docs: Update documentation by beatrizsavinhas · Pull Request #48 · Clinical-Genomics/oncorefiner

beatrizsavinhas · 2026-03-12T13:40:45Z

Closes #28.

Changed

Added .github/CONTRIBUTING.md to the list of files for lint ignore since it no longer follows the nf-core template.

Fixed

Updated template description in .nf-core.yml.
Updated parameters.md by running pre-commit.
Fix formatting and typos and added missing information in CHANGELOG.md.
Updated .github/CONTRIBUTING.md:
- Added instructions on how to install dependencies for development.
- Added instructions on how to update the nf-core tools template.
- Added information on PR conventions and review process.
- Moved to the main root to make the file easier to find.
Updated README.md:
- Added placeholder logo.
- Filled in introduction section.
- Added contributors.
- Updated Usage section.
Updated CITATIONS.md.
Updated docs/usage.md. Input information will be updated when the input file structure is decided.
Updated docs/output.md with an example. To be expanded when output file structure is decided.

github-actions · 2026-03-12T13:40:56Z

PR checklist

Fill in description of the PR and link to any relevant issues.
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool, follow the pipeline conventions in the contribution docs.
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
README.md is updated (including new tool citations and authors/contributors).

github-actions · 2026-03-12T13:50:56Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 46e2fe0

+| ✅ 179 tests passed       |+
#| ❔  15 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  18 tests had warnings |!
-| ❌   1 tests failed       |-

Details

❌ Test failures:

files_exist - File not found: .github/CONTRIBUTING.md

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - actions_awstest
actions_awsfulltest - actions_awsfulltest
multiqc_config - multiqc_config

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-oncorefiner_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-oncorefiner_logo_light.png
files_exist - File found: docs/images/nf-core-oncorefiner_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-oncorefiner_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowOncorefiner.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with Clinical-Genomics/
nextflow_config - Config variable manifest.homePage began with https://github.com/Clinical-Genomics/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.0.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.genome= GRCh38
nextflow_config - Config default value correct: params.species= homo_sapiens
nextflow_config - Config default value correct: params.vep_cache_version= 112
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/Clinical-Genomics/test-datasets/refs/heads/oncorefiner/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 25.10.0, Config: 25.10.0
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: add_pr_checklist_comment.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: conventional_pr_title.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: update_changelog.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBLVEP_SNV found in conf/modules.config and Nextflow scripts.
modules_config - VCFANNO found in conf/modules.config and Nextflow scripts.
modules_config - RESEARCH_FILTERING found in conf/modules.config and Nextflow scripts.
modules_config - CLINICAL_FILTERING found in conf/modules.config and Nextflow scripts.
modules_config - SVDB_QUERY_DB found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBLVEP_SV found in conf/modules.config and Nextflow scripts.
modules_config - RESEARCH_FILTERING_SV found in conf/modules.config and Nextflow scripts.
modules_config - CLINICAL_FILTERING_SV found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-20 13:50:24

beatrizsavinhas · 2026-03-16T09:55:00Z

CHANGELOG.md

Moved PR link to the beginning of the line as I think it makes it easier to read when rendered. Thoughts?

beatrizsavinhas · 2026-03-16T15:50:15Z

README.md

 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use Clinical-Genomics/oncorefiner for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->


This is to be updated after the first release!

beatrizsavinhas · 2026-03-16T15:50:42Z

README.md

 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use Clinical-Genomics/oncorefiner for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->

-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->


Added to CITATIONS.md which is mentioned in the next line.
If we use additional data in the pipeline in the future, we should document that here.

beatrizsavinhas · 2026-03-16T15:51:40Z

README.md

 nextflow run Clinical-Genomics/oncorefiner \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>


Are there any other parameters required for a minimal run? See comment above.

beatrizsavinhas · 2026-03-16T16:08:03Z

README.md

+1. Process SNV VCF files
+   1. Annotate with [`Vcfanno`](https://github.com/brentp/vcfanno)
+   1. Filter according to call quality with [`bcftools`](https://github.com/samtools/bcftools)
+   1. Filter according to user provided list of research relevant variant with [`bcftools`](https://github.com/samtools/bcftools)
+   1. Annotate with [`VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html)
+   1. Filter according to user provided list of clinically relevant variants with [`bcftools`](https://github.com/samtools/bcftools)
+
+1. Process SV VCF files
+   1. SVDB QUERY ???
+   1. Filter according to call quality with ???
+   1. Filter according to user provided list of research relevant variant with [`bcftools`](https://github.com/samtools/bcftools)
+   1. Annotate with [`VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html)
+   1. Filter according to user provided list of clinically relevant variants with [`bcftools`](https://github.com/samtools/bcftools)
+
+1. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))


Can you check this information and fill in the missing parts marked with ????

beatrizsavinhas · 2026-03-17T12:14:03Z

README.md

 ## Introduction

-**Clinical-Genomics/oncorefiner** is a bioinformatics pipeline that ...
+**Clinical-Genomics/oncorefiner** is a customizable post-processing and extension layer for Oncoanalyser that adapts its outputs according to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser's robust core.


Added the same text that is in .nf-core.yml. We could provide a bit more information about the processes and the output when the issues mentioned above are cleared out.

beatrizsavinhas · 2026-03-17T12:54:03Z

docs/usage.md


-<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
-
 ## Samplesheet input


This information is general for the use of samplesheets. For oncorefiner, this will change when we decide on an input file strategy in https://github.com/Clinical-Genomics/CancerBioInfo/issues/101. Same for usage information in README.md. Added that as acceptance criterion for the issue.

Do you want to include the input VCF file parameters here already or should we leave this for when we figure things out in the issue above?

beatrizsavinhas · 2026-03-17T13:16:05Z

docs/output.md

All of this would be changed once the issue to Clean up pipeline output structure and file naming is cleared out. I think we should wait to write this until after that and keep what is here as a placeholder for now. I have included updating the documentation as an acceptance criterion for the issue above.

beatrizsavinhas · 2026-03-19T12:24:59Z

.github/ISSUE_TEMPLATE/config.yml

This is not present in the acceptance criteria or PR description since I wanted to hear your opinions first!

I thought it would be nice to add a link to the contributing guidelines when you are about to create an issue. What do you think? 🙂

beatrizsavinhas · 2026-03-19T12:40:03Z

README.md

+
+1. Process SNV VCF files
+   1. Annotate with [`Vcfanno`](https://github.com/brentp/vcfanno)
+   1. Filter according to call quality with [`bcftools`](https://github.com/samtools/bcftools)
+   1. Filter according to user provided list of research relevant variant with [`bcftools`](https://github.com/samtools/bcftools)
+   1. Annotate with [`Ensembl VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html)
+   1. Filter according to user provided list of clinically relevant variants with [`bcftools`](https://github.com/samtools/bcftools)
+
+1. Process SV VCF files
+   1. SVDB QUERY ???
+   1. Filter according to call quality with ???
+   1. Filter according to user provided list of research relevant variant with [`bcftools`](https://github.com/samtools/bcftools)
+   1. Annotate with [`Ensembl VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html)
+   1. Filter according to user provided list of clinically relevant variants with [`bcftools`](https://github.com/samtools/bcftools)
+
+1. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+
+### Summary of tools and version used in the pipeline
+
+| Step                  | Tool          | Version |
+| --------------------- | ------------- | ------- |
+| Clinical Filtering    | bcftools      | 1.22    |
+| Clinical Filtering SV | bcftools      | 1.22    |
+| EnsemblVEP SNV        | ensemblvep    | 115.2   |
+| EnsemblVEP SNV        | perl-math-cdf | 0.1     |
+| EnsemblVEP SNV        | tabix         | 1.21    |
+| EnsemblVEP SV         | ensemblvep    | 115.2   |
+| EnsemblVEP SV         | perl-math-cdf | 0.1     |
+| EnsemblVEP SV         | tabix         | 1.21    |
+| Research Filtering    | bcftools      | 1.22    |
+| Research Filtering SV | bcftools      | 1.22    |
+| SVDB Query DB         | svdb          | 2.8.4   |
+| Untar VEP Cache       | untar         | 1.34    |
+| Vcfanno               | vcfanno       | 0.3.7   |


Another option for the structure of this section is following what /nf-core/raredisease did!
But perhaps the versions are still relevant to include? You can always see them in the pipeline_info/*versions.yml but it can be nice to have it written here and not have to run the pipeline to get it.

beatrizsavinhas · 2026-03-19T12:48:25Z

CONTRIBUTING.md

I think we should adopt a lot of things from the raredisease contributing guidelines!

Thoughts?
This will give us more merge conflicts when the template is updated, but I think it's worth it since it's very important information.

update project description in .nf-core.yml

d30a2da

Merge branch 'dev' into 28-update-documentation

e008c65

beatrizsavinhas changed the title ~~Update documentation~~ docs: Update documentation Mar 12, 2026

beatrizsavinhas added 2 commits March 12, 2026 14:48

update parameters.md

da7f3d9

pre-commit

9149209

beatrizsavinhas added 13 commits March 12, 2026 14:52

update changelog

6ea0452

update changelog

bad6f1c

add template update instructions to contributing.md

f3fcb3c

add template update instructions to contributing.md

d2a98bd

Add installation instructions to contributing

617bf49

update installation instructions to contributing

acb8b3c

update contributors

5465fa5

re-arrange contributing.md

53a82b3

add information on PR and reviews in contributing

7a2c865

fix linting issues

f2edb4e

update changelog

fb07914

update CONTRIBUTING.md

4a374da

refactor changelog

7752749

beatrizsavinhas commented Mar 16, 2026

View reviewed changes

beatrizsavinhas added 4 commits March 16, 2026 13:33

Merge branch 'dev' into 28-update-documentation

5d93dbc

pre-commit to update parameters.md

ede68d2

Add Felix as contributor

7548675

update README.md usage

068d74d

beatrizsavinhas commented Mar 16, 2026

View reviewed changes

Fill in introduction in README.md

17c2903

beatrizsavinhas commented Mar 16, 2026

View reviewed changes

beatrizsavinhas added 3 commits March 16, 2026 17:10

Add logo code

3c85e5f

add note to CITATIONS.md

1b7885e

Added introduction to README.md

0f68e0f

beatrizsavinhas commented Mar 17, 2026

View reviewed changes

beatrizsavinhas added 3 commits March 17, 2026 13:26

update citations

5c75381

update usage

0ba2b3e

update usage

4a899ad

beatrizsavinhas commented Mar 17, 2026

View reviewed changes

Add output example.

356575d

beatrizsavinhas commented Mar 17, 2026

View reviewed changes

beatrizsavinhas added 4 commits March 17, 2026 14:22

update CHANGELOG.md

4c5204e

Merge branch 'dev' into 28-update-documentation

8bdbcbb

update CHANGELOG.md

efd6985

update ISSUE_TEMPLATE/config

de8eb66

beatrizsavinhas commented Mar 19, 2026

View reviewed changes

beatrizsavinhas added 2 commits March 19, 2026 13:45

Update CITATIONS.md

ed01899

Update CITATIONS.md

21ca245

beatrizsavinhas commented Mar 19, 2026

View reviewed changes

beatrizsavinhas added 2 commits March 19, 2026 17:00

Move contributing to root directory

913441f

update docker installation link

46e2fe0

		<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
		<!-- If you use Clinical-Genomics/oncorefiner for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->


		<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->

		## Samplesheet input

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beatrizsavinhas commented Mar 12, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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beatrizsavinhas commented Mar 12, 2026 •

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edited by beatrizsavinhas

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`nf-core pipelines lint` overall result: Failed ❌

beatrizsavinhas Mar 16, 2026 •

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