From 021ec5ff2c26accac0a79d7d1824b35360cbae95 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:20:12 +0200 Subject: [PATCH 01/10] fix(sort): fix issue with sorting false on gcp --- workflows/sarek/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf index 5062470373..d28aabff4c 100644 --- a/workflows/sarek/main.nf +++ b/workflows/sarek/main.nf @@ -879,7 +879,7 @@ workflow SAREK { ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(version_yaml) ch_multiqc_files = ch_multiqc_files.mix(reports) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)) MULTIQC ( ch_multiqc_files.collect(), From b7e352332b851b97ff154704e47af02f7f379504 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:20:55 +0200 Subject: [PATCH 02/10] fix(doi): fix multiple doi print --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index afd58a8cc2..282ff83651 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -280,7 +280,13 @@ def methodsDescriptionText(mqc_methods_yaml) { meta["manifest_map"] = workflow.manifest.toMap() // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + if (meta.manifest_map.doi) { + def temp_doi_ref = "" + String[] manifest_doi = meta.manifest_map.doi.split(",") + for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref}), " + meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) + } + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " // Tool references From adb0ecd3f00fbdcb9afd83cf2fabed1e45d1279c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:21:24 +0200 Subject: [PATCH 03/10] fix(manifest): fix doi in manifest --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index e32da2cb94..447e219cd9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -391,7 +391,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '3.5.0dev' - doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' + doi = '10.12688/f1000research.16665.2,10.1093/nargab/lqae031,10.5281/zenodo.3476425' } // Load modules.config for DSL2 module specific options From c8817f919faf373adc183f65ac445a9e6b75aadb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:42:56 +0200 Subject: [PATCH 04/10] code polish --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index 282ff83651..21ed197041 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -285,10 +285,10 @@ def methodsDescriptionText(mqc_methods_yaml) { String[] manifest_doi = meta.manifest_map.doi.split(",") for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref}), " meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) + } else { + meta["nodoi_text"] = "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " } - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - // Tool references meta["tool_citations"] = "" meta["tool_bibliography"] = "" From ce2460b5dbc20397e87e1fdc1315566a3318be37 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 11:46:52 +0200 Subject: [PATCH 05/10] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe9a52fb8e..eac887999e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline` +- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491) +- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix multiple DOI handling in manifest ### Removed From 9f6903e484aed63d93c2274eb81a29cb1ec07477 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 2 May 2024 12:03:49 +0200 Subject: [PATCH 06/10] Update subworkflows/local/utils_nfcore_sarek_pipeline/main.nf --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index 21ed197041..a9ae9cbe93 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -285,9 +285,8 @@ def methodsDescriptionText(mqc_methods_yaml) { String[] manifest_doi = meta.manifest_map.doi.split(",") for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref}), " meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) - } else { - meta["nodoi_text"] = "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - } + } else meta["doi_text"] = "" + meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " // Tool references meta["tool_citations"] = "" From 7a8a860b82306f82b1bf2b224d510a9cb41a1456 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 15:07:02 +0200 Subject: [PATCH 07/10] let's keep the space and just handle them --- nextflow.config | 2 +- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 447e219cd9..e32da2cb94 100644 --- a/nextflow.config +++ b/nextflow.config @@ -391,7 +391,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '3.5.0dev' - doi = '10.12688/f1000research.16665.2,10.1093/nargab/lqae031,10.5281/zenodo.3476425' + doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425' } // Load modules.config for DSL2 module specific options diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index a9ae9cbe93..fc81f2f67b 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -283,7 +283,7 @@ def methodsDescriptionText(mqc_methods_yaml) { if (meta.manifest_map.doi) { def temp_doi_ref = "" String[] manifest_doi = meta.manifest_map.doi.split(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref}), " + for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace(" ", "")}), " meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " From 0f682d5fcff664a6a7c0787ad14f9f8013936efa Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 16:12:26 +0200 Subject: [PATCH 08/10] deal with multiple DOI properly --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 2 +- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index fc81f2f67b..67d455863c 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -282,7 +282,7 @@ def methodsDescriptionText(mqc_methods_yaml) { // Pipeline DOI if (meta.manifest_map.doi) { def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.split(",") + String[] manifest_doi = meta.manifest_map.doi.tokenize(",") for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace(" ", "")}), " meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) } else meta["doi_text"] = "" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a8b55d6fe1..f70b89fd29 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -65,9 +65,12 @@ def checkProfileProvided(nextflow_cli_args) { // Citation string for pipeline // def workflowCitation() { + def temp_doi_ref = "" + String[] manifest_doi = workflow.manifest.doi.tokenize(",") + for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace(" ", "")}\n" return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + - " ${workflow.manifest.doi}\n\n" + + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + From 6a4a1891f962c5b4c7fdad41b3e542f807c12d64 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 18:26:01 +0200 Subject: [PATCH 09/10] update CHANGELOG --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index eac887999e..5ea71806d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,7 +24,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline` - [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491) -- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix multiple DOI handling in manifest ### Removed From c7138909c308b5ebbc1e62decf1ee817801d413a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 2 May 2024 18:27:55 +0200 Subject: [PATCH 10/10] revert changes --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 9 ++------- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 5 +---- 2 files changed, 3 insertions(+), 11 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index 67d455863c..afd58a8cc2 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -280,13 +280,8 @@ def methodsDescriptionText(mqc_methods_yaml) { meta["manifest_map"] = workflow.manifest.toMap() // Pipeline DOI - if (meta.manifest_map.doi) { - def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace(" ", "")}), " - meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2) - } else meta["doi_text"] = "" - meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " // Tool references meta["tool_citations"] = "" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index f70b89fd29..a8b55d6fe1 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -65,12 +65,9 @@ def checkProfileProvided(nextflow_cli_args) { // Citation string for pipeline // def workflowCitation() { - def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace(" ", "")}\n" return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + - temp_doi_ref + "\n" + + " ${workflow.manifest.doi}\n\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" +