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ASCAT exome/targeted sequencing resource file generation #981

Merged
merged 9 commits into from
Mar 29, 2023
Merged

ASCAT exome/targeted sequencing resource file generation #981

merged 9 commits into from
Mar 29, 2023

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ameynert
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Added instructions to generate resource files for running ASCAT on exome or targeted sequencing data. Tested resulting files on TWIST exome capture kit targets and a set of 74 tumour-normal pairs.

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/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 --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 Mar 28, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 1ab65eb

+| ✅ 152 tests passed       |+
#| ❔   8 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-29 08:18:16

@FriederikeHanssen
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❤️ Loooooooove it! Thank you so much! I am not going to reproduce this, but it looks great!

@FriederikeHanssen
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Can you update the changelog?

ameynert added 2 commits March 28, 2023 16:19
Merge pull request #1 from nf-core/dev
11dbc19 
Merge from dev into forked dev
nf-core#981
7cf0c1f
@ameynert
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Can you update the changelog?

Done!

@SusiJo
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SusiJo commented Mar 28, 2023

Hi @ameynert, don't forget to add yourself to the contributors in the Readme :)

lassefolkersen
lassefolkersen requested changes Mar 28, 2023
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Nice work. Very useful 😄
One comment about the now expanded sarek/usage.md section on ASCAT usage: It seems like it's skipping on any mention of whole-genome sequencing. As I recall, that is possible out-of-the-box. Or not, I'm unsure. But regardless, it feels like if there is a long and detailed point about ASCAT exome data, then there should at least be a sentence saying what to do with ASCAT whole genome data, even if that sentence is just "it works out of the box":

@ameynert
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Nice work. Very useful 😄 One comment about the now expanded sarek/usage.md section on ASCAT usage: It seems like it's skipping on any mention of whole-genome sequencing. As I recall, that is possible out-of-the-box. Or not, I'm unsure. But regardless, it feels like if there is a long and detailed point about ASCAT exome data, then there should at least be a sentence saying what to do with ASCAT whole genome data, even if that sentence is just "it works out of the box":

Good shout. I've added a sentence at the start of that section to clarify.

lassefolkersen
lassefolkersen approved these changes Mar 29, 2023
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LGTM 👍

@ameynert ameynert merged commit 56a8de5 into nf-core:dev Mar 29, 2023
@FriederikeHanssen
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😱 what is going on with all the failing tests

@FriederikeHanssen FriederikeHanssen mentioned this pull request Mar 30, 2023
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@lassefolkersen lassefolkersen lassefolkersen approved these changes

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

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4 participants
@ameynert @FriederikeHanssen @SusiJo @lassefolkersen