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update tiddit/sv#581

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maxulysse merged 19 commits intonf-core:devfrom
maxulysse:dev_tiddit
Jun 16, 2022
Merged

update tiddit/sv#581
maxulysse merged 19 commits intonf-core:devfrom
maxulysse:dev_tiddit

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@maxulysse maxulysse commented Jun 8, 2022

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • 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 Jun 8, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit dfd73f5

+| ✅ 144 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_description - No description provided in schema for parameter: umi_read_structure
  • schema_description - No description provided in schema for parameter: group_by_umi_strategy

❔ Tests ignored:

  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-16 13:35:32

@maxulysse maxulysse marked this pull request as ready for review June 13, 2022 15:37
FriederikeHanssen
FriederikeHanssen reviewed Jun 13, 2022
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Comment thread CHANGELOG.md
FriederikeHanssen
FriederikeHanssen approved these changes Jun 14, 2022
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Comment thread conf/modules.config Outdated
Comment thread subworkflows/nf-core/variantcalling/tiddit/main.nf Outdated
emit:
versions = ch_versions

tiddit_vcf = tiddit_vcf_gz_tbi
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@FriederikeHanssen FriederikeHanssen Jun 14, 2022

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For the annotation, I think we need just the vcf.gz, not the tbi

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@FriederikeHanssen FriederikeHanssen Jun 16, 2022

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What about this one?

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@maxulysse maxulysse Jun 16, 2022

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oh yeah, I forgot about it, so we want only vcf.gz here, not the tbi?

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@FriederikeHanssen FriederikeHanssen Jun 16, 2022

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sorry for the late reply, didn't check my emails. 🙈 yes only vcf.gz, apaprently the annotation tools don't wnat the tbi

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@maxulysse maxulysse Jun 16, 2022

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no worries

Comment thread workflows/sarek.nf
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FriederikeHanssen commented Jun 14, 2022

oh: Tiddit test still needs to be include in the ci.yml to run

@maxulysse maxulysse merged commit db638bd into nf-core:dev Jun 16, 2022
@maxulysse maxulysse deleted the dev_tiddit branch June 16, 2022 14:03
This was referenced Jun 22, 2022
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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