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Avoid publishing from SENTIEON_GVCFTYPER #1064

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merged 1 commit into from
Jun 5, 2023

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@asp8200 asp8200 commented Jun 4, 2023

Change similar to the one done for 'GATK4_GENOTYPEGVCFS in #1061

Without this change, the following test

 nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --skip_tools haplotyper_filter --outdir results --sentieon_haplotyper_out_format gvcf

publishes the following files:

-rw-r--r--  1 ubuntu ubuntu 1662 Jun  4 17:27 chr22_2-15000.vcf.gz
-rw-r--r--  1 ubuntu ubuntu   99 Jun  4 17:27 chr22_2-15000.vcf.gz.tbi
-rw-r--r--  1 ubuntu ubuntu 1262 Jun  4 17:26 chr22_20001-40001.vcf.gz

under results/sentieon.

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).

@asp8200 asp8200 requested a review from maxulysse as a code owner June 4, 2023 17:41
@asp8200 asp8200 merged commit b3fb0d8 into sentieon Jun 5, 2023
@asp8200 asp8200 deleted the sentieon_avoid_publishing branch June 5, 2023 08:34
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3 participants