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Template update nf-core tools v2.8 #274

Merged
merged 7 commits into from
May 5, 2023
Merged

Template update nf-core tools v2.8 #274

merged 7 commits into from
May 5, 2023

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JoseEspinosa
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Template update nf-core tools v2.8

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/atacseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented May 4, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0aee372

+| ✅ 158 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 23]
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 36]
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 41]

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-05 09:13:24

@JoseEspinosa JoseEspinosa marked this pull request as ready for review May 4, 2023 20:24
mashehu
mashehu approved these changes May 5, 2023
View reviewed changes
README.md
nextflow run nf-core/atacseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```

See [usage docs](https://nf-co.re/atacseq/usage) for all of the available options when running the pipeline.
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you somehow lost the links to the usage and parameter docs from the template: For more details, please refer to the [usage documentation](https://nf-co.re/{{ short_name }}/usage) and the [parameter documentation](https://nf-co.re/{{ short_name }}/parameters).

modules/local/tss_extract.nf Outdated
@@ -3,7 +3,7 @@ process TSS_EXTRACT {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
'docker.io/ubuntu:20.04' }"
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Suggested change
'docker.io/ubuntu:20.04' }"
'docker.io/library/ubuntu:20.04' }"

see nf-core/modules#3358

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Thanks!

modules/local/multiqc_custom_peaks.nf Outdated
@@ -3,7 +3,7 @@ process MULTIQC_CUSTOM_PEAKS {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
'docker.io/ubuntu:20.04' }"
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Suggested change
'docker.io/ubuntu:20.04' }"
'docker.io/library/ubuntu:20.04' }"

see nf-core/modules#3358

@JoseEspinosa JoseEspinosa merged commit daa5a6b into nf-core:dev May 5, 2023
@JoseEspinosa JoseEspinosa deleted the template-update-v2.8 branch May 5, 2023 10:02
@maxulysse maxulysse mentioned this pull request May 22, 2023
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@mashehu mashehu mashehu approved these changes

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@JoseEspinosa @mashehu @nf-core-bot