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Add new version syntax based on yml files to the pipeline #119

Merged
merged 25 commits into from
Nov 12, 2021
Merged

Add new version syntax based on yml files to the pipeline #119

merged 25 commits into from
Nov 12, 2021

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JoseEspinosa
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@JoseEspinosa JoseEspinosa commented Nov 9, 2021 •
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This PR implements the new way of outputing software versions. Software version(s) are now reported for every module imported during a given pipeline execution that is emitted in a versions.yml file.
Other minor changes:

  • params.skip_mirdeep switch is implemented on smrnaseq.nf instead of inside the modules involved in MIRDEEP2 subworkflow.
  • Remove hostnames to avoid error in json schema validation in new Nextflow releases (see here JSON schema validation error with 21.10.0-SNAPSHOT  tools#1304)
  • Update mirbase urls
  • Update singularity container of modules/local/bowtie_map_mirna.nf to match docker one.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • CHANGELOG.md is updated.

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github-actions bot commented Nov 9, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0019e48

+| ✅ 127 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.0.0'
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

  • files_exist - File is ignored: bin/scrape_software_versions.py
  • files_exist - File is ignored: modules/local/get_software_versions.nf
  • files_unchanged - File ignored due to lint config: .markdownlint.yml
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File does not exist: bin/scrape_software_versions.py
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-12 15:28:38

@JoseEspinosa JoseEspinosa marked this pull request as ready for review November 9, 2021 16:57
FriederikeHanssen
FriederikeHanssen reviewed Nov 10, 2021
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Nice looks good. Just a couple of things about open TODO statements and having initOptions left here and there.

modules/local/bowtie_map_mirna.nf Outdated Show resolved Hide resolved
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FriederikeHanssen
FriederikeHanssen approved these changes Nov 10, 2021
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lgtm

@JoseEspinosa
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I think I have addressed now all @FriederikeHanssen suggestions (very nicely spotted 😄 ) + I updated the files from mirbase in the nextflow.config as discussed on slack.

@lpantano lpantano merged commit 3e25b1c into nf-core:dev Nov 12, 2021
nschcolnicov pushed a commit that referenced this pull request Oct 10, 2024
@matthdsm
Merge pull request #119 from adamrtalbot/re_add_aws_tower_profile
e57768d 
Re-add aws_tower config for running on Tower
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@lpantano lpantano lpantano approved these changes

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@JoseEspinosa @lpantano @FriederikeHanssen