,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/concatRuns", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 3700b689..41f51e32 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -168,7 +168,7 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 fe8372bb..b490e4ff 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -3239,7 +3239,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/utils/save_params/.config.vsh.yaml b/target/nextflow/utils/save_params/.config.vsh.yaml index 8ace0cef..a2ce9d21 100644 --- a/target/nextflow/utils/save_params/.config.vsh.yaml +++ b/target/nextflow/utils/save_params/.config.vsh.yaml @@ -146,7 +146,7 @@ build_info: output: "target/nextflow/utils/save_params" executable: "target/nextflow/utils/save_params/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/utils/save_params/main.nf b/target/nextflow/utils/save_params/main.nf index 4edf72bc..3a2a0c41 100644 --- a/target/nextflow/utils/save_params/main.nf +++ b/target/nextflow/utils/save_params/main.nf @@ -3221,7 +3221,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/utils/save_params", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3320,18 +3320,9 @@ def decode_params_yaml(encoded_yaml): return yaml_data -# def replace_id(value, sample_id): -# if isinstance(value, str): -# return value.replace('\\$id', sample_id) -# elif isinstance(value, list): -# return [replace_id(item, sample_id) for item in value] -# return value - print(par['params_yaml']) params = decode_params_yaml(par['params_yaml']) -# for key, value in params.items(): -# params[key] = replace_id(value, par["id"]) with open(par["output"], 'w') as f: yaml.dump(params, f, default_flow_style=False, Dumper=Dumper) diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index fd8850d2..ea937178 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -342,7 +342,7 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 aa3afb8d..414d92be 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -3484,7 +3484,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 78936e03..4cd371b8 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -221,7 +221,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 a7e6dc1b..17ced7b8 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -3317,7 +3317,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 7ede8518..991f2982 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -214,7 +214,7 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 ced4a9eb..61bff408 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -3319,7 +3319,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "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 bc4fca31..3fc1c2d1 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -212,7 +212,7 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.2" - git_commit: "b9a380acae42705fc901f8d9e73e698ef55f4b65" + git_commit: "afdc3f4ed8c09d39a40ba036f794b7061a689bd6" 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 9e838375..21559e77 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -3299,7 +3299,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.2", - "git_commit" : "b9a380acae42705fc901f8d9e73e698ef55f4b65", + "git_commit" : "afdc3f4ed8c09d39a40ba036f794b7061a689bd6", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : {