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Intervals #609

Merged
merged 9 commits into from
Jun 28, 2022
Merged

Intervals #609

merged 9 commits into from
Jun 28, 2022

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FriederikeHanssen
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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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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 Jun 28, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b66c573

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-28 16:36:16

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review June 28, 2022 12:14
ggabernet
ggabernet approved these changes Jun 28, 2022
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LGTM!

SusiJo
SusiJo reviewed Jun 28, 2022
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workflows/sarek.nf
@@ -52,7 +52,7 @@ for (param in checkPathParamList) if (param) file(param, checkIfExists: true)
// Set input, can either be from --input or from automatic retrieval in WorkflowSarek.groovy
ch_input_sample = extract_csv(file(params.input, checkIfExists: true))

if (params.wes) {
if (params.wes && !params.step == 'annotate') {
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Ah, so you fixed it already 👍

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yeah since it was a one liner at roughly fit into the theme: fix intervals :D

@SusiJo
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SusiJo commented Jun 28, 2022

Controlfreec was not failing before, right? Do your changes affect something there?

@FriederikeHanssen
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Controlfreec was not failing before, right? Do your changes affect something there?

must. I'll take a look now. thanks for reviewing :)

@FriederikeHanssen
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Controlfreec was not failing before, right? Do your changes affect something there?

was actually a bug, the interval was always used 😱 . However it fails with no intervals because controlfreec fails if it doesn't find enough. I cannot see the bed file aymore in the config

@FriederikeHanssen FriederikeHanssen merged commit ffd1100 into nf-core:dev Jun 28, 2022
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@SusiJo SusiJo SusiJo left review comments

@ggabernet ggabernet ggabernet approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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3 participants
@FriederikeHanssen @SusiJo @ggabernet