From f59c5f3b78087c9e42444988d237a8f9eaa0ce33 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 11 Oct 2024 11:09:31 +0200 Subject: [PATCH 1/5] fix pre-commit lining failing on pipelines template --- .../.github/workflows/download_pipeline.yml | 3 +-- nf_core/pipeline-template/CITATIONS.md | 9 ++++++--- nf_core/pipeline-template/docs/output.md | 2 +- nf_core/pipeline-template/main.nf | 3 ++- nf_core/pipeline-template/nextflow.config | 4 ++-- .../local/utils_nfcore_pipeline_pipeline/main.nf | 8 +++++--- nf_core/pipeline-template/workflows/pipeline.nf | 5 +++-- 7 files changed, 20 insertions(+), 14 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 29b994754..fdd5492ca 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -116,5 +116,4 @@ jobs: exit 1 else echo "The pipeline can be downloaded successfully!" - fi - {% endraw %}{% endif %} + fi{% endraw %}{% endif %} diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md index 01e97c141..16da9a420 100644 --- a/nf_core/pipeline-template/CITATIONS.md +++ b/nf_core/pipeline-template/CITATIONS.md @@ -15,12 +15,14 @@ {% if fastqc %}- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. -> {% endif %} + +{%- endif %} {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. -> {% endif %} + +{%- endif %} ## Software packaging/containerisation tools @@ -43,4 +45,5 @@ - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. - > {%- endif %} + + {%- endif %} diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md index 1becf24b6..83d5d23fe 100644 --- a/nf_core/pipeline-template/docs/output.md +++ b/nf_core/pipeline-template/docs/output.md @@ -64,7 +64,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - `pipeline_info/` - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. {%- if email %} - - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %} + - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.{% endif %} - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - Parameters used by the pipeline run: `params.json`. diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf index 6516ebf90..f908ec934 100644 --- a/nf_core/pipeline-template/main.nf +++ b/nf_core/pipeline-template/main.nf @@ -84,7 +84,8 @@ workflow { params.outdir, params.input ) - {% endif %} + {-% endif %} + // // WORKFLOW: Run main workflow // diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index f2bcda097..052a5d8b1 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -288,10 +288,10 @@ validation { """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x + https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/${manifest.name}/blob/master/CITATIONS.md """{% endif %} }{% if is_nfcore %} summary { diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index bcf2f4a9a..78fed1fcf 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -51,7 +51,8 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) - {% if nf_schema %} + {%- if nf_schema %} + // // Validate parameters and generate parameter summary to stdout // @@ -60,7 +61,7 @@ workflow PIPELINE_INITIALISATION { validate_params, null ) - {% endif %} + {%- endif %} // // Check config provided to the pipeline @@ -70,6 +71,7 @@ workflow PIPELINE_INITIALISATION { ) {%- if igenomes %} + // // Custom validation for pipeline parameters // @@ -123,7 +125,7 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML - {% endif %} + {%- endif %} outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output {% if adaptivecard or slackreport %}hook_url // string: hook URL for notifications{% endif %} diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index f878bb31a..adad7a6a0 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -65,13 +65,14 @@ workflow {{ short_name|upper }} { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - {% if nf_schema %} + {%- if nf_schema %} + summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - {% endif %} + {%- endif %} {%- if citations %} ch_multiqc_custom_methods_description = params.multiqc_methods_description ? From 12084b4bd3953f47c26b27c2db1788d026e1ce47 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 11 Oct 2024 11:14:23 +0200 Subject: [PATCH 2/5] use multi-line string for local swf --- .../nf-core/utils_nextflow_pipeline/main.nf | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67a6..ea5b7aaa1 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -115,8 +115,17 @@ def checkCondaChannels() { } if (channels_missing | channel_priority_violation) { - log.warn( - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - ) + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } From f2339a32bcb493384942a8ca17ee7972ac22f49a Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 11 Oct 2024 11:15:09 +0200 Subject: [PATCH 3/5] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5073fa670..5ad584d68 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ - Add null/ to .gitignore ([#3191](https://github.com/nf-core/tools/pull/3191)) - Parallelize pipeline GHA tests over docker/conda/singularity ([#3214](https://github.com/nf-core/tools/pull/3214)) - Fix `template_version_comment.yml` github action ([#3212](https://github.com/nf-core/tools/pull/3212)) +- Fix pre-commit linting on pipeline template ([#3218](https://github.com/nf-core/tools/pull/3218)) ### Linting From cc713d8411e5d78796f99f230f8b0270fe8e7ad1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 11 Oct 2024 12:01:18 +0200 Subject: [PATCH 4/5] update template components --- nf_core/pipeline-template/modules.json | 6 +++--- .../modules/nf-core/multiqc/main.nf | 2 +- .../nf-core/utils_nextflow_pipeline/main.nf | 17 +++++------------ .../nf-core/utils_nfcore_pipeline/main.nf | 10 +++++----- 4 files changed, 14 insertions(+), 21 deletions(-) diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index fa4651ee1..f714eb1d9 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -13,7 +13,7 @@ }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %} "multiqc": { "branch": "master", - "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] } {%- endif %} @@ -23,12 +23,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }{% if nf_schema %}, "utils_nfschema_plugin": { diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf index 9724d2f34..cc0643e1d 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf @@ -52,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ea5b7aaa1..0fcbf7b3f 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -106,19 +106,12 @@ def checkCondaChannels() { def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - - required_channels_in_order.eachWithIndex { channel, index -> - if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) - } - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { log.warn """\ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ There is a problem with your Conda configuration! - You will need to set-up the conda-forge and bioconda channels correctly. Please refer to https://bioconda.github.io/ The observed channel order is diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index b78273ca4..5cb7bafef 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) { def workflowCitation() { def temp_doi_ref = "" def manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list manifest_doi.each { doi_ref -> From 658f77bf519afce85117310cf1ab73136b14f1e0 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 11 Oct 2024 12:05:07 +0200 Subject: [PATCH 5/5] fix small typo --- nf_core/pipeline-template/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf index f908ec934..6644d74a2 100644 --- a/nf_core/pipeline-template/main.nf +++ b/nf_core/pipeline-template/main.nf @@ -84,7 +84,7 @@ workflow { params.outdir, params.input ) - {-% endif %} + {%- endif %} // // WORKFLOW: Run main workflow