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Fix sorting in overall_summary.tsv #750

Merged
merged 3 commits into from
Jun 18, 2024
Merged

Fix sorting in overall_summary.tsv #750

merged 3 commits into from
Jun 18, 2024

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d4straub
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@d4straub d4straub commented Jun 17, 2024 •
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overall_summary.tsv had sometimes misleading numbers in 2.9.0. This was due to a new sorting method added in #717 (necessary due to bad forward & reverse read pairing due to edge case sample names).

This PR makes sure that all tables that are merged are identically sorted (merged by cbind rather than merge due to different row names (contain sampleID), e.g. sample1.trimmed_1.trim.fastq.gz & sample1_1.filt.fastq.gz & sample1_2.filt.fastq.gz).
I also considered correcting the row names for each table and subsequently apply merge, but because row names are so divers, that seems not great. I do have the feeling correcting row names and use merge might be safer, but I couldnt find any example where it would matter, but I am open to change the implementation.

Using the example above, the sorting should be fine:

> sort( c("sample1.trimmed_1.trim.fastq.gz","sample2.trimmed_1.trim.fastq.gz","sample10.trimmed_1.trim.fastq.gz","sample10_1.trimmed_1.trim.fastq.gz") )
[1] "sample1.trimmed_1.trim.fastq.gz"    "sample10_1.trimmed_1.trim.fastq.gz"
[3] "sample10.trimmed_1.trim.fastq.gz"   "sample2.trimmed_1.trim.fastq.gz"   
> sort( c("sample1_1.filt.fastq.gz","sample2_1.filt.fastq.gz","sample10_1.filt.fastq.gz","sample10_1_1.filt.fastq.gz") )
[1] "sample1_1.filt.fastq.gz"    "sample10_1_1.filt.fastq.gz"
[3] "sample10_1.filt.fastq.gz"   "sample2_1.filt.fastq.gz"

Closes #742.

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github-actions bot commented Jun 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6f520a9

+| ✅ 281 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-17 13:33:35

@d4straub d4straub mentioned this pull request Jun 17, 2024
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erikrikarddaniel
erikrikarddaniel approved these changes Jun 17, 2024
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d4straub and others added 2 commits June 17, 2024 15:26
@d4straub @erikrikarddaniel
Update CHANGELOG.md
5c8382d 
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
@d4straub
Merge branch 'dev' into fix-overall_summary.tsv-sorting
6f520a9
@d4straub d4straub merged commit 2c464fd into nf-core:dev Jun 18, 2024
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@d4straub d4straub deleted the fix-overall_summary.tsv-sorting branch June 18, 2024 11:43
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