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Bwamemory #166

Merged
merged 4 commits into from
Oct 15, 2024
Merged

Bwamemory #166

merged 4 commits into from
Oct 15, 2024

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edmundmiller
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@edmundmiller edmundmiller commented Sep 26, 2024 •
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  • Updated to include dynamic memory memory adjustments for bwa and bwamem2 index
  • Add a hisat2 hg19 build

Waiting for nf-core/modules#6628 to merge, but that will just be a nf-core modules update later, but have a few PRs that are based off this one.

@edmundmiller edmundmiller self-assigned this Sep 30, 2024
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github-actions bot commented Sep 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5cf681d

+| ✅ 199 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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:

  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-30 12:40:45

@edmundmiller edmundmiller marked this pull request as ready for review September 30, 2024 16:19
itrujnara
itrujnara reviewed Oct 15, 2024
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One question, otherwise looks good

conf/igenomes.config
@@ -295,6 +295,7 @@ params {
bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
hisat2 = "s3://genome-idx/hisat/hg19_genome.tar.gz"
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Is there a reason this one must use a separate URL rather than the base?

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Yeah, it does because it's not hosted under igenomes.

https://daehwankimlab.github.io/hisat2/download/

We could move it under igenomes, but I'm trying to avoid shaving that yak until we work on nf-core/references a bit more.

@edmundmiller edmundmiller merged commit f61aac0 into dev Oct 15, 2024
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@edmundmiller edmundmiller deleted the bwamemory branch October 15, 2024 18:22
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@itrujnara itrujnara itrujnara left review comments

@sateeshperi sateeshperi sateeshperi approved these changes

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@edmundmiller @sateeshperi @itrujnara