From 51f37561bf9555202803c23494959f8cec7e1ae3 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 5 Aug 2024 15:27:13 +0200 Subject: [PATCH 1/6] add option to exclude citations for custom pipeline template --- .../create-test-lint-wf-template.yml | 5 + nf_core/pipeline-template/nextflow.config | 3 +- .../pipeline-template/nextflow_schema.json | 4 +- .../pipeline-template/workflows/pipeline.nf | 4 + nf_core/pipelines/create/create.py | 2 + nf_core/pipelines/create/custompipeline.py | 13 + tests/__snapshots__/test_create_app.ambr | 511 +++++++++--------- tests/data/pipeline_create_template_skip.yml | 1 + 8 files changed, 284 insertions(+), 259 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index cfa0a50079..818c206167 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -42,6 +42,7 @@ jobs: - "template_skip_igenomes.yml" - "template_skip_ci.yml" - "template_skip_code_linters.yml" + - "template_skip_citations.yml" runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} @@ -107,6 +108,10 @@ jobs: run: | printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml + - name: Create template skip citations + run: | + printf "org: my-prefix\nskip: citations" > create-test-lint-wf/template_skip_citations.yml + # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} run: | diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 2e6a56b001..f622205a12 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -25,7 +25,8 @@ params { multiqc_title = null multiqc_logo = null max_multiqc_email_size = '25.MB' - multiqc_methods_description = null + {%- if citations %} + multiqc_methods_description = null{% endif %} // Boilerplate options outdir = null diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 18bad71b76..0bd4443675 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -234,12 +234,12 @@ "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", "fa_icon": "fas fa-image", "hidden": true - }, + },{% if citations %} "multiqc_methods_description": { "type": "string", "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" - }, + },{% endif %} "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index de0f21fe38..765b97c68e 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -63,21 +63,25 @@ workflow {{ short_name|upper }} { workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + {%- if citations %} ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) + {%- endif %} ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + {%- if citations %} ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( name: 'methods_description_mqc.yaml', sort: true ) ) + {%- endif %} MULTIQC ( ch_multiqc_files.collect(), diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 42e4a6ad7b..86ca1763fc 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -101,6 +101,7 @@ def __init__( ".prettierrc.yml", ".github/workflows/fix-linting.yml", ], + "citations": ["CITATIONS.md", "assets/methods_description_template.yml"], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) @@ -210,6 +211,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): "igenomes": {"file": True, "content": True}, "nf_core_configs": {"file": False, "content": True}, "code_linters": {"file": True, "content": True}, + "citations": {"file": True, "content": True}, } # Set the parameters for the jinja template diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 0925fb5bab..1dd6134848 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -51,6 +51,13 @@ - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). """ +markdown_citations = """ +If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. + +Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to describe a Materials & Methods section describing the tools used in the pieline, +and the logics to add this section to the output MultiQC report (if the report is generated). +""" + class CustomPipeline(Screen): """Select if the pipeline will use genomic data.""" @@ -96,6 +103,12 @@ def compose(self) -> ComposeResult: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.", "code_linters", ), + PipelineFeature( + markdown_citations, + "Include citations", + "Include a CITATIONS.md file to add pipeline tools citations.", + "citations", + ), classes="features-container", ) yield Center( diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 5e5b005de0..531ea098bf 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-2778615119-matrix { + .terminal-4194849765-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2778615119-title { + .terminal-4194849765-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2778615119-r1 { fill: #c5c8c6 } - .terminal-2778615119-r2 { fill: #e3e3e3 } - .terminal-2778615119-r3 { fill: #989898 } - .terminal-2778615119-r4 { fill: #e1e1e1 } - .terminal-2778615119-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2778615119-r6 { fill: #1e1e1e } - .terminal-2778615119-r7 { fill: #0178d4 } - .terminal-2778615119-r8 { fill: #454a50 } - .terminal-2778615119-r9 { fill: #e2e2e2 } - .terminal-2778615119-r10 { fill: #808080 } - .terminal-2778615119-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-2778615119-r12 { fill: #000000 } - .terminal-2778615119-r13 { fill: #e4e4e4 } - .terminal-2778615119-r14 { fill: #14191f } - .terminal-2778615119-r15 { fill: #507bb3 } - .terminal-2778615119-r16 { fill: #dde6ed;font-weight: bold } - .terminal-2778615119-r17 { fill: #001541 } - .terminal-2778615119-r18 { fill: #7ae998 } - .terminal-2778615119-r19 { fill: #0a180e;font-weight: bold } - .terminal-2778615119-r20 { fill: #008139 } - .terminal-2778615119-r21 { fill: #fea62b;font-weight: bold } - .terminal-2778615119-r22 { fill: #a7a9ab } - .terminal-2778615119-r23 { fill: #e2e3e3 } + .terminal-4194849765-r1 { fill: #c5c8c6 } + .terminal-4194849765-r2 { fill: #e3e3e3 } + .terminal-4194849765-r3 { fill: #989898 } + .terminal-4194849765-r4 { fill: #e1e1e1 } + .terminal-4194849765-r5 { fill: #4ebf71;font-weight: bold } + .terminal-4194849765-r6 { fill: #1e1e1e } + .terminal-4194849765-r7 { fill: #0178d4 } + .terminal-4194849765-r8 { fill: #454a50 } + .terminal-4194849765-r9 { fill: #e2e2e2 } + .terminal-4194849765-r10 { fill: #808080 } + .terminal-4194849765-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-4194849765-r12 { fill: #000000 } + .terminal-4194849765-r13 { fill: #e4e4e4 } + .terminal-4194849765-r14 { fill: #14191f } + .terminal-4194849765-r15 { fill: #507bb3 } + .terminal-4194849765-r16 { fill: #dde6ed;font-weight: bold } + .terminal-4194849765-r17 { fill: #001541 } + .terminal-4194849765-r18 { fill: #7ae998 } + .terminal-4194849765-r19 { fill: #0a180e;font-weight: bold } + .terminal-4194849765-r20 { fill: #008139 } + .terminal-4194849765-r21 { fill: #fea62b;font-weight: bold } + .terminal-4194849765-r22 { fill: #a7a9ab } + .terminal-4194849765-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + ▃▃ + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,254 @@ font-weight: 700; } - .terminal-763408100-matrix { + .terminal-423998432-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-763408100-title { + .terminal-423998432-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-763408100-r1 { fill: #c5c8c6 } - .terminal-763408100-r2 { fill: #e3e3e3 } - .terminal-763408100-r3 { fill: #989898 } - .terminal-763408100-r4 { fill: #e1e1e1 } - .terminal-763408100-r5 { fill: #4ebf71;font-weight: bold } - .terminal-763408100-r6 { fill: #1e1e1e } - .terminal-763408100-r7 { fill: #507bb3 } - .terminal-763408100-r8 { fill: #e2e2e2 } - .terminal-763408100-r9 { fill: #808080 } - .terminal-763408100-r10 { fill: #dde6ed;font-weight: bold } - .terminal-763408100-r11 { fill: #001541 } - .terminal-763408100-r12 { fill: #14191f } - .terminal-763408100-r13 { fill: #454a50 } - .terminal-763408100-r14 { fill: #7ae998 } - .terminal-763408100-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-763408100-r16 { fill: #0a180e;font-weight: bold } - .terminal-763408100-r17 { fill: #000000 } - .terminal-763408100-r18 { fill: #008139 } - .terminal-763408100-r19 { fill: #fea62b;font-weight: bold } - .terminal-763408100-r20 { fill: #a7a9ab } - .terminal-763408100-r21 { fill: #e2e3e3 } + .terminal-423998432-r1 { fill: #c5c8c6 } + .terminal-423998432-r2 { fill: #e3e3e3 } + .terminal-423998432-r3 { fill: #989898 } + .terminal-423998432-r4 { fill: #e1e1e1 } + .terminal-423998432-r5 { fill: #4ebf71;font-weight: bold } + .terminal-423998432-r6 { fill: #1e1e1e } + .terminal-423998432-r7 { fill: #507bb3 } + .terminal-423998432-r8 { fill: #e2e2e2 } + .terminal-423998432-r9 { fill: #808080 } + .terminal-423998432-r10 { fill: #dde6ed;font-weight: bold } + .terminal-423998432-r11 { fill: #001541 } + .terminal-423998432-r12 { fill: #454a50 } + .terminal-423998432-r13 { fill: #7ae998 } + .terminal-423998432-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-423998432-r15 { fill: #0a180e;font-weight: bold } + .terminal-423998432-r16 { fill: #000000 } + .terminal-423998432-r17 { fill: #008139 } + .terminal-423998432-r18 { fill: #fea62b;font-weight: bold } + .terminal-423998432-r19 { fill: #a7a9ab } + .terminal-423998432-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different ▁▁ - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml index d9ef405c51..06e01cc7f2 100644 --- a/tests/data/pipeline_create_template_skip.yml +++ b/tests/data/pipeline_create_template_skip.yml @@ -12,3 +12,4 @@ skip_features: - igenomes - nf_core_configs - code_linters + - citations From 74bd318ef0785108f122bc1f14f4d9d668f57b35 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 5 Aug 2024 13:29:41 +0000 Subject: [PATCH 2/6] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aea91cb51a..a723bd3283 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) +- add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101)) ### Linting From 9182530d2a4356fa2924798b5aa2025fed793dd0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 5 Aug 2024 16:13:37 +0200 Subject: [PATCH 3/6] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/custompipeline.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 1dd6134848..d5bcf04bc7 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -54,7 +54,7 @@ markdown_citations = """ If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. -Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to describe a Materials & Methods section describing the tools used in the pieline, +Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, and the logics to add this section to the output MultiQC report (if the report is generated). """ @@ -106,7 +106,7 @@ def compose(self) -> ComposeResult: PipelineFeature( markdown_citations, "Include citations", - "Include a CITATIONS.md file to add pipeline tools citations.", + "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled).", "citations", ), classes="features-container", From b0d07609507ef60ba79179e810b0cac1f308108a Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 5 Aug 2024 16:23:54 +0200 Subject: [PATCH 4/6] exclude content of CITATIONS.md instead of the whole file --- nf_core/pipeline-template/CITATIONS.md | 3 +++ nf_core/pipeline-template/README.md | 4 ++-- .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 2 ++ nf_core/pipeline-template/workflows/pipeline.nf | 2 +- nf_core/pipelines/create/create.py | 2 +- 5 files changed, 9 insertions(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md index 6edf8f620c..c0c0729277 100644 --- a/nf_core/pipeline-template/CITATIONS.md +++ b/nf_core/pipeline-template/CITATIONS.md @@ -8,6 +8,8 @@ > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. +{%- if citations %} + ## Pipeline tools - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) @@ -39,3 +41,4 @@ - [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 %} diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index feece399b5..4efa88d5f6 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -116,10 +116,10 @@ For further information or help, don't hesitate to get in touch on the [Slack `# - +{% if citations %} An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. - +{% endif %} {% if is_nfcore -%} You can cite the `nf-core` publication as follows: 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 a4bfb9f8be..0c2e1d8b0a 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 @@ -207,6 +207,7 @@ def genomeExistsError() { } {%- endif %} +{%- if citations %} // // Generate methods description for MultiQC // @@ -270,3 +271,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } +{% endif %} diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 765b97c68e..8ce3637e4e 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -9,7 +9,7 @@ include { MULTIQC } from '../modules/nf-core/multiqc/main' include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline' +{% if citations %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 86ca1763fc..3adeec60b7 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -101,7 +101,7 @@ def __init__( ".prettierrc.yml", ".github/workflows/fix-linting.yml", ], - "citations": ["CITATIONS.md", "assets/methods_description_template.yml"], + "citations": ["assets/methods_description_template.yml"], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) From 138ecb793ab57f34b7fb124a81df04512f0b36fd Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 5 Aug 2024 16:58:50 +0200 Subject: [PATCH 5/6] update snapshot --- tests/__snapshots__/test_create_app.ambr | 511 ++++++++++++----------- 1 file changed, 256 insertions(+), 255 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 531ea098bf..940a875839 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-4194849765-matrix { + .terminal-2433570258-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4194849765-title { + .terminal-2433570258-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4194849765-r1 { fill: #c5c8c6 } - .terminal-4194849765-r2 { fill: #e3e3e3 } - .terminal-4194849765-r3 { fill: #989898 } - .terminal-4194849765-r4 { fill: #e1e1e1 } - .terminal-4194849765-r5 { fill: #4ebf71;font-weight: bold } - .terminal-4194849765-r6 { fill: #1e1e1e } - .terminal-4194849765-r7 { fill: #0178d4 } - .terminal-4194849765-r8 { fill: #454a50 } - .terminal-4194849765-r9 { fill: #e2e2e2 } - .terminal-4194849765-r10 { fill: #808080 } - .terminal-4194849765-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-4194849765-r12 { fill: #000000 } - .terminal-4194849765-r13 { fill: #e4e4e4 } - .terminal-4194849765-r14 { fill: #14191f } - .terminal-4194849765-r15 { fill: #507bb3 } - .terminal-4194849765-r16 { fill: #dde6ed;font-weight: bold } - .terminal-4194849765-r17 { fill: #001541 } - .terminal-4194849765-r18 { fill: #7ae998 } - .terminal-4194849765-r19 { fill: #0a180e;font-weight: bold } - .terminal-4194849765-r20 { fill: #008139 } - .terminal-4194849765-r21 { fill: #fea62b;font-weight: bold } - .terminal-4194849765-r22 { fill: #a7a9ab } - .terminal-4194849765-r23 { fill: #e2e3e3 } + .terminal-2433570258-r1 { fill: #c5c8c6 } + .terminal-2433570258-r2 { fill: #e3e3e3 } + .terminal-2433570258-r3 { fill: #989898 } + .terminal-2433570258-r4 { fill: #e1e1e1 } + .terminal-2433570258-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2433570258-r6 { fill: #1e1e1e } + .terminal-2433570258-r7 { fill: #0178d4 } + .terminal-2433570258-r8 { fill: #454a50 } + .terminal-2433570258-r9 { fill: #e2e2e2 } + .terminal-2433570258-r10 { fill: #808080 } + .terminal-2433570258-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-2433570258-r12 { fill: #000000 } + .terminal-2433570258-r13 { fill: #e4e4e4 } + .terminal-2433570258-r14 { fill: #14191f } + .terminal-2433570258-r15 { fill: #507bb3 } + .terminal-2433570258-r16 { fill: #dde6ed;font-weight: bold } + .terminal-2433570258-r17 { fill: #001541 } + .terminal-2433570258-r18 { fill: #7ae998 } + .terminal-2433570258-r19 { fill: #0a180e;font-weight: bold } + .terminal-2433570258-r20 { fill: #008139 } + .terminal-2433570258-r21 { fill: #fea62b;font-weight: bold } + .terminal-2433570258-r22 { fill: #a7a9ab } + .terminal-2433570258-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - ▃▃ - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + ▃▃ + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,254 +2233,255 @@ font-weight: 700; } - .terminal-423998432-matrix { + .terminal-1630976143-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-423998432-title { + .terminal-1630976143-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-423998432-r1 { fill: #c5c8c6 } - .terminal-423998432-r2 { fill: #e3e3e3 } - .terminal-423998432-r3 { fill: #989898 } - .terminal-423998432-r4 { fill: #e1e1e1 } - .terminal-423998432-r5 { fill: #4ebf71;font-weight: bold } - .terminal-423998432-r6 { fill: #1e1e1e } - .terminal-423998432-r7 { fill: #507bb3 } - .terminal-423998432-r8 { fill: #e2e2e2 } - .terminal-423998432-r9 { fill: #808080 } - .terminal-423998432-r10 { fill: #dde6ed;font-weight: bold } - .terminal-423998432-r11 { fill: #001541 } - .terminal-423998432-r12 { fill: #454a50 } - .terminal-423998432-r13 { fill: #7ae998 } - .terminal-423998432-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-423998432-r15 { fill: #0a180e;font-weight: bold } - .terminal-423998432-r16 { fill: #000000 } - .terminal-423998432-r17 { fill: #008139 } - .terminal-423998432-r18 { fill: #fea62b;font-weight: bold } - .terminal-423998432-r19 { fill: #a7a9ab } - .terminal-423998432-r20 { fill: #e2e3e3 } + .terminal-1630976143-r1 { fill: #c5c8c6 } + .terminal-1630976143-r2 { fill: #e3e3e3 } + .terminal-1630976143-r3 { fill: #989898 } + .terminal-1630976143-r4 { fill: #e1e1e1 } + .terminal-1630976143-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1630976143-r6 { fill: #1e1e1e } + .terminal-1630976143-r7 { fill: #507bb3 } + .terminal-1630976143-r8 { fill: #e2e2e2 } + .terminal-1630976143-r9 { fill: #808080 } + .terminal-1630976143-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1630976143-r11 { fill: #001541 } + .terminal-1630976143-r12 { fill: #14191f } + .terminal-1630976143-r13 { fill: #454a50 } + .terminal-1630976143-r14 { fill: #7ae998 } + .terminal-1630976143-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-1630976143-r16 { fill: #0a180e;font-weight: bold } + .terminal-1630976143-r17 { fill: #000000 } + .terminal-1630976143-r18 { fill: #008139 } + .terminal-1630976143-r19 { fill: #fea62b;font-weight: bold } + .terminal-1630976143-r20 { fill: #a7a9ab } + .terminal-1630976143-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles ▆▆ + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 88a354fa73a657570496fd9cc6343d7e75aeaba7 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 09:29:48 +0200 Subject: [PATCH 6/6] update textual snapshots --- tests/__snapshots__/test_create_app.ambr | 511 ++++++++++++----------- 1 file changed, 256 insertions(+), 255 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index ed597e46b6..57e4258ef8 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-4194849765-matrix { + .terminal-3843971496-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4194849765-title { + .terminal-3843971496-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4194849765-r1 { fill: #c5c8c6 } - .terminal-4194849765-r2 { fill: #e3e3e3 } - .terminal-4194849765-r3 { fill: #989898 } - .terminal-4194849765-r4 { fill: #e1e1e1 } - .terminal-4194849765-r5 { fill: #4ebf71;font-weight: bold } - .terminal-4194849765-r6 { fill: #1e1e1e } - .terminal-4194849765-r7 { fill: #0178d4 } - .terminal-4194849765-r8 { fill: #454a50 } - .terminal-4194849765-r9 { fill: #e2e2e2 } - .terminal-4194849765-r10 { fill: #808080 } - .terminal-4194849765-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-4194849765-r12 { fill: #000000 } - .terminal-4194849765-r13 { fill: #e4e4e4 } - .terminal-4194849765-r14 { fill: #14191f } - .terminal-4194849765-r15 { fill: #507bb3 } - .terminal-4194849765-r16 { fill: #dde6ed;font-weight: bold } - .terminal-4194849765-r17 { fill: #001541 } - .terminal-4194849765-r18 { fill: #7ae998 } - .terminal-4194849765-r19 { fill: #0a180e;font-weight: bold } - .terminal-4194849765-r20 { fill: #008139 } - .terminal-4194849765-r21 { fill: #fea62b;font-weight: bold } - .terminal-4194849765-r22 { fill: #a7a9ab } - .terminal-4194849765-r23 { fill: #e2e3e3 } + .terminal-3843971496-r1 { fill: #c5c8c6 } + .terminal-3843971496-r2 { fill: #e3e3e3 } + .terminal-3843971496-r3 { fill: #989898 } + .terminal-3843971496-r4 { fill: #e1e1e1 } + .terminal-3843971496-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3843971496-r6 { fill: #1e1e1e } + .terminal-3843971496-r7 { fill: #0178d4 } + .terminal-3843971496-r8 { fill: #454a50 } + .terminal-3843971496-r9 { fill: #e2e2e2 } + .terminal-3843971496-r10 { fill: #808080 } + .terminal-3843971496-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-3843971496-r12 { fill: #000000 } + .terminal-3843971496-r13 { fill: #e4e4e4 } + .terminal-3843971496-r14 { fill: #14191f } + .terminal-3843971496-r15 { fill: #507bb3 } + .terminal-3843971496-r16 { fill: #dde6ed;font-weight: bold } + .terminal-3843971496-r17 { fill: #001541 } + .terminal-3843971496-r18 { fill: #7ae998 } + .terminal-3843971496-r19 { fill: #0a180e;font-weight: bold } + .terminal-3843971496-r20 { fill: #008139 } + .terminal-3843971496-r21 { fill: #fea62b;font-weight: bold } + .terminal-3843971496-r22 { fill: #a7a9ab } + .terminal-3843971496-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - ▃▃ - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files.▁▁ + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,254 +2233,255 @@ font-weight: 700; } - .terminal-423998432-matrix { + .terminal-1616690770-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-423998432-title { + .terminal-1616690770-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-423998432-r1 { fill: #c5c8c6 } - .terminal-423998432-r2 { fill: #e3e3e3 } - .terminal-423998432-r3 { fill: #989898 } - .terminal-423998432-r4 { fill: #e1e1e1 } - .terminal-423998432-r5 { fill: #4ebf71;font-weight: bold } - .terminal-423998432-r6 { fill: #1e1e1e } - .terminal-423998432-r7 { fill: #507bb3 } - .terminal-423998432-r8 { fill: #e2e2e2 } - .terminal-423998432-r9 { fill: #808080 } - .terminal-423998432-r10 { fill: #dde6ed;font-weight: bold } - .terminal-423998432-r11 { fill: #001541 } - .terminal-423998432-r12 { fill: #454a50 } - .terminal-423998432-r13 { fill: #7ae998 } - .terminal-423998432-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-423998432-r15 { fill: #0a180e;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help ▄▄ + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit