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Add option to download cache for annotation #936

Merged
merged 14 commits into from
Feb 8, 2023
Merged

Add option to download cache for annotation #936

merged 14 commits into from
Feb 8, 2023

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maxulysse
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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 Feb 7, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit ae480e5

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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-02-08 13:17:49

@maxulysse
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maxulysse commented Feb 7, 2023 •
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Need to:

  • Fix Linting (so fix snpeff/download module mainly).
  • Add some tests
  • And make sure that the params are actually logical.

but looking good:

[8c/927316] process > NFCORE_SAREK:SAREK:PREPARE_CACHE:ENSEMBLVEP_DOWNLOAD (WBcel235.106)               [100%] 1 of 1 ✔
[45/9bfef3] process > NFCORE_SAREK:SAREK:PREPARE_CACHE:SNPEFF_DOWNLOAD (WBcel235.105)                   [100%] 1 of 1 ✔
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX                                   -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX                                   -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                               -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY                  -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                               -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX                                  -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP                                     -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE                         -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS                                -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS                              -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON                                       -
[-        ] process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS                        -
[-        ] process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT                   -
[-        ] process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL                    -
[-        ] process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY                      -
[3e/c41f9f] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (test)      [100%] 1 of 1 ✔
[5f/c6abb3] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX (test)   [100%] 1 of 1 ✔
[44/9ac2e4] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP (test)      [100%] 1 of 1 ✔
[d2/a35cfe] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:TABIX_TABIX (test)         [100%] 1 of 1 ✔
[c3/9c66cd] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP (test) [100%] 1 of 1 ✔
[86/e9d8de] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX (test)    [100%] 1 of 1 ✔
[ac/d5f9d2] process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS (1)                                [100%] 1 of 1 ✔
[54/097e69] process > NFCORE_SAREK:SAREK:MULTIQC                                                        [100%] 1 of 1 ✔
-[nf-core/sarek] Pipeline completed successfully-
Completed at: 07-Feb-2023 22:59:04
Duration    : 1m 31s
CPU hours   : 0.1
Succeeded   : 10

EDIT: Add checklist

nvnieuwk
nvnieuwk approved these changes Feb 8, 2023
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I love it!

FriederikeHanssen
FriederikeHanssen reviewed Feb 8, 2023
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conf/modules/prepare_cache.config
// VEP
withName: 'ENSEMBLVEP_DOWNLOAD' {
ext.when = { params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge')) }
ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
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quick question: how does it work to fetch the correct version, since it is not specified here?

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correct version of what?

FriederikeHanssen
FriederikeHanssen reviewed Feb 8, 2023
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Looks good to me overall. Can we have a section in the FAQs about this? I always have a hard time wrapping my head around it and there already is a section about custom cache that could be extended with this I think

@maxulysse maxulysse mentioned this pull request Feb 8, 2023
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Looks good to me overall. Can we have a section in the FAQs about this? I always have a hard time wrapping my head around it and there already is a section about custom cache that could be extended with this I think

Need to merge it and try it out properly on tower as well, so I can see if it works as expected, so will add docs in a separate PR, but before release

@maxulysse maxulysse merged commit ef1ec74 into nf-core:dev Feb 8, 2023
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@nvnieuwk nvnieuwk nvnieuwk approved these changes

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3 participants
@maxulysse @FriederikeHanssen @nvnieuwk