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Fix unique lanes for freebayes, groupKey, add new indices, copy meta maps #549

Merged
merged 39 commits into from
May 23, 2022
Merged

Fix unique lanes for freebayes, groupKey, add new indices, copy meta maps #549

merged 39 commits into from
May 23, 2022

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FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented May 16, 2022 •
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Closes #311
closes #340 & #542

This PR got quite big now:

  • Fixes Freebayes unique lanes issue
  • Adds PON & dragmap to the igenomes.config; indices for both + bwamem2 are now also available on igenomes
  • Fix groupKey: actually using it for grouping
  • Copy all the meta maps and not just clone. more people raninto this weird issue: https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339
  • Add freebayes tests that work with the CI

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).

@FriederikeHanssen
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This is ready for review from my POV. There is some un-used code in there at the moment. I would leave it until we ultimately decided on something and remove before merge.

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review May 18, 2022 13:34
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This is ready for review from my POV. There is some un-used code in there at the moment. I would leave it until we ultimately decided on something and remove before merge.

Alright, actually got the flowcell code to work.

SusiJo
SusiJo reviewed May 19, 2022
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modules.json
@@ -130,7 +133,7 @@
"git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
},
"gatk4/markduplicates": {
"git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
"git_sha": "df2620cfc7e4c21b14ed03c1c928f09fbabf83c4"
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was that expected to be different?

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yeah module update. Someone changed the default ressource usage, which makes sense IMO

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right, i see 👍

SusiJo
SusiJo reviewed May 19, 2022
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tests/csv/3.0/fastq_pair.csv
@@ -1,3 +1,3 @@
patient,gender,status,sample,lane,fastq_1,fastq_2
test,XX,0,test,test_L1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz
test,XX,1,test2,test2_L1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz
test,XX,1,test2,test_L1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz
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could you please explain why this was changed to test rather than test2?

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Because the test_paired.csv was updated to have the same lane ID for both samples. That way I can test that the feature fixed in this PR is actually fixed.

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okay great!

SusiJo
SusiJo approved these changes May 19, 2022
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@FriederikeHanssen LGTM as far as i can tell 👍

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Vielen Dank 😊

@FriederikeHanssen FriederikeHanssen changed the title Fix unique lanes issue Fix unique lanes for freebayes, groupKey, add new indices, copy al meta maps May 23, 2022
@FriederikeHanssen FriederikeHanssen changed the title Fix unique lanes for freebayes, groupKey, add new indices, copy al meta maps Fix unique lanes for freebayes, groupKey, add new indices, copy meta maps May 23, 2022
maxulysse
maxulysse approved these changes May 23, 2022
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👍

workflows/sarek.nf Outdated Show resolved Hide resolved
@FriederikeHanssen FriederikeHanssen merged commit 769b38b into nf-core:dev May 23, 2022
This was referenced May 23, 2022
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@SusiJo SusiJo SusiJo approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse @SusiJo