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update Dragmap #1350

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wants to merge 3 commits into from
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update Dragmap #1350

wants to merge 3 commits into from

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maxulysse
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close #1348

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github-actions bot commented Dec 8, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 59f5550

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-08 13:22:59

@maxulysse
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test are working locally, but not on GHA apparently 🤦

@maxulysse
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No idea what is happening there

.command.sh: line 8:    26 Segmentation fault      (core dumped) dragen-os -r dragmap --RGSM test_test --RGID "@RG\tID:null.test.test_L1\tPU:test_L1\tSM:test_test\tLB:test\tDS:[https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta\tPL:ILLUMINA](https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta/tPL:ILLUMINA)" --num-threads 2 -1 test_1.fastq.gz -2 test_2.fastq.gz 2> >(tee test-test_L1.sorted.dragmap.log 1>&2)
          28 Done                    | samtools sort --threads 2 -o test-test_L1.sorted.bam -

@FriederikeHanssen
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well I was too excited. Looks like the segmentation fault reported here is still not fixed.

@maxulysse
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ok, nevermind, was not running the right tests, I can reproduce locally

@maxulysse
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well I was too excited. Looks like the segmentation fault reported here is still not fixed.

I agree with you

@maxulysse
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won't merge, so let's kill it until dragmap is actually fixed

@maxulysse maxulysse closed this Dec 8, 2023
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen