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Fixes for PR #264 #265

Merged
merged 8 commits into from
Jan 31, 2022
Merged

Fixes for PR #264 #265

merged 8 commits into from
Jan 31, 2022

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drpatelh
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github-actions bot commented Jan 31, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e48bef7

+| ✅ 132 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yaml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowViralrecon.groovy

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-01-31 15:54:09

@drpatelh drpatelh mentioned this pull request Jan 31, 2022
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saramonzon
saramonzon approved these changes Jan 31, 2022
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docs/output.md Outdated
<summary>Output files</summary>

* `variants/<CALLER>/consensus/bcftools/`
* `*.consensus.fa`: Consensus Fasta file generated by integrating the variants called by BCFTools into the reference genome.
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Shouldn't it be the variants called by it could be bcftools or ivar right?
Also another output here would be the variants with AF> threshold?

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Good spot. Fixed in e48bef7

Yep, the variants with AF > threshold are defined in the line below that one. They will be called <SAMPLE>.filtered.vcf.gz

@drpatelh drpatelh merged commit a50c5c2 into nf-core:dev Jan 31, 2022
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@saramonzon saramonzon saramonzon approved these changes

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@drpatelh @saramonzon