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Hi, I have 4 PRs to fix the last linting issues in...
# request-review
l
Hi, I have 4 PRs to fix the last linting issues in the modules repository • https://github.com/nf-core/modules/pull/10109 (SRA_TOOLS) • https://github.com/nf-core/modules/pull/10123 (small subworkflow cleanup) • https://github.com/nf-core/modules/pull/10124 (NARFMAP) • https://github.com/nf-core/modules/pull/10129 (template argument modules)
✅ 1
@Maxime Garcia and @Simon Pearce could I have a review on these ?
m
Give me 5 to get me a coffee
l
I'm not in a hurry 😉
m
ok, so let's skip the failing tests on NARFMAP
anyway, this tool is due for an update, and I know that @Edmund is busy for now, so it'll happen later I'm afraid, but in the meanwhile, let's just have ✅
And let's open an issue in the original repo to remind us of doing the fix
l
Okay, I will do so !
m
I think the issue is actually there already https://github.com/bioinformaticsorphanage/NARFMAP/issues/10
l
But it's not the same issue ? The one I have is only an out of memory on the CI/CD test with docker, singularity and conda are fine. I just guess that 
<https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa>
is too big.
m
it's a single chromosome it shouldn't be
s
How have I never heard of the https://github.com/orgs/bioinformaticsorphanage ?
l
@Maxime Garcia what I could do otherwise, would be to reduce the size of the genome used by the hashtable setup process, or do we really want to test a whole chromosome on the CI/CD ?
m
yeah, maybe try a smaller fasta file
what do we use for bwa mem?
l
what do we use for bwa mem?
Only sarscov2 data Switching to 
params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz'
does fix the issue OOM issue.
🙌 1
m
then good enough for me for now
👍 2
l
Ready for review 😉
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Repositories/modules$ nextflow lint modules/
Nextflow linting complete!
 ✅ 2672 files had no errors
Repositories/modules$ nextflow lint subworkflows/
Nextflow linting complete!
 ✅ 483 files had no errors
🎉 2
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