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Additional checks of sample sheet #623

Merged
merged 5 commits into from
Jul 8, 2022
Merged

Additional checks of sample sheet #623

merged 5 commits into from
Jul 8, 2022

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asp8200
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@asp8200 asp8200 commented Jul 7, 2022 •
edited by carpanz
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Related to #93

With this PR, I've tried adding checks for the following:

  1. The sample sheet should not contain several rows with the same combination of patient, sample and lane, and
  2. A sample should not be associated to several patients.

I have some ideas or questions for additional checks, but let's first see if the two above-mentioned checks are a step in the right direction.

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
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    • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
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github-actions bot commented Jul 7, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 337adea

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_description - No description provided in schema for parameter: ascat_chromosomes

❔ 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 2022-07-08 11:59:27

maxulysse
maxulysse reviewed Jul 7, 2022
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@maxulysse maxulysse changed the title DRAFT: Additional checks of sample sheet Additional checks of sample sheet Jul 8, 2022
@maxulysse maxulysse marked this pull request as ready for review July 8, 2022 07:05
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Just need to update the CHANGELOG and we're good to go

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asp8200 commented Jul 8, 2022

Just need to update the CHANGELOG and we're good to go

Sound good 🙏 Should we go even further and add some checks like:

A) Each sample should correspond to a unique set of fastq-files (see example below),

B) Each fastq-file should only be associated with one sample.

The purpose of (A) is to detect an error in the sample sheet like this:

patient,sex,sample,fastq_1,fastq_2
p1, XX,s1, f1_R1.fastq.gz, f1_R2.fastq.gz
p2, XX,s1, f2_R1.fastq.gz, f2_R2.fastq.gz

(Here the s1 in the last row should have been s2.)
Similar, the purpose of (B) is to detect an error in the sample sheet like this:

patient,sex,sample,fastq_1,fastq_2
p1, XX,s1, f1_R1.fastq.gz, f1_R2.fastq.gz
p2, XX,s2, f1_R1.fastq.gz, f2_R2.fastq.gz

(Here the f1_R1.fastq.gz in the last row should have been f2_R1.fastq.gz.)

Let me know what you think. Cheers

@maxulysse
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what about the lane information in these cases?

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asp8200 commented Jul 8, 2022

what about the lane information in these cases?

These two new proposed checks don't involve the lanes, but perhaps they should? Or other checks should be made involving the lanes? I'm not sure what one would want to check for the lane-data, perhaps you know?

lassefolkersen
lassefolkersen reviewed Jul 8, 2022
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Very nice to have patient-sample-lane checked for uniqueness.
Just wanted to pipe in that I often run the pipeline with the same fastq-file for different patients, or somatic/germline or such. It comes out with no differences, but it actually runs. I wouldn't be able to run such test-setups if you disallow same fastq. Maybe it's more of a log.warning thing?

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asp8200 commented Jul 8, 2022

Very nice to have patient-sample-lane checked for uniqueness. Just wanted to pipe in that I often run the pipeline with the same fastq-file for different patients, or somatic/germline or such. It comes out with no differences, but it actually runs. I wouldn't be able to run such test-setups if you disallow same fastq. Maybe it's more of a log.warning thing?

@lassefolkersen and @maxulysse : So maybe we should just keep it to those checks which are implemented in this PR?

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Very nice to have patient-sample-lane checked for uniqueness. Just wanted to pipe in that I often run the pipeline with the same fastq-file for different patients, or somatic/germline or such. It comes out with no differences, but it actually runs. I wouldn't be able to run such test-setups if you disallow same fastq. Maybe it's more of a log.warning thing?

@lassefolkersen and @maxulysse : So maybe we should just keep it to those checks which are implemented in this PR?

Yes, let's keep it that way for now, I feel like it's good and enough already

@maxulysse maxulysse merged commit 7383196 into nf-core:dev Jul 8, 2022
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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@asp8200 @maxulysse @lassefolkersen