From 02a96cab1c40560fc31698403899a472462e869d Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sun, 14 Aug 2022 08:09:34 +0200 Subject: [PATCH 01/20] Add new custom groovy library to generate a methods section for MultiQC --- .../assets/methods_description_template.yml | 25 +++++++++++++++++++ .../assets/multiqc_config.yml | 6 +++-- .../lib/WorkflowPipeline.groovy | 15 +++++++++++ nf_core/pipeline-template/nextflow.config | 8 +++--- .../pipeline-template/workflows/pipeline.nf | 9 +++++-- 5 files changed, 56 insertions(+), 7 deletions(-) create mode 100644 nf_core/pipeline-template/assets/methods_description_template.yml diff --git a/nf_core/pipeline-template/assets/methods_description_template.yml b/nf_core/pipeline-template/assets/methods_description_template.yml new file mode 100644 index 0000000000..e330e51615 --- /dev/null +++ b/nf_core/pipeline-template/assets/methods_description_template.yml @@ -0,0 +1,25 @@ +id: "${workflow.manifest.name.replace('/', '-')}-methods-description" +description: "Suggested methods description text of pipeline usage" +section_name: "${ workflow.manifest.name } Methods Description" +section_href: "https://github.com/${workflow.manifest.name}" +plot_type: "html" +## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## You inject any metadata in the Nextflow '${workflow}' object +data: | + Methods +

Data was processed using the ${workflow.manifest.name} (v${workflow.manifest.version}, doi: ${workflow.manifest.doi}) of the nf-core collection of workflows (Ewels et al. 2020).

+

The pipeline was executed with Nextflow (v${workflow.nextflow.version}; Di Tommaso et al. 2017) with the following command:

+
${workflow.commandLine}
+ References + +
+ Notes:
+ +
diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml index a9cc6cdb35..89c8b9146d 100644 --- a/nf_core/pipeline-template/assets/multiqc_config.yml +++ b/nf_core/pipeline-template/assets/multiqc_config.yml @@ -3,9 +3,11 @@ report_comment: > analysis pipeline.{% if branded %} For information about how to interpret these results, please see the documentation.{% endif %} report_section_order: - software_versions: + "{{ name.lower().replace('/', '-') }}-methods-description": order: -1000 - "{{ name.lower().replace('/', '-') }}-summary": + software_versions: order: -1001 + "{{ name.lower().replace('/', '-') }}-summary": + order: -1002 export_plots: true diff --git a/nf_core/pipeline-template/lib/WorkflowPipeline.groovy b/nf_core/pipeline-template/lib/WorkflowPipeline.groovy index ba9199e6fc..618af77050 100755 --- a/nf_core/pipeline-template/lib/WorkflowPipeline.groovy +++ b/nf_core/pipeline-template/lib/WorkflowPipeline.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the workflow/{{ short_name }}.nf in the {{ name }} pipeline // +import groovy.text.SimpleTemplateEngine + class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} { // @@ -45,6 +47,19 @@ class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} { return yaml_file_text } + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = run_workflow.toMap() + + def methods_text = mqc_methods_yaml.text + + def engine = new SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html + } + {%- if igenomes -%} // // Exit pipeline if incorrect --genome key provided diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index fb9db8f03d..336cc86355 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -21,9 +21,10 @@ params { {% endif -%} // MultiQC options - multiqc_config = null - multiqc_title = null - max_multiqc_email_size = '25.MB' + multiqc_config = null + multiqc_title = null + max_multiqc_email_size = '25.MB' + multiqc_methods_description = null // Boilerplate options outdir = null @@ -191,6 +192,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' version = '{{ version }}' + doi = '' } // Load modules.config for DSL2 module specific options diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 97e80b7c3a..57a56f9734 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -23,8 +23,9 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() +ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) +ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() +ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -89,10 +90,14 @@ workflow {{ short_name|upper }} { workflow_summary = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) + methods_description = WorkflowTestpipeline.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + ch_methods_description = Channel.value(methods_description) + ch_multiqc_files = Channel.empty() ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config)) ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) From 63e3df6f00237e6956fe0e9661dd97d50c4e894e Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sun, 14 Aug 2022 08:17:54 +0200 Subject: [PATCH 02/20] Changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1fd26d065b..728396bb03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ - Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705)) - Convert `console` snippets to `bash` snippets in the template where applicable ([#1729](https://github.com/nf-core/tools/pull/1729)) - Add `branch` field to module entries in `modules.json` to record what branch a module was installed from ([#1728](https://github.com/nf-core/tools/issues/1728)) +- Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications ### Linting From d9a30d54ea84749dd950a19356d4109a0efa0ac5 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sun, 14 Aug 2022 08:22:36 +0200 Subject: [PATCH 03/20] Add to schema --- nf_core/pipeline-template/nextflow_schema.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 5cd8ac489a..0f261ea55f 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -219,6 +219,12 @@ "fa_icon": "fas fa-cog", "hidden": true }, + "multiqc_methods_description": { + "type": "string", + "description": "Custom MultiQC yaml file containing HTML including a methods description.", + "fa_icon": "fas fa-cog", + "hidden": true + }, "tracedir": { "type": "string", "description": "Directory to keep pipeline Nextflow logs and reports.", From de682fb329bc7085885259e2660eff200f02cc8e Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 17 Aug 2022 11:18:02 +0200 Subject: [PATCH 04/20] Update nf_core/pipeline-template/assets/methods_description_template.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- .../pipeline-template/assets/methods_description_template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/assets/methods_description_template.yml b/nf_core/pipeline-template/assets/methods_description_template.yml index e330e51615..e0d6f5ba26 100644 --- a/nf_core/pipeline-template/assets/methods_description_template.yml +++ b/nf_core/pipeline-template/assets/methods_description_template.yml @@ -1,5 +1,5 @@ id: "${workflow.manifest.name.replace('/', '-')}-methods-description" -description: "Suggested methods description text of pipeline usage" +description: "Suggested methods description text of pipeline usage." section_name: "${ workflow.manifest.name } Methods Description" section_href: "https://github.com/${workflow.manifest.name}" plot_type: "html" From b2c5f1e8ba71905a6d83e3192aaa30e43317b4b3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 17 Aug 2022 15:04:16 +0200 Subject: [PATCH 05/20] Apply suggestions from code review Co-authored-by: Phil Ewels --- CHANGELOG.md | 2 +- .../assets/methods_description_template.yml | 30 +++++++++---------- .../assets/multiqc_config.yml | 4 +-- 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 728396bb03..3683071e56 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ - Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705)) - Convert `console` snippets to `bash` snippets in the template where applicable ([#1729](https://github.com/nf-core/tools/pull/1729)) - Add `branch` field to module entries in `modules.json` to record what branch a module was installed from ([#1728](https://github.com/nf-core/tools/issues/1728)) -- Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications +- Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications ([#1749](https://github.com/nf-core/tools/pull/1749)) ### Linting diff --git a/nf_core/pipeline-template/assets/methods_description_template.yml b/nf_core/pipeline-template/assets/methods_description_template.yml index e0d6f5ba26..ac15db072b 100644 --- a/nf_core/pipeline-template/assets/methods_description_template.yml +++ b/nf_core/pipeline-template/assets/methods_description_template.yml @@ -1,25 +1,25 @@ -id: "${workflow.manifest.name.replace('/', '-')}-methods-description" +id: "{{ name_noslash }}-methods-description" description: "Suggested methods description text of pipeline usage." -section_name: "${ workflow.manifest.name } Methods Description" -section_href: "https://github.com/${workflow.manifest.name}" +section_name: "{{ name }} Methods Description" +section_href: "https://github.com/{{ name }}" plot_type: "html" ## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: | - Methods -

Data was processed using the ${workflow.manifest.name} (v${workflow.manifest.version}, doi: ${workflow.manifest.doi}) of the nf-core collection of workflows (Ewels et al. 2020).

-

The pipeline was executed with Nextflow (v${workflow.nextflow.version}; Di Tommaso et al. 2017) with the following command:

+

Methods

+

Data was processed using {{ name }} v${workflow.manifest.version} (DOI: ${workflow.manifest.doi}) of the nf-core collection of workflows (Ewels et al., 2020).

+

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}
- References +

References

    -
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
  • -
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
  • +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
  • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
- Notes:
-
    -
  • If present, make sure to replace the pipeline DOI with correct reference information.
  • -
  • The command above does not include parameters contained in any configs pr profiles that may have been used. Ensure the config file is also uploaded with your publication!
  • -
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
  • -
+
Notes:
+
    +
  • If present, make sure to replace the pipeline DOI with correct reference information.
  • +
  • The command above does not include parameters contained in any configs pr profiles that may have been used. Ensure the config file is also uploaded with your publication!
  • +
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
  • +
diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml index 89c8b9146d..440b0b9a3a 100644 --- a/nf_core/pipeline-template/assets/multiqc_config.yml +++ b/nf_core/pipeline-template/assets/multiqc_config.yml @@ -3,11 +3,11 @@ report_comment: > analysis pipeline.{% if branded %} For information about how to interpret these results, please see the documentation.{% endif %} report_section_order: - "{{ name.lower().replace('/', '-') }}-methods-description": + "{{ name_noslash }}-methods-description": order: -1000 software_versions: order: -1001 - "{{ name.lower().replace('/', '-') }}-summary": + "{{ name_noslash }}-summary": order: -1002 export_plots: true From 6f13ab2795182c9be89c1919a63d203f958fa200 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 23 Aug 2022 15:29:06 +0200 Subject: [PATCH 06/20] Apply suggestions from code review Co-authored-by: Phil Ewels --- .../assets/methods_description_template.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/assets/methods_description_template.yml b/nf_core/pipeline-template/assets/methods_description_template.yml index ac15db072b..7ee7c142a2 100644 --- a/nf_core/pipeline-template/assets/methods_description_template.yml +++ b/nf_core/pipeline-template/assets/methods_description_template.yml @@ -12,14 +12,14 @@ data: |
${workflow.commandLine}

References

    -
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
  • -
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
  • +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
  • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
-
+
Notes:
  • If present, make sure to replace the pipeline DOI with correct reference information.
  • The command above does not include parameters contained in any configs pr profiles that may have been used. Ensure the config file is also uploaded with your publication!
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
-
+ From 4da8e9f0969f7cec0ca84383b4827b5546bb8d0b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 23 Aug 2022 15:41:02 +0200 Subject: [PATCH 07/20] Update nf_core/pipeline-template/assets/methods_description_template.yml --- .../pipeline-template/assets/methods_description_template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/assets/methods_description_template.yml b/nf_core/pipeline-template/assets/methods_description_template.yml index 7ee7c142a2..d3a78d3fa3 100644 --- a/nf_core/pipeline-template/assets/methods_description_template.yml +++ b/nf_core/pipeline-template/assets/methods_description_template.yml @@ -19,7 +19,7 @@ data: |
Notes:
  • If present, make sure to replace the pipeline DOI with correct reference information.
  • -
  • The command above does not include parameters contained in any configs pr profiles that may have been used. Ensure the config file is also uploaded with your publication!
  • +
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
From 98eacbc0775e38ce3ed1cc68a60c717d2997a32f Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 23 Aug 2022 16:41:59 +0200 Subject: [PATCH 08/20] Add conditional DOI --- .../pipeline-template/assets/methods_description_template.yml | 4 ++-- nf_core/pipeline-template/lib/WorkflowPipeline.groovy | 3 +++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/assets/methods_description_template.yml b/nf_core/pipeline-template/assets/methods_description_template.yml index 7ee7c142a2..daa6fdf47c 100644 --- a/nf_core/pipeline-template/assets/methods_description_template.yml +++ b/nf_core/pipeline-template/assets/methods_description_template.yml @@ -7,7 +7,7 @@ plot_type: "html" ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using {{ name }} v${workflow.manifest.version} (DOI: ${workflow.manifest.doi}) of the nf-core collection of workflows (Ewels et al., 2020).

+

Data was processed using {{ name }} v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}

References

@@ -19,7 +19,7 @@ data: |
Notes:
  • If present, make sure to replace the pipeline DOI with correct reference information.
  • -
  • The command above does not include parameters contained in any configs pr profiles that may have been used. Ensure the config file is also uploaded with your publication!
  • +
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
diff --git a/nf_core/pipeline-template/lib/WorkflowPipeline.groovy b/nf_core/pipeline-template/lib/WorkflowPipeline.groovy index 618af77050..2cd2dceff4 100755 --- a/nf_core/pipeline-template/lib/WorkflowPipeline.groovy +++ b/nf_core/pipeline-template/lib/WorkflowPipeline.groovy @@ -51,6 +51,9 @@ class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} { // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = run_workflow.toMap() + meta["manifest_map"] = run_workflow.manifest.toMap() + + meta["doi_text"] = meta.manifest_map.doi ? "(DOI: ${meta.manifest_map.doi})" : "" def methods_text = mqc_methods_yaml.text From d94c50b7ae886ac741702d45412a877ff8156922 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 25 Aug 2022 09:04:04 +0000 Subject: [PATCH 09/20] Generate new screengrabs with rich-codex --- docs/images/nf-core-modules-lint.svg | 252 ++++++++------------ docs/images/nf-core-modules-list-local.svg | 132 +++++----- docs/images/nf-core-modules-list-remote.svg | 132 +++++----- docs/images/nf-core-modules-remove.svg | 72 +++--- docs/images/nf-core-schema-build.svg | 84 +++---- docs/images/nf-core-schema-lint.svg | 78 +++--- 6 files changed, 347 insertions(+), 403 deletions(-) diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index d0503aac4d..8a4d1f6113 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Linting modules repo: '.'__init__.py:195 -INFO     Linting module: 'multiqc'__init__.py:199 - -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc - - -╭─[!] 1 Module Test Warning ──────────────────────────────────────────────────╮ -                                           ╷                ╷                  -Module name                              File path     Test message    -╶──────────────────────────────────────────┼────────────────┼────────────────╴ -multiqcmodules/multi…Conda update:  -bioconda::mult… -1.10 -> 1.13a -                                           ╵                ╵                  -╰──────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────╮ -LINT RESULTS SUMMARY -├──────────────────────┤ -[✔]  22 Tests Passed -[!]   1 Test Warning -[✗]   0 Tests Failed -╰──────────────────────╯ + + + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Linting modules repo: '.'__init__.py:195 +INFO     Linting module: 'multiqc'__init__.py:199 + +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc + + +╭─[!] 1 Module Test Warning ──────────────────────────────────────────────────╮ +                                           ╷                ╷                  +Module name                              File path     Test message    +╶──────────────────────────────────────────┼────────────────┼────────────────╴ +multiqcmodules/multi…Conda update:  +bioconda::mult… +1.10 -> 1.13a +                                           ╵                ╵                  +╰──────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────╮ +LINT RESULTS SUMMARY +├──────────────────────┤ +[✔]  22 Tests Passed +[!]   1 Test Warning +[✗]   0 Tests Failed +╰──────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index e53839201b..9297ec424b 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,109 +19,109 @@ font-weight: 700; } - .terminal-2388969700-matrix { + .terminal-1989200096-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2388969700-title { + .terminal-1989200096-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2388969700-r1 { fill: #c5c8c6 } -.terminal-2388969700-r2 { fill: #98a84b } -.terminal-2388969700-r3 { fill: #9a9b99 } -.terminal-2388969700-r4 { fill: #608ab1 } -.terminal-2388969700-r5 { fill: #d0b344 } -.terminal-2388969700-r6 { fill: #868887 } -.terminal-2388969700-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-2388969700-r8 { fill: #868887;font-style: italic; } + .terminal-1989200096-r1 { fill: #c5c8c6 } +.terminal-1989200096-r2 { fill: #98a84b } +.terminal-1989200096-r3 { fill: #9a9b99 } +.terminal-1989200096-r4 { fill: #608ab1 } +.terminal-1989200096-r5 { fill: #d0b344 } +.terminal-1989200096-r6 { fill: #868887 } +.terminal-1989200096-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-1989200096-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Modules installed in '.':                                   list.py:128 - -┏━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -Module Name  Repository    Version SHA  Message       Date       -┡━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumps… │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -│               │                │               │ in yaml files, │            │ -│               │                │               │ add yamllint   │            │ -│               │                │               │ config (#1279) │            │ -│ fastqc        │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -│               │                │               │ in yaml files, │            │ -│               │                │               │ add yamllint   │            │ -│               │                │               │ config (#1279) │            │ -│ multiqc       │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Modules installed in '.':                                   list.py:124 + +┏━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +Module Name  Repository    Version SHA  Message       Date       +┡━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumps… │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ +│               │                │               │ in yaml files, │            │ +│               │                │               │ add yamllint   │            │ +│               │                │               │ config (#1279) │            │ +│ fastqc        │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ +│               │                │               │ in yaml files, │            │ +│               │                │               │ add yamllint   │            │ +│               │                │               │ config (#1279) │            │ +│ multiqc       │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index 328d5f100f..e26dcf52b8 100644 --- a/docs/images/nf-core-modules-list-remote.svg +++ b/docs/images/nf-core-modules-list-remote.svg @@ -19,109 +19,109 @@ font-weight: 700; } - .terminal-1590927372-matrix { + .terminal-1871028241-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1590927372-title { + .terminal-1871028241-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1590927372-r1 { fill: #c5c8c6 } -.terminal-1590927372-r2 { fill: #98a84b } -.terminal-1590927372-r3 { fill: #9a9b99 } -.terminal-1590927372-r4 { fill: #608ab1 } -.terminal-1590927372-r5 { fill: #d0b344 } -.terminal-1590927372-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1590927372-r7 { fill: #868887 } -.terminal-1590927372-r8 { fill: #868887;font-style: italic; } + .terminal-1871028241-r1 { fill: #c5c8c6 } +.terminal-1871028241-r2 { fill: #98a84b } +.terminal-1871028241-r3 { fill: #9a9b99 } +.terminal-1871028241-r4 { fill: #608ab1 } +.terminal-1871028241-r5 { fill: #d0b344 } +.terminal-1871028241-r6 { fill: #c5c8c6;font-weight: bold } +.terminal-1871028241-r7 { fill: #868887 } +.terminal-1871028241-r8 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +133,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Modules available from nf-core/modules (master):            list.py:123 - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -Module Name                              -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                   │ -│ abricate/run                             │ -│ abricate/summary                         │ -│ adapterremoval                           │ -│ adapterremovalfixprefix                  │ -│ agrvate                                  │ -│ allelecounter                            │ -│ ampir                                    │ -│ amplify/predict                          │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Modules available from nf-core/modules (master):            list.py:119 + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +Module Name                              +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                   │ +│ abricate/run                             │ +│ abricate/summary                         │ +│ adapterremoval                           │ +│ adapterremovalfixprefix                  │ +│ agrvate                                  │ +│ allelecounter                            │ +│ ampir                                    │ +│ amplify/predict                          │ +[..truncated..] diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index 2c9d755ab1..a8b3b7a17a 100644 --- a/docs/images/nf-core-modules-remove.svg +++ b/docs/images/nf-core-modules-remove.svg @@ -19,65 +19,65 @@ font-weight: 700; } - .terminal-623533593-matrix { + .terminal-623664666-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-623533593-title { + .terminal-623664666-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-623533593-r1 { fill: #c5c8c6 } -.terminal-623533593-r2 { fill: #98a84b } -.terminal-623533593-r3 { fill: #9a9b99 } -.terminal-623533593-r4 { fill: #608ab1 } -.terminal-623533593-r5 { fill: #d0b344 } -.terminal-623533593-r6 { fill: #868887 } + .terminal-623664666-r1 { fill: #c5c8c6 } +.terminal-623664666-r2 { fill: #98a84b } +.terminal-623664666-r3 { fill: #9a9b99 } +.terminal-623664666-r4 { fill: #608ab1 } +.terminal-623664666-r5 { fill: #d0b344 } +.terminal-623664666-r6 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -89,22 +89,22 @@ - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Removing abacas                                            remove.py:51 + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + + +INFO     Removing abacas                                            remove.py:52 diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index 3d1e555dc6..67ba38633a 100644 --- a/docs/images/nf-core-schema-build.svg +++ b/docs/images/nf-core-schema-build.svg @@ -19,72 +19,72 @@ font-weight: 700; } - .terminal-4157447415-matrix { + .terminal-4168195321-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4157447415-title { + .terminal-4168195321-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4157447415-r1 { fill: #c5c8c6 } -.terminal-4157447415-r2 { fill: #98a84b } -.terminal-4157447415-r3 { fill: #9a9b99 } -.terminal-4157447415-r4 { fill: #608ab1 } -.terminal-4157447415-r5 { fill: #d0b344 } -.terminal-4157447415-r6 { fill: #98a84b;font-weight: bold } -.terminal-4157447415-r7 { fill: #868887 } -.terminal-4157447415-r8 { fill: #868887;font-weight: bold } -.terminal-4157447415-r9 { fill: #4e707b;font-weight: bold } -.terminal-4157447415-r10 { fill: #68a0b3;font-weight: bold } + .terminal-4168195321-r1 { fill: #c5c8c6 } +.terminal-4168195321-r2 { fill: #98a84b } +.terminal-4168195321-r3 { fill: #9a9b99 } +.terminal-4168195321-r4 { fill: #608ab1 } +.terminal-4168195321-r5 { fill: #d0b344 } +.terminal-4168195321-r6 { fill: #98a84b;font-weight: bold } +.terminal-4168195321-r7 { fill: #868887 } +.terminal-4168195321-r8 { fill: #868887;font-weight: bold } +.terminal-4168195321-r9 { fill: #4e707b;font-weight: bold } +.terminal-4168195321-r10 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -96,23 +96,23 @@ - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [] Default parameters match schema validationschema.py:237 -INFO    [] Pipeline schema looks valid(found 27 params)schema.py:95 -INFO     Writing schema with 28 params: './nextflow_schema.json'schema.py:173 + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO    [] Default parameters match schema validationschema.py:237 +INFO    [] Pipeline schema looks valid(found 28 params)schema.py:95 +INFO     Writing schema with 29 params: './nextflow_schema.json'schema.py:173 diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index 0e70f4518b..fcb19b9919 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -19,68 +19,68 @@ font-weight: 700; } - .terminal-691504655-matrix { + .terminal-693601808-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-691504655-title { + .terminal-693601808-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-691504655-r1 { fill: #c5c8c6 } -.terminal-691504655-r2 { fill: #98a84b } -.terminal-691504655-r3 { fill: #9a9b99 } -.terminal-691504655-r4 { fill: #608ab1 } -.terminal-691504655-r5 { fill: #d0b344 } -.terminal-691504655-r6 { fill: #98a84b;font-weight: bold } -.terminal-691504655-r7 { fill: #868887 } -.terminal-691504655-r8 { fill: #868887;font-weight: bold } -.terminal-691504655-r9 { fill: #4e707b;font-weight: bold } + .terminal-693601808-r1 { fill: #c5c8c6 } +.terminal-693601808-r2 { fill: #98a84b } +.terminal-693601808-r3 { fill: #9a9b99 } +.terminal-693601808-r4 { fill: #608ab1 } +.terminal-693601808-r5 { fill: #d0b344 } +.terminal-693601808-r6 { fill: #98a84b;font-weight: bold } +.terminal-693601808-r7 { fill: #868887 } +.terminal-693601808-r8 { fill: #868887;font-weight: bold } +.terminal-693601808-r9 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -92,22 +92,22 @@ - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [] Default parameters match schema validationschema.py:237 -INFO    [] Pipeline schema looks valid(found 28 params)schema.py:95 + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re + + +INFO    [] Default parameters match schema validationschema.py:237 +INFO    [] Pipeline schema looks valid(found 29 params)schema.py:95 From 25d73bf4754a7260bc9152d4e59d061c54e41a5f Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 8 Sep 2022 09:20:12 +0200 Subject: [PATCH 10/20] Update MultiQC and insert config correctly --- nf_core/pipeline-template/modules.json | 12 ++++---- .../modules/nf-core/modules/multiqc/main.nf | 29 +++++++++++++++---- .../modules/nf-core/modules/multiqc/meta.yml | 8 +++++ .../pipeline-template/workflows/pipeline.nf | 13 +++++---- 4 files changed, 46 insertions(+), 16 deletions(-) diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 9c8d724aef..d17e160448 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -6,16 +6,16 @@ "git_url": "https://github.com/nf-core/modules.git", "modules": { "custom/dumpsoftwareversions": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" + "branch": "master", + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "fastqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" + "branch": "master", + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "multiqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" + "branch": "master", + "git_sha": "31166227d3dbc949f5403fb4c0ce2d65fb8107a4" } } } diff --git a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf index 1264aac1eb..c8e6acee30 100644 --- a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf @@ -1,13 +1,15 @@ process MULTIQC { label 'process_medium' - conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' : + 'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }" input: - path multiqc_files + path multiqc_files, stageAs: "?/*" + path(multiqc_config) + path(multiqc_logo) output: path "*multiqc_report.html", emit: report @@ -20,8 +22,25 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def config = multiqc_config ? "--config $multiqc_config" : '' """ - multiqc -f $args . + multiqc \\ + --force \\ + $config \\ + $args \\ + . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ + + stub: + """ + touch multiqc_data + touch multiqc_plots + touch multiqc_report.html cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml index 6fa891efc2..46cb92abe8 100644 --- a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml @@ -17,6 +17,14 @@ input: type: file description: | List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" output: - report: type: file diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 24f78e7746..3bb18ed81d 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -23,8 +23,11 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() +ch_multiqc_config = params.multiqc_config ? file(params.multiqc_config, checkIfExists: true) : file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + +// TODO nf-core: replace empty list with path to pipeline logo +ch_multiqc_logo = [] + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -90,14 +93,14 @@ workflow {{ short_name|upper }} { ch_workflow_summary = Channel.value(workflow_summary) ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config)) - ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) MULTIQC ( - ch_multiqc_files.collect() + ch_multiqc_files.collect(), + ch_multiqc_config, + ch_multiqc_logo ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) From 720f8ed38cd49a0017014f9ecb8b382fbc34e076 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 8 Sep 2022 09:21:40 +0200 Subject: [PATCH 11/20] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7ee1a97beb..4fdfd456e3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ - Add `actions/upload-artifact` step to the awstest workflows, to expose the debug log file - Bioconda incompatible conda channel setups now result in more informative error messages ([#1812](https://github.com/nf-core/tools/pull/1812)) +- Update MultiQC module and correctly supply default MultiQC config file ### Linting From 3edfa5f05f42bd860b25ccf94ecb6387a88385b6 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 8 Sep 2022 09:23:09 +0200 Subject: [PATCH 12/20] Improve message re logo --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 3bb18ed81d..88b095ce66 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -25,7 +25,7 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ch_multiqc_config = params.multiqc_config ? file(params.multiqc_config, checkIfExists: true) : file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -// TODO nf-core: replace empty list with path to pipeline logo +// TODO nf-core: replace empty list with path to pipeline logo. Will require adding logo file name to MultiQC config to be displayed. ch_multiqc_logo = [] From 5fe2e8f5b41f57ed73e1af2179bff8539961974d Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 8 Sep 2022 09:24:55 +0200 Subject: [PATCH 13/20] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4fdfd456e3..07b1bb79cf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ - Add `actions/upload-artifact` step to the awstest workflows, to expose the debug log file - Bioconda incompatible conda channel setups now result in more informative error messages ([#1812](https://github.com/nf-core/tools/pull/1812)) -- Update MultiQC module and correctly supply default MultiQC config file +- Update MultiQC module, update supplying MultiQC default and custom config files to module ### Linting From f19641ed9c9c5b9e0de2c47c2d7cb21e28bd46ae Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 8 Sep 2022 09:58:31 +0200 Subject: [PATCH 14/20] Try adding custom logo path parameter --- nf_core/pipeline-template/nextflow.config | 1 + nf_core/pipeline-template/nextflow_schema.json | 5 +++++ nf_core/pipeline-template/workflows/pipeline.nf | 4 ++-- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index ba808b1d50..1f5ebf13f3 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -23,6 +23,7 @@ params { // MultiQC options multiqc_config = null multiqc_title = null + multiqc_logo = "${projectDir}/assets/*_logo_light.png" max_multiqc_email_size = '25.MB' // Boilerplate options diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 2be134ba08..d3b77e5d50 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -39,6 +39,11 @@ "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", "fa_icon": "fas fa-file-signature" + }, + "multiqc_logo": { + "type": "string", + "description": "Path to custom logo for display in MultiQC report", + "fa_icon": "fas fa-image" } } }, diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 88b095ce66..8d48f37abc 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -23,10 +23,10 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = params.multiqc_config ? file(params.multiqc_config, checkIfExists: true) : file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) +ch_multiqc_config = params.multiqc_config ? file( params.multiqc_config, checkIfExists: true ) : file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) // TODO nf-core: replace empty list with path to pipeline logo. Will require adding logo file name to MultiQC config to be displayed. -ch_multiqc_logo = [] +ch_multiqc_logo = file( params.multiqc_logo, checkIfExists: true ) /* From e3ec6dce10a241de5b3660d58852b75ee3bb89bb Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 8 Sep 2022 10:48:21 +0200 Subject: [PATCH 15/20] Remove MultiQC logo --- nf_core/pipeline-template/nextflow.config | 1 - nf_core/pipeline-template/nextflow_schema.json | 5 ----- nf_core/pipeline-template/workflows/pipeline.nf | 7 +------ 3 files changed, 1 insertion(+), 12 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 1f5ebf13f3..ba808b1d50 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -23,7 +23,6 @@ params { // MultiQC options multiqc_config = null multiqc_title = null - multiqc_logo = "${projectDir}/assets/*_logo_light.png" max_multiqc_email_size = '25.MB' // Boilerplate options diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index d3b77e5d50..2be134ba08 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -39,11 +39,6 @@ "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", "fa_icon": "fas fa-file-signature" - }, - "multiqc_logo": { - "type": "string", - "description": "Path to custom logo for display in MultiQC report", - "fa_icon": "fas fa-image" } } }, diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 8d48f37abc..a546ce50cb 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -25,10 +25,6 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ch_multiqc_config = params.multiqc_config ? file( params.multiqc_config, checkIfExists: true ) : file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -// TODO nf-core: replace empty list with path to pipeline logo. Will require adding logo file name to MultiQC config to be displayed. -ch_multiqc_logo = file( params.multiqc_logo, checkIfExists: true ) - - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT LOCAL MODULES/SUBWORKFLOWS @@ -99,8 +95,7 @@ workflow {{ short_name|upper }} { MULTIQC ( ch_multiqc_files.collect(), - ch_multiqc_config, - ch_multiqc_logo + ch_multiqc_config ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) From e5dafc840c1298ea35adec30783c4872d75972d4 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 8 Sep 2022 10:59:51 +0200 Subject: [PATCH 16/20] Remove MultiQC logo from pipeline --- nf_core/pipeline-template/modules.json | 2 +- .../modules/nf-core/modules/multiqc/main.nf | 1 - .../modules/nf-core/modules/multiqc/meta.yml | 7 +++---- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index d17e160448..091b45d81d 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -15,7 +15,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "31166227d3dbc949f5403fb4c0ce2d65fb8107a4" + "git_sha": "8d2fedadff6b741a6bcf5144443035e1498b9640" } } } diff --git a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf index c8e6acee30..c83ebf8587 100644 --- a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf @@ -9,7 +9,6 @@ process MULTIQC { input: path multiqc_files, stageAs: "?/*" path(multiqc_config) - path(multiqc_logo) output: path "*multiqc_report.html", emit: report diff --git a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml index 46cb92abe8..574f293efe 100644 --- a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + input: - multiqc_files: type: file @@ -21,10 +22,7 @@ input: type: file description: Optional config yml for MultiQC pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + output: - report: type: file @@ -46,3 +44,4 @@ authors: - "@abhi18av" - "@bunop" - "@drpatelh" + - "@jfy133" From 19c22f25b4f7216bf7c5d474938f543e464b6396 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 8 Sep 2022 12:42:19 +0200 Subject: [PATCH 17/20] Re-add logo --- nf_core/pipeline-template/modules.json | 2 +- .../modules/nf-core/modules/multiqc/main.nf | 1 + .../modules/nf-core/modules/multiqc/meta.yml | 4 ++++ nf_core/pipeline-template/nextflow.config | 1 + nf_core/pipeline-template/nextflow_schema.json | 6 ++++++ nf_core/pipeline-template/workflows/pipeline.nf | 4 +++- 6 files changed, 16 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 091b45d81d..2a804dc1d0 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -15,7 +15,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "8d2fedadff6b741a6bcf5144443035e1498b9640" + "git_sha": "16eee433b87b303bda650131ac5a0b1ad725e166" } } } diff --git a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf index c83ebf8587..c8e6acee30 100644 --- a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf @@ -9,6 +9,7 @@ process MULTIQC { input: path multiqc_files, stageAs: "?/*" path(multiqc_config) + path(multiqc_logo) output: path "*multiqc_report.html", emit: report diff --git a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml index 574f293efe..a1029f3366 100644 --- a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml @@ -22,6 +22,10 @@ input: type: file description: Optional config yml for MultiQC pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" output: - report: diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index ba808b1d50..c70f3a2e06 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -23,6 +23,7 @@ params { // MultiQC options multiqc_config = null multiqc_title = null + multiqc_logo = null max_multiqc_email_size = '25.MB' // Boilerplate options diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 2be134ba08..a4abd9b099 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -226,6 +226,12 @@ "fa_icon": "fas fa-cog", "hidden": true }, + "multiqc_logo": { + "type": "string", + "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 + }, "tracedir": { "type": "string", "description": "Directory to keep pipeline Nextflow logs and reports.", diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index a546ce50cb..605f1cb6c5 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -24,6 +24,7 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample */ ch_multiqc_config = params.multiqc_config ? file( params.multiqc_config, checkIfExists: true ) : file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) +ch_multiqc_logo = params.multiqc_logo ? file( params.multiqc_logo, checkIfExists: true ) : [] /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -95,7 +96,8 @@ workflow {{ short_name|upper }} { MULTIQC ( ch_multiqc_files.collect(), - ch_multiqc_config + ch_multiqc_config, + ch_multiqc_logo ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) From b9ff86ddfd3b47e364763498cba3c702bacd903f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 9 Sep 2022 09:57:48 +0200 Subject: [PATCH 18/20] Update nf_core/pipeline-template/assets/methods_description_template.yml Co-authored-by: Phil Ewels --- .../pipeline-template/assets/methods_description_template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/assets/methods_description_template.yml b/nf_core/pipeline-template/assets/methods_description_template.yml index daa6fdf47c..f479bd0b31 100644 --- a/nf_core/pipeline-template/assets/methods_description_template.yml +++ b/nf_core/pipeline-template/assets/methods_description_template.yml @@ -1,5 +1,5 @@ id: "{{ name_noslash }}-methods-description" -description: "Suggested methods description text of pipeline usage." +description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." section_name: "{{ name }} Methods Description" section_href: "https://github.com/{{ name }}" plot_type: "html" From 3b8c3035e99e065fab6a90089100933cabd9a42f Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 9 Sep 2022 08:01:52 +0000 Subject: [PATCH 19/20] Generate new screengrabs with rich-codex --- docs/images/nf-core-bump-version.svg | 101 ++++---- docs/images/nf-core-create.svg | 173 +++++++------- docs/images/nf-core-download.svg | 99 ++++---- docs/images/nf-core-launch-rnaseq.svg | 95 ++++---- docs/images/nf-core-licences.svg | 147 ++++++------ docs/images/nf-core-list-rna.svg | 129 ++++++----- docs/images/nf-core-list-stars.svg | 105 ++++----- docs/images/nf-core-list.svg | 109 ++++----- docs/images/nf-core-modules-bump-version.svg | 117 +++++----- docs/images/nf-core-modules-create.svg | 153 ++++++------ docs/images/nf-core-modules-info.svg | 231 ++++++++++--------- docs/images/nf-core-modules-install.svg | 93 ++++---- docs/images/nf-core-modules-lint.svg | 209 +++++++++-------- docs/images/nf-core-modules-list-local.svg | 133 +++++------ docs/images/nf-core-modules-list-remote.svg | 133 +++++------ docs/images/nf-core-modules-mulled.svg | 95 ++++---- docs/images/nf-core-modules-patch.svg | 161 ++++++------- docs/images/nf-core-modules-remove.svg | 83 +++---- docs/images/nf-core-modules-test.svg | 87 +++---- docs/images/nf-core-modules-update.svg | 99 ++++---- docs/images/nf-core-schema-build.svg | 95 ++++---- docs/images/nf-core-schema-lint.svg | 89 +++---- docs/images/nf-core-schema-validate.svg | 93 ++++---- docs/images/nf-core-sync.svg | 103 +++++---- 24 files changed, 1522 insertions(+), 1410 deletions(-) diff --git a/docs/images/nf-core-bump-version.svg b/docs/images/nf-core-bump-version.svg index f42cb69e5f..e302e5ad91 100644 --- a/docs/images/nf-core-bump-version.svg +++ b/docs/images/nf-core-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core bump-version 1.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Changing version number from '1.0dev' to '1.1'bump_version.py:35 -INFO     Updated version in 'nextflow.config'bump_version.py:164 - - version         = '1.0dev' - + version = '1.1' - - + + $ nf-core bump-version 1.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO     Changing version number from '1.0dev' to '1.1'bump_version.py:35 +INFO     Updated version in 'nextflow.config'bump_version.py:164 + - version         = '1.0dev' + + version = '1.1' + + diff --git a/docs/images/nf-core-create.svg b/docs/images/nf-core-create.svg index d90cdfdaa7..47ac15e503 100644 --- a/docs/images/nf-core-create.svg +++ b/docs/images/nf-core-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - - - - $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next  -big omics technique" -a "Big Steve" --plain - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing'create.py:226 -INFO     Initialising pipeline git repository                      create.py:518 -INFO     Done. Remember to add a remote and push to GitHub:        create.py:525 - cd  -/home/runner/work/nf-core-tools/nf-core-tools/tmp/nf-core --nextbigthing - git remote add origin  -git@github.com:USERNAME/REPO_NAME.git  - git push --all origin                                    -INFO     This will also push your newly created dev branch and the create.py:531 -         TEMPLATE branch for syncing.                               -INFO    !!!!!! IMPORTANT !!!!!!create.py:217 - -If you are interested in adding your pipeline to the  -nf-core community, -PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE  -WRITING ANY CODE! - -Please read:  -https://nf-co.re/developers/adding_pipelines#join-the-com -munity + + + + $ nf-core create -n nextbigthing -d "This pipeline analyses data from the next  +big omics technique" -a "Big Steve" --plain + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO     Creating new nf-core pipeline: 'nf-core/nextbigthing'create.py:226 +INFO     Initialising pipeline git repository                      create.py:518 +INFO     Done. Remember to add a remote and push to GitHub:        create.py:525 + cd  +/home/runner/work/nf-core-tools/nf-core-tools/tmp/nf-core +-nextbigthing + git remote add origin  +git@github.com:USERNAME/REPO_NAME.git  + git push --all origin                                    +INFO     This will also push your newly created dev branch and the create.py:531 +         TEMPLATE branch for syncing.                               +INFO    !!!!!! IMPORTANT !!!!!!create.py:217 + +If you are interested in adding your pipeline to the  +nf-core community, +PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE  +WRITING ANY CODE! + +Please read:  +https://nf-co.re/developers/adding_pipelines#join-the-com +munity diff --git a/docs/images/nf-core-download.svg b/docs/images/nf-core-download.svg index 5b479971ae..50335f3a6f 100644 --- a/docs/images/nf-core-download.svg +++ b/docs/images/nf-core-download.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Saving 'nf-core/rnaseq'download.py:158 -          Pipeline revision: '3.8' -          Pull containers: 'none' -          Output directory: 'nf-core-rnaseq' -INFO     Downloading workflow files from GitHub                  download.py:161 -INFO     Downloading centralised configs from GitHub             download.py:165 + + $ nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -c none + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO     Saving 'nf-core/rnaseq'download.py:158 +          Pipeline revision: '3.8' +          Pull containers: 'none' +          Output directory: 'nf-core-rnaseq' +INFO     Downloading workflow files from GitHub                  download.py:161 +INFO     Downloading centralised configs from GitHub             download.py:165 diff --git a/docs/images/nf-core-launch-rnaseq.svg b/docs/images/nf-core-launch-rnaseq.svg index f60ff94212..319de71823 100644 --- a/docs/images/nf-core-launch-rnaseq.svg +++ b/docs/images/nf-core-launch-rnaseq.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core launch rnaseq -r 3.8.1 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     NOTE: This tool ignores any pipeline parameter defaults   launch.py:131 -         overwritten by Nextflow config files or profiles           - -INFO     Downloading workflow: nf-core/rnaseq (3.8.1)list.py:67 + + $ nf-core launch rnaseq -r 3.8.1 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO     NOTE: This tool ignores any pipeline parameter defaults   launch.py:131 +         overwritten by Nextflow config files or profiles           + +INFO     Downloading workflow: nf-core/rnaseq (3.8.1)list.py:67 diff --git a/docs/images/nf-core-licences.svg b/docs/images/nf-core-licences.svg index ced30525e1..7639066972 100644 --- a/docs/images/nf-core-licences.svg +++ b/docs/images/nf-core-licences.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core licences deepvariant - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Fetching licence information for 8 tools                 licences.py:77 -INFO     Warning: This tool only prints licence information for   licences.py:98 -         the software tools packaged using conda.                  -INFO     The pipeline may use other software and dependencies not licences.py:99 -         described here.                                           -┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ -Package NameVersionLicence -┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ -│ lbzip2       │ 2.5     │ GPL v3  │ -│ deepvariant  │ 0.7.0   │ MIT     │ -│ htslib       │ 1.9     │ MIT     │ -│ picard       │ 2.18.7  │ MIT     │ -│ pip          │ 10.0.1  │ MIT     │ -│ samtools     │ 1.9     │ MIT     │ -│ python       │ 2.7.15  │ PSF     │ -│ bzip2        │ 1.0.6   │ bzip2   │ -└──────────────┴─────────┴─────────┘ + + $ nf-core licences deepvariant + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO     Fetching licence information for 8 tools                 licences.py:77 +INFO     Warning: This tool only prints licence information for   licences.py:98 +         the software tools packaged using conda.                  +INFO     The pipeline may use other software and dependencies not licences.py:99 +         described here.                                           +┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓ +Package NameVersionLicence +┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩ +│ lbzip2       │ 2.5     │ GPL v3  │ +│ deepvariant  │ 0.7.0   │ MIT     │ +│ htslib       │ 1.9     │ MIT     │ +│ picard       │ 2.18.7  │ MIT     │ +│ pip          │ 10.0.1  │ MIT     │ +│ samtools     │ 1.9     │ MIT     │ +│ python       │ 2.7.15  │ PSF     │ +│ bzip2        │ 1.0.6   │ bzip2   │ +└──────────────┴─────────┴─────────┘ diff --git a/docs/images/nf-core-list-rna.svg b/docs/images/nf-core-list-rna.svg index 235b4a479a..db5e49cd52 100644 --- a/docs/images/nf-core-list-rna.svg +++ b/docs/images/nf-core-list-rna.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core list rna rna-seq - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┓ -Pipeline        LatestHave latest -Name       Stars    Release    ReleasedLast Pulledrelease?    -┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━┩ -│ rnafusion   │    76 │       2.1.0 │ 1 months ago │           - │ -           │ -│ smrnaseq    │    42 │       2.0.0 │ 3 months ago │           - │ -           │ -│ rnaseq      │   499 │       3.8.1 │ 3 months ago │           - │ -           │ -│ dualrnaseq  │     7 │       1.0.0 │  2 years ago │           - │ -           │ -│ circrna     │    19 │         dev │            - │           - │ -           │ -│ lncpipe     │    23 │         dev │            - │           - │ -           │ -│ scflow      │    12 │         dev │            - │           - │ -           │ -│ spatialtra… │    10 │         dev │            - │           - │ -           │ -└─────────────┴───────┴─────────────┴──────────────┴─────────────┴─────────────┘ + + $ nf-core list rna rna-seq + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┓ +Pipeline        LatestHave latest +Name       Stars    Release    ReleasedLast Pulledrelease?    +┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━┩ +│ rnafusion   │    78 │       2.1.0 │ 2 months ago │           - │ -           │ +│ smrnaseq    │    43 │       2.0.0 │ 3 months ago │           - │ -           │ +│ rnaseq      │   503 │       3.8.1 │ 3 months ago │           - │ -           │ +│ dualrnaseq  │     7 │       1.0.0 │  2 years ago │           - │ -           │ +│ circrna     │    19 │         dev │            - │           - │ -           │ +│ lncpipe     │    22 │         dev │            - │           - │ -           │ +│ scflow      │    12 │         dev │            - │           - │ -           │ +│ spatialtra… │    10 │         dev │            - │           - │ -           │ +└─────────────┴───────┴─────────────┴──────────────┴─────────────┴─────────────┘ diff --git a/docs/images/nf-core-list-stars.svg b/docs/images/nf-core-list-stars.svg index cf4b23118e..74870d8f8b 100644 --- a/docs/images/nf-core-list-stars.svg +++ b/docs/images/nf-core-list-stars.svg @@ -19,88 +19,89 @@ font-weight: 700; } - .terminal-2036675850-matrix { + .terminal-3543478864-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2036675850-title { + .terminal-3543478864-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2036675850-r1 { fill: #c5c8c6 } -.terminal-2036675850-r2 { fill: #98a84b } -.terminal-2036675850-r3 { fill: #9a9b99 } -.terminal-2036675850-r4 { fill: #608ab1 } -.terminal-2036675850-r5 { fill: #d0b344 } -.terminal-2036675850-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2036675850-r7 { fill: #868887 } -.terminal-2036675850-r8 { fill: #868887;font-style: italic; } + .terminal-3543478864-r1 { fill: #c5c8c6 } +.terminal-3543478864-r2 { fill: #98a84b } +.terminal-3543478864-r3 { fill: #9a9b99 } +.terminal-3543478864-r4 { fill: #608ab1 } +.terminal-3543478864-r5 { fill: #d0b344 } +.terminal-3543478864-r6 { fill: #d08442;font-weight: bold } +.terminal-3543478864-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-3543478864-r8 { fill: #868887 } +.terminal-3543478864-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,29 +113,29 @@ - + - - $ nf-core list -s stars - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ -Pipeline        LatestHave latest  -Name       Stars    Release   ReleasedLast Pulledrelease?     -┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩ -│ rnaseq      │   499 │       3.8.1 │    3 months │           - │ -            │ -│             │       │             │         ago │             │              │ -│ sarek       │   186 │       3.0.1 │  6 days ago │           - │ -            │ -│ chipseq     │   121 │       1.2.2 │ 1 years ago │           - │ -            │ -[..truncated..] + + $ nf-core list -s stars + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┓ +Pipeline        LatestHave latest +Name       Stars    Release    ReleasedLast Pulledrelease?    +┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━┩ +│ rnaseq      │   503 │       3.8.1 │ 3 months ago │           - │ -           │ +│ sarek       │   188 │       3.0.1 │  3 weeks ago │           - │ -           │ +│ chipseq     │   125 │       1.2.2 │  1 years ago │           - │ -           │ +[..truncated..] diff --git a/docs/images/nf-core-list.svg b/docs/images/nf-core-list.svg index 5b0721e32e..19cadbc2a7 100644 --- a/docs/images/nf-core-list.svg +++ b/docs/images/nf-core-list.svg @@ -19,91 +19,92 @@ font-weight: 700; } - .terminal-2123714818-matrix { + .terminal-2167229852-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2123714818-title { + .terminal-2167229852-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2123714818-r1 { fill: #c5c8c6 } -.terminal-2123714818-r2 { fill: #98a84b } -.terminal-2123714818-r3 { fill: #9a9b99 } -.terminal-2123714818-r4 { fill: #608ab1 } -.terminal-2123714818-r5 { fill: #d0b344 } -.terminal-2123714818-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-2123714818-r7 { fill: #868887 } -.terminal-2123714818-r8 { fill: #868887;font-style: italic; } + .terminal-2167229852-r1 { fill: #c5c8c6 } +.terminal-2167229852-r2 { fill: #98a84b } +.terminal-2167229852-r3 { fill: #9a9b99 } +.terminal-2167229852-r4 { fill: #608ab1 } +.terminal-2167229852-r5 { fill: #d0b344 } +.terminal-2167229852-r6 { fill: #d08442;font-weight: bold } +.terminal-2167229852-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2167229852-r8 { fill: #868887 } +.terminal-2167229852-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -115,30 +116,30 @@ - + - - $ nf-core list - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓ -Pipeline        LatestHave latest  -Name       Stars    Release   ReleasedLast Pulledrelease?     -┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩ -│ sarek       │   186 │       3.0.1 │  6 days ago │           - │ -            │ -│ epitopepre… │    22 │       2.1.0 │ 3 weeks ago │           - │ -            │ -│ eager       │    70 │       2.4.5 │ 3 weeks ago │           - │ -            │ -│ viralrecon  │    74 │         2.5 │    1 months │           - │ -            │ -│             │       │             │         ago │             │              │ -[..truncated..] + + $ nf-core list + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +┏━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┓ +Pipeline        LatestHave latest +Name       Stars    Release    ReleasedLast Pulledrelease?    +┡━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━┩ +│ ampliseq    │    93 │       2.4.0 │    yesterday │           - │ -           │ +│ mag         │   100 │       2.2.1 │  2 weeks ago │           - │ -           │ +│ sarek       │   188 │       3.0.1 │  3 weeks ago │           - │ -           │ +│ epitopepre… │    22 │       2.1.0 │ 1 months ago │           - │ -           │ +[..truncated..] diff --git a/docs/images/nf-core-modules-bump-version.svg b/docs/images/nf-core-modules-bump-version.svg index 8ac0040588..0caa1f45af 100644 --- a/docs/images/nf-core-modules-bump-version.svg +++ b/docs/images/nf-core-modules-bump-version.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules bump-versions fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - - -╭──────────────────────────────────────────────────────────────────────────────╮ -[!] 1 Module version up to date. -╰──────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────────────────────────┬───────────────────────────────────╮ -Module name                             Update Message                    -├──────────────────────────────────────────┼───────────────────────────────────┤ - fastqc                                    Module version up to date: fastqc  -╰──────────────────────────────────────────┴───────────────────────────────────╯ + + $ nf-core modules bump-versions fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + + +╭──────────────────────────────────────────────────────────────────────────────╮ +[!] 1 Module version up to date. +╰──────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────────────────────────┬───────────────────────────────────╮ +Module name                             Update Message                    +├──────────────────────────────────────────┼───────────────────────────────────┤ + fastqc                                    Module version up to date: fastqc  +╰──────────────────────────────────────────┴───────────────────────────────────╯ diff --git a/docs/images/nf-core-modules-create.svg b/docs/images/nf-core-modules-create.svg index 69b382a0ad..abab34af2e 100644 --- a/docs/images/nf-core-modules-create.svg +++ b/docs/images/nf-core-modules-create.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules create fastqc --author @nf-core-bot  --label process_low  ---meta --force - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Repository type: modulescreate.py:93 -INFO    Press enter to use default values (shown in brackets)or create.py:97 -type your own responses. ctrl+click underlined text to  -open links. -INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165 -INFO     Using Docker container:                                   create.py:191 -'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1' -INFO     Using Singularity container:                              create.py:192 -'https://depot.galaxyproject.org/singularity/fastqc:0.11. -9--hdfd78af_1' -INFO     Created / edited following files:                         create.py:270 -           ./modules/fastqc/main.nf -           ./modules/fastqc/meta.yml -           ./tests/modules/fastqc/main.nf -           ./tests/modules/fastqc/test.yml -           ./tests/modules/fastqc/nextflow.config -           ./tests/config/pytest_modules.yml + + $ nf-core modules create fastqc --author @nf-core-bot  --label process_low  +--meta --force + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO     Repository type: modulescreate.py:93 +INFO    Press enter to use default values (shown in brackets)or create.py:97 +type your own responses. ctrl+click underlined text to  +open links. +INFO     Using Bioconda package: 'bioconda::fastqc=0.11.9'create.py:165 +INFO     Using Docker container:                                   create.py:191 +'quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1' +INFO     Using Singularity container:                              create.py:192 +'https://depot.galaxyproject.org/singularity/fastqc:0.11. +9--hdfd78af_1' +INFO     Created / edited following files:                         create.py:270 +           ./modules/fastqc/main.nf +           ./modules/fastqc/meta.yml +           ./tests/modules/fastqc/main.nf +           ./tests/modules/fastqc/test.yml +           ./tests/modules/fastqc/nextflow.config +           ./tests/config/pytest_modules.yml diff --git a/docs/images/nf-core-modules-info.svg b/docs/images/nf-core-modules-info.svg index 69b4109b23..5b293e9c52 100644 --- a/docs/images/nf-core-modules-info.svg +++ b/docs/images/nf-core-modules-info.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - - - - $ nf-core modules info abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -╭─ Module: abacas  ────────────────────────────────────────────────────────────╮ -│ 🌐 Repository: https://github.com/nf-core/modules.git                        │ -│ 🔧 Tools: abacas                                                             │ -│ 📖 Description: contiguate draft genome assembly                             │ -╰──────────────────────────────────────────────────────────────────────────────╯ -                  ╷                                               ╷              -📥 Inputs        Description                                         Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [│ -                  │id:'test', single_end:false ]                  │ -╶─────────────────┼───────────────────────────────────────────────┼────────────╴ - scaffold  (file)│Fasta file containing scaffold                 │*.{fasta,fa} -╶─────────────────┼───────────────────────────────────────────────┼────────────╴ - fasta  (file)   │FASTA reference file                           │*.{fasta,fa} -                  ╵                                               ╵              -                  ╷                                               ╷              -📤 Outputs       Description                                         Pattern -╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ - meta  (map)     │Groovy Map containing sample information e.g. [│ -                  │id:'test', single_end:false ]                  │ -╶─────────────────┼───────────────────────────────────────────────┼────────────╴ - results  (files)│List containing abacas output files [          │ *.{abacas}* -                  │'test.abacas.bin', 'test.abacas.fasta',        │ -                  │'test.abacas.gaps', 'test.abacas.gaps.tab',    │ -                  │'test.abacas.nucmer.delta',                    │ -                  │'test.abacas.nucmer.filtered.delta',           │ -                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',│ -                  │'test.abacas.unused.contigs.out',              │ -                  │'test.abacas.MULTIFASTA.fa' ]                  │ -╶─────────────────┼───────────────────────────────────────────────┼────────────╴ - versions  (file)│File containing software versions              │versions.yml -                  ╵                                               ╵              - - 💻  Installation command: nf-core modules install abacas - + + + + $ nf-core modules info abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +╭─ Module: abacas  ────────────────────────────────────────────────────────────╮ +│ 🌐 Repository: https://github.com/nf-core/modules.git                        │ +│ 🔧 Tools: abacas                                                             │ +│ 📖 Description: contiguate draft genome assembly                             │ +╰──────────────────────────────────────────────────────────────────────────────╯ +                  ╷                                               ╷              +📥 Inputs        Description                                         Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [│ +                  │id:'test', single_end:false ]                  │ +╶─────────────────┼───────────────────────────────────────────────┼────────────╴ + scaffold  (file)│Fasta file containing scaffold                 │*.{fasta,fa} +╶─────────────────┼───────────────────────────────────────────────┼────────────╴ + fasta  (file)   │FASTA reference file                           │*.{fasta,fa} +                  ╵                                               ╵              +                  ╷                                               ╷              +📤 Outputs       Description                                         Pattern +╺━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┿━━━━━━━━━━━━╸ + meta  (map)     │Groovy Map containing sample information e.g. [│ +                  │id:'test', single_end:false ]                  │ +╶─────────────────┼───────────────────────────────────────────────┼────────────╴ + results  (files)│List containing abacas output files [          │ *.{abacas}* +                  │'test.abacas.bin', 'test.abacas.fasta',        │ +                  │'test.abacas.gaps', 'test.abacas.gaps.tab',    │ +                  │'test.abacas.nucmer.delta',                    │ +                  │'test.abacas.nucmer.filtered.delta',           │ +                  │'test.abacas.nucmer.tiling', 'test.abacas.tab',│ +                  │'test.abacas.unused.contigs.out',              │ +                  │'test.abacas.MULTIFASTA.fa' ]                  │ +╶─────────────────┼───────────────────────────────────────────────┼────────────╴ + versions  (file)│File containing software versions              │versions.yml +                  ╵                                               ╵              + + 💻  Installation command: nf-core modules install abacas + diff --git a/docs/images/nf-core-modules-install.svg b/docs/images/nf-core-modules-install.svg index 9a57d28b44..ddf4808be3 100644 --- a/docs/images/nf-core-modules-install.svg +++ b/docs/images/nf-core-modules-install.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules install abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Installing 'abacas'install.py:116 -INFO     Include statement: include { ABACAS } from               install.py:125 -'../modules/nf-core/modules/abacas/main' + + $ nf-core modules install abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +INFO     Installing 'abacas'install.py:116 +INFO     Include statement: include { ABACAS } from               install.py:125 +'../modules/nf-core/modules/abacas/main' diff --git a/docs/images/nf-core-modules-lint.svg b/docs/images/nf-core-modules-lint.svg index 8a4d1f6113..08cc7e2612 100644 --- a/docs/images/nf-core-modules-lint.svg +++ b/docs/images/nf-core-modules-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + - + - - - - $ nf-core modules lint multiqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Linting modules repo: '.'__init__.py:195 -INFO     Linting module: 'multiqc'__init__.py:199 - -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc -Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc - - -╭─[!] 1 Module Test Warning ──────────────────────────────────────────────────╮ -                                           ╷                ╷                  -Module name                              File path     Test message    -╶──────────────────────────────────────────┼────────────────┼────────────────╴ -multiqcmodules/multi…Conda update:  -bioconda::mult… -1.10 -> 1.13a -                                           ╵                ╵                  -╰──────────────────────────────────────────────────────────────────────────────╯ -╭──────────────────────╮ -LINT RESULTS SUMMARY -├──────────────────────┤ -[✔]  22 Tests Passed -[!]   1 Test Warning -[✗]   0 Tests Failed -╰──────────────────────╯ + + + + $ nf-core modules lint multiqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +INFO     Linting modules repo: '.'__init__.py:195 +INFO     Linting module: 'multiqc'__init__.py:199 + +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━0 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc +Linting nf-core modules━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━1 of 1 » multiqc + + +╭─[!] 1 Module Test Warning ──────────────────────────────────────────────────╮ +                                           ╷                ╷                  +Module name                              File path     Test message    +╶──────────────────────────────────────────┼────────────────┼────────────────╴ +multiqcmodules/multi…Conda update:  +bioconda::mult… +1.10 -> 1.13 +                                           ╵                ╵                  +╰──────────────────────────────────────────────────────────────────────────────╯ +╭──────────────────────╮ +LINT RESULTS SUMMARY +├──────────────────────┤ +[✔]  22 Tests Passed +[!]   1 Test Warning +[✗]   0 Tests Failed +╰──────────────────────╯ diff --git a/docs/images/nf-core-modules-list-local.svg b/docs/images/nf-core-modules-list-local.svg index 9297ec424b..eb0fd4ff36 100644 --- a/docs/images/nf-core-modules-list-local.svg +++ b/docs/images/nf-core-modules-list-local.svg @@ -19,109 +19,110 @@ font-weight: 700; } - .terminal-1989200096-matrix { + .terminal-2362882186-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1989200096-title { + .terminal-2362882186-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1989200096-r1 { fill: #c5c8c6 } -.terminal-1989200096-r2 { fill: #98a84b } -.terminal-1989200096-r3 { fill: #9a9b99 } -.terminal-1989200096-r4 { fill: #608ab1 } -.terminal-1989200096-r5 { fill: #d0b344 } -.terminal-1989200096-r6 { fill: #868887 } -.terminal-1989200096-r7 { fill: #c5c8c6;font-weight: bold } -.terminal-1989200096-r8 { fill: #868887;font-style: italic; } + .terminal-2362882186-r1 { fill: #c5c8c6 } +.terminal-2362882186-r2 { fill: #98a84b } +.terminal-2362882186-r3 { fill: #9a9b99 } +.terminal-2362882186-r4 { fill: #608ab1 } +.terminal-2362882186-r5 { fill: #d0b344 } +.terminal-2362882186-r6 { fill: #d08442;font-weight: bold } +.terminal-2362882186-r7 { fill: #868887 } +.terminal-2362882186-r8 { fill: #c5c8c6;font-weight: bold } +.terminal-2362882186-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +134,36 @@ - + - - $ nf-core modules list local - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Modules installed in '.':                                   list.py:124 - -┏━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ -Module Name  Repository    Version SHA  Message       Date       -┡━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ -│ custom/dumps… │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -│               │                │               │ in yaml files, │            │ -│               │                │               │ add yamllint   │            │ -│               │                │               │ config (#1279) │            │ -│ fastqc        │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -│               │                │               │ in yaml files, │            │ -│               │                │               │ add yamllint   │            │ -│               │                │               │ config (#1279) │            │ -│ multiqc       │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ -[..truncated..] + + $ nf-core modules list local + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +INFO     Modules installed in '.':                                   list.py:124 + +┏━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓ +Module Name  Repository    Version SHA  Message       Date       +┡━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩ +│ custom/dumps… │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ +│               │                │               │ in yaml files, │            │ +│               │                │               │ add yamllint   │            │ +│               │                │               │ config (#1279) │            │ +│ fastqc        │ nf-core/modul… │ e745e167c102… │ Fix formatting │ 2022-02-15 │ +│               │                │               │ in yaml files, │            │ +│               │                │               │ add yamllint   │            │ +│               │                │               │ config (#1279) │            │ +[..truncated..] diff --git a/docs/images/nf-core-modules-list-remote.svg b/docs/images/nf-core-modules-list-remote.svg index e26dcf52b8..a2e2177d84 100644 --- a/docs/images/nf-core-modules-list-remote.svg +++ b/docs/images/nf-core-modules-list-remote.svg @@ -19,109 +19,110 @@ font-weight: 700; } - .terminal-1871028241-matrix { + .terminal-2129569440-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1871028241-title { + .terminal-2129569440-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1871028241-r1 { fill: #c5c8c6 } -.terminal-1871028241-r2 { fill: #98a84b } -.terminal-1871028241-r3 { fill: #9a9b99 } -.terminal-1871028241-r4 { fill: #608ab1 } -.terminal-1871028241-r5 { fill: #d0b344 } -.terminal-1871028241-r6 { fill: #c5c8c6;font-weight: bold } -.terminal-1871028241-r7 { fill: #868887 } -.terminal-1871028241-r8 { fill: #868887;font-style: italic; } + .terminal-2129569440-r1 { fill: #c5c8c6 } +.terminal-2129569440-r2 { fill: #98a84b } +.terminal-2129569440-r3 { fill: #9a9b99 } +.terminal-2129569440-r4 { fill: #608ab1 } +.terminal-2129569440-r5 { fill: #d0b344 } +.terminal-2129569440-r6 { fill: #d08442;font-weight: bold } +.terminal-2129569440-r7 { fill: #c5c8c6;font-weight: bold } +.terminal-2129569440-r8 { fill: #868887 } +.terminal-2129569440-r9 { fill: #868887;font-style: italic; } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -133,36 +134,36 @@ - + - - $ nf-core modules list remote - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Modules available from nf-core/modules (master):            list.py:119 - -┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ -Module Name                              -┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ -│ abacas                                   │ -│ abricate/run                             │ -│ abricate/summary                         │ -│ adapterremoval                           │ -│ adapterremovalfixprefix                  │ -│ agrvate                                  │ -│ allelecounter                            │ -│ ampir                                    │ -│ amplify/predict                          │ -[..truncated..] + + $ nf-core modules list remote + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +INFO     Modules available from nf-core/modules (master):            list.py:119 + +┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ +Module Name                              +┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ +│ abacas                                   │ +│ abricate/run                             │ +│ abricate/summary                         │ +│ adapterremoval                           │ +│ adapterremovalfixprefix                  │ +│ agrvate                                  │ +│ allelecounter                            │ +│ ampir                                    │ +[..truncated..] diff --git a/docs/images/nf-core-modules-mulled.svg b/docs/images/nf-core-modules-mulled.svg index 0fcd819ed8..b1421cf115 100644 --- a/docs/images/nf-core-modules-mulled.svg +++ b/docs/images/nf-core-modules-mulled.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Found docker image on quay.io! ✨                          mulled.py:68 -INFO     Mulled container hash:                                  __main__.py:810 -mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f -5ac4481e91f-0 + + $ nf-core modules mulled pysam==0.16.0.1 biopython==1.78 + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO     Found docker image on quay.io! ✨                          mulled.py:68 +INFO     Mulled container hash:                                  __main__.py:810 +mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f +5ac4481e91f-0 diff --git a/docs/images/nf-core-modules-patch.svg b/docs/images/nf-core-modules-patch.svg index ef6bf2f2ff..c56a5a1789 100644 --- a/docs/images/nf-core-modules-patch.svg +++ b/docs/images/nf-core-modules-patch.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules patch fastqc - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Changes in module 'nf-core/modules/fastqc'modules_differ.py:252 -INFO    'modules/nf-core/modules/fastqc/meta.yml' is      modules_differ.py:257 -         unchanged                                          -INFO     Changes in 'fastqc/main.nf':                      modules_differ.py:266 - ---- modules/nf-core/modules/fastqc/main.nf -+++ modules/nf-core/modules/fastqc/main.nf -@@ -1,6 +1,6 @@ -process FASTQC {                                                               -    tag "$meta.id"                                                             --    label 'process_medium' -+    label 'process_low' - -    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)             -    container "${ workflow.containerEngine == 'singularity' && !task.ext.sing  - - -INFO     Patch file of 'nf-core/modules/fastqc' written to          patch.py:115 -'modules/nf-core/modules/fastqc/fastqc.diff' + + $ nf-core modules patch fastqc + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +INFO     Changes in module 'nf-core/modules/fastqc'modules_differ.py:252 +INFO    'modules/nf-core/modules/fastqc/meta.yml' is      modules_differ.py:257 +         unchanged                                          +INFO     Changes in 'fastqc/main.nf':                      modules_differ.py:266 + +--- modules/nf-core/modules/fastqc/main.nf ++++ modules/nf-core/modules/fastqc/main.nf +@@ -1,6 +1,6 @@ +process FASTQC {                                                               +    tag "$meta.id"                                                             +-    label 'process_medium' ++    label 'process_low' + +    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)             +    container "${ workflow.containerEngine == 'singularity' && !task.ext.sing  + + +INFO     Patch file of 'nf-core/modules/fastqc' written to          patch.py:115 +'modules/nf-core/modules/fastqc/fastqc.diff' diff --git a/docs/images/nf-core-modules-remove.svg b/docs/images/nf-core-modules-remove.svg index a8b3b7a17a..ca71c79a65 100644 --- a/docs/images/nf-core-modules-remove.svg +++ b/docs/images/nf-core-modules-remove.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules remove abacas - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO     Removing abacas                                            remove.py:52 + + $ nf-core modules remove abacas + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +INFO     Removing abacas                                            remove.py:52 diff --git a/docs/images/nf-core-modules-test.svg b/docs/images/nf-core-modules-test.svg index b08d0f3039..9d662ddd85 100644 --- a/docs/images/nf-core-modules-test.svg +++ b/docs/images/nf-core-modules-test.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules test samtools/view --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -──────────────────────────────── samtools/view ───────────────────────────────── -INFO     Running pytest for module 'samtools/view'module_test.py:184 + + $ nf-core modules test samtools/view --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +──────────────────────────────── samtools/view ───────────────────────────────── +INFO     Running pytest for module 'samtools/view'module_test.py:184 diff --git a/docs/images/nf-core-modules-update.svg b/docs/images/nf-core-modules-update.svg index 559506e75e..40f7eb2403 100644 --- a/docs/images/nf-core-modules-update.svg +++ b/docs/images/nf-core-modules-update.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core modules update --all --no-preview - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - - -INFO    'nf-core/modules/abacas' is already up to date            update.py:160 -INFO     Updating 'nf-core/modules/custom/dumpsoftwareversions'update.py:516 -INFO     Updating 'nf-core/modules/fastqc'update.py:516 -INFO     Updating 'nf-core/modules/multiqc'update.py:516 -INFO     Updates complete ✨                                       update.py:242 + + $ nf-core modules update --all --no-preview + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + + +INFO    'nf-core/modules/abacas' is already up to date            update.py:160 +INFO     Updating 'nf-core/modules/custom/dumpsoftwareversions'update.py:516 +INFO     Updating 'nf-core/modules/fastqc'update.py:516 +INFO     Updating 'nf-core/modules/multiqc'update.py:516 +INFO     Updates complete ✨                                       update.py:242 diff --git a/docs/images/nf-core-schema-build.svg b/docs/images/nf-core-schema-build.svg index 67ba38633a..4c2be1800d 100644 --- a/docs/images/nf-core-schema-build.svg +++ b/docs/images/nf-core-schema-build.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core schema build --no-prompts - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [] Default parameters match schema validationschema.py:237 -INFO    [] Pipeline schema looks valid(found 28 params)schema.py:95 -INFO     Writing schema with 29 params: './nextflow_schema.json'schema.py:173 + + $ nf-core schema build --no-prompts + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO    [] Default parameters match schema validationschema.py:237 +INFO    [] Pipeline schema looks valid(found 28 params)schema.py:95 +INFO     Writing schema with 29 params: './nextflow_schema.json'schema.py:173 diff --git a/docs/images/nf-core-schema-lint.svg b/docs/images/nf-core-schema-lint.svg index fcb19b9919..5177b75fe0 100644 --- a/docs/images/nf-core-schema-lint.svg +++ b/docs/images/nf-core-schema-lint.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core schema lint nextflow_schema.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [] Default parameters match schema validationschema.py:237 -INFO    [] Pipeline schema looks valid(found 29 params)schema.py:95 + + $ nf-core schema lint nextflow_schema.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO    [] Default parameters match schema validationschema.py:237 +INFO    [] Pipeline schema looks valid(found 29 params)schema.py:95 diff --git a/docs/images/nf-core-schema-validate.svg b/docs/images/nf-core-schema-validate.svg index 8ba9a2d519..9836f61564 100644 --- a/docs/images/nf-core-schema-validate.svg +++ b/docs/images/nf-core-schema-validate.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO    [] Default parameters match schema validationschema.py:237 -INFO    [] Pipeline schema looks valid(found 93 params)schema.py:95 -INFO    [] Input parameters look validschema.py:213 + + $ nf-core schema validate nf-core-rnaseq/workflow nf-params.json + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO    [] Default parameters match schema validationschema.py:237 +INFO    [] Pipeline schema looks valid(found 93 params)schema.py:95 +INFO    [] Input parameters look validschema.py:213 diff --git a/docs/images/nf-core-sync.svg b/docs/images/nf-core-sync.svg index 81f992bf71..3183d11846 100644 --- a/docs/images/nf-core-sync.svg +++ b/docs/images/nf-core-sync.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ nf-core sync - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\ -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -    nf-core/tools version 2.5.dev0 - https://nf-co.re - - -INFO     Pipeline directory:                                          sync.py:95 -/home/runner/work/nf-core-tools/nf-core-tools/tmp/nf-core-ne -xtbigthing -INFO     Original pipeline repository branch is 'master'sync.py:149 -INFO     Deleting all files in 'TEMPLATE' branch                     sync.py:205 -INFO     Making a new template pipeline using pipeline variables     sync.py:223 + + $ nf-core sync + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\ +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +    nf-core/tools version 2.5.dev0 - https://nf-co.re +    There is a new version of nf-core/tools available! (2.5.1) + + +INFO     Pipeline directory:                                          sync.py:95 +/home/runner/work/nf-core-tools/nf-core-tools/tmp/nf-core-ne +xtbigthing +INFO     Original pipeline repository branch is 'master'sync.py:149 +INFO     Deleting all files in 'TEMPLATE' branch                     sync.py:205 +INFO     Making a new template pipeline using pipeline variables     sync.py:223 From c74af0187da3ee5d3f568d682107d65e596c3cab Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 9 Sep 2022 10:36:07 +0200 Subject: [PATCH 20/20] Make DOI notice a condition --- .../pipeline-template/assets/methods_description_template.yml | 2 +- nf_core/pipeline-template/lib/WorkflowPipeline.groovy | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/assets/methods_description_template.yml b/nf_core/pipeline-template/assets/methods_description_template.yml index f479bd0b31..b2dc0a99c1 100644 --- a/nf_core/pipeline-template/assets/methods_description_template.yml +++ b/nf_core/pipeline-template/assets/methods_description_template.yml @@ -18,7 +18,7 @@ data: |
Notes:
    -
  • If present, make sure to replace the pipeline DOI with correct reference information.
  • + ${nodoi_text}
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
diff --git a/nf_core/pipeline-template/lib/WorkflowPipeline.groovy b/nf_core/pipeline-template/lib/WorkflowPipeline.groovy index 2cd2dceff4..252f127d80 100755 --- a/nf_core/pipeline-template/lib/WorkflowPipeline.groovy +++ b/nf_core/pipeline-template/lib/WorkflowPipeline.groovy @@ -53,7 +53,8 @@ class Workflow{{ short_name[0]|upper }}{{ short_name[1:] }} { meta.workflow = run_workflow.toMap() meta["manifest_map"] = run_workflow.manifest.toMap() - meta["doi_text"] = meta.manifest_map.doi ? "(DOI: ${meta.manifest_map.doi})" : "" + 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.
  • " def methods_text = mqc_methods_yaml.text