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Change the workflow to take MAGeCK MLE as a default and add tests #99

Merged
merged 9 commits into from
Jan 15, 2024
Merged

Change the workflow to take MAGeCK MLE as a default and add tests #99

merged 9 commits into from
Jan 15, 2024

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LaurenceKuhl
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I changed the parameters and the workflow so as to have MAGeCK MLE set as a default and the user has to explicitely use the RRA parameter.
BAGEL2 will be run as soon as contrasts are given.

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github-actions bot commented Dec 12, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 08269c2

+| ✅ 158 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/crisprseq/tree/dev" target="_blank">nf-core/crisprseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/crisprseq/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/crisprseq/releases/tag/dev" target="_blank">nf-core/crisprseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/crisprseq/dev/docs/output" target="_blank">documentation</a>.

❗ Test warnings:

  • 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 WorkflowCrisprseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-15 13:58:28

@mirpedrol mirpedrol self-requested a review January 9, 2024 14:06
mirpedrol
mirpedrol approved these changes Jan 10, 2024
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LGTM!
Don't forget to update the CHANGELOG.md and the documentation if needed :)

modules/local/matricescreation.nf Show resolved Hide resolved
modules/local/matricescreation.nf Outdated
#### Orient a reference sequence according to reads orientation.

data <- read.table("$contrasts", header = TRUE, sep = ";", stringsAsFactors = FALSE)
print(data)
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remove the print?

nextflow_schema.json Outdated Show resolved Hide resolved
@LaurenceKuhl @mirpedrol
Update nextflow_schema.json
32493db 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@LaurenceKuhl LaurenceKuhl merged commit 8781f5a into nf-core:dev Jan 15, 2024
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@mirpedrol mirpedrol mirpedrol approved these changes

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@LaurenceKuhl @mirpedrol