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Important! Template update for nf-core/tools v2.9 #52

Merged
merged 10 commits into from
Jul 14, 2023
Merged

Important! Template update for nf-core/tools v2.9 #52

merged 10 commits into from
Jul 14, 2023

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nf-core-bot
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Version 2.9 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.9 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/developers/sync.

For more information about this release of nf-core/tools, please see the v2.9 release page.

@mirpedrol mirpedrol modified the milestones: 2.0.1, 2.1.0 Jul 3, 2023
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github-actions bot commented Jul 7, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit ef705d7

+| ✅ 156 tests passed       |+
#| ❔  16 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-14 07:53:25

mirpedrol
mirpedrol reviewed Jul 13, 2023
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nextflow_schema.json Outdated
Comment on lines 152 to 176
"mle_design_matrix": {
"type": "string",
"format": "file-path",
"exists": true,
"description": "Design matrix used for MAGeCK MLE to call essential genes under multiple conditions while considering sgRNA knockout efficiency"
},
"rra_contrasts": {
"type": "string",
"format": "file-path",
"exists": true,
"description": "Comma-separated file with the conditions to be compared. The first one will be the reference (control)"
},
"count_table": {
"type": "string",
"format": "file-path",
"exists": true,
"description": "Please provide your count table if the mageck test should be skipped."
},
"library": {
"type": "string",
"format": "file-path",
"exists": true,
"fa_icon": "far fa-address-book",
"description": "sgRNA sequences and targeting genes"
},
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@LaurenceKuhl I have added the validation of these parameters, they must be files and they must exist. Could you check if it's correct? And if they have a pattern, like ending with .csv for example, we can also add it.

LaurenceKuhl
LaurenceKuhl reviewed Jul 14, 2023
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LaurenceKuhl
LaurenceKuhl reviewed Jul 14, 2023
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@mirpedrol @LaurenceKuhl
Apply suggestions from code review
ef705d7 
Co-authored-by: LaurenceKuhl <laurence.kuhlburger@gmail.com>
@mirpedrol mirpedrol merged commit ddddf26 into dev Jul 14, 2023
@mirpedrol mirpedrol deleted the nf-core-template-merge-2.9 branch July 14, 2023 08:09
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@mirpedrol mirpedrol mirpedrol approved these changes

@LaurenceKuhl LaurenceKuhl LaurenceKuhl approved these changes

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@nf-core-bot @mirpedrol @LaurenceKuhl