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Refactor with fixes from Champagne QC #32

Merged
merged 29 commits into from
Nov 1, 2023
Merged

Refactor with fixes from Champagne QC #32

merged 29 commits into from
Nov 1, 2023

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kelly-sovacool
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@kelly-sovacool kelly-sovacool commented Oct 27, 2023 •
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Changes

  • Add custom/countfastq modules that counts fastq records w/ biopython.
  • Use custom/countfastq in filter_blacklist subworkflow.
  • Minor changes to other modules.

Issues

NA

PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • Write unit tests for any new features, bug fixes, or other code changes.
  • Update docs if there are any API changes.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

@kelly-sovacool
fix: refactor from QC fixes for CHAMPAGNE
25e6e67
@kelly-sovacool
feat: create custom module to count fastq reads
e14e086
@kelly-sovacool
docs: metadata for countfastq module
4e307e4
@kelly-sovacool
docs: update filter_blacklist meta w/ custom/countfastq component
bdaaa94
@kelly-sovacool
fix: path to custom/countfastq module
50585e6
@kelly-sovacool
fix: CUSTOM_COUNTFASTQ module name
aeaea74
@kelly-sovacool
fix: get flagstat of filtered bam
5da73d0
@kelly-sovacool
fix: use biopython to count fastqs
9c344c9
@kelly-sovacool
fix: use standard process label
f2ac212
@kelly-sovacool
fix: increase resources for samtools sort
d2bd2d9
@kelly-sovacool
fix: input type integer->value
5ae0b73
@kelly-sovacool
fix: count fastq records w/ Biopython instead of grep
01a4371 
quality scores can contain `@` and may sometimes appear as the first
character on a line, so using `grep "^@"` over counts records
@kelly-sovacool
refactor: use custom count fastq
62154da 
flagstat doesn't work here since we keep reads that are unaligned
@kelly-sovacool
chore: Merge branch 'champagne-qc-fixes' of https://github.com/CCBR/n…
efb52e3 
…f-modules into champagne-qc-fixes
@kelly-sovacool
test: create test infra for custom/countfastq
8fe1fba
@kelly-sovacool
test: create blank gzip file
61917fd
@kelly-sovacool
fix: Revert "fix: input type integer->value"
1f9d7fd 
This reverts commit 5ae0b73.
@kelly-sovacool
fix: add 'when' condition
0261535
@kelly-sovacool
fix: add custom/countfastq to tags
3aa030c
@kelly-sovacool
test: fix path to custom test data config
6e78b46
@kelly-sovacool
fix: stub for custom_countfastq
19cb4b7
@kelly-sovacool
docs: add biopython to keywords
a3c88a4
@kelly-sovacool
feat: output versions in countfastq
3bd6cd8
@kelly-sovacool
refactor: make write_versions() function
9879888
@kelly-sovacool
fix: touch versions.yml in stub
48ff180
@kelly-sovacool
feat: include versions from custom/countfastq
b776437
@kelly-sovacool
test: create test.yml for custom/countfastq
450fdb3
@kelly-sovacool
docs: add custom/countfastq to changelog
f7722ee
@kelly-sovacool
fix: linting errors
2ccd43e
@kelly-sovacool kelly-sovacool marked this pull request as ready for review November 1, 2023 17:47
@kelly-sovacool kelly-sovacool merged commit ad8b993 into main Nov 1, 2023
13 checks passed
@kelly-sovacool kelly-sovacool deleted the champagne-qc-fixes branch November 1, 2023 17:47
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@kelly-sovacool