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insert check for one line sample sheet #591

Merged
merged 6 commits into from
Jun 17, 2022
Merged

insert check for one line sample sheet #591

merged 6 commits into from
Jun 17, 2022

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lassefolkersen
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@lassefolkersen lassefolkersen commented Jun 15, 2022 •
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This fixes #589 by checking that sample sheet is at least two lines. If it's only 1 line, the subsequent splitCsv(header: true) call will read it as empty and skip all other samplesheet checks. Also - upgraded missing patient and sample cases from log.warn to log.error.

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.
  • Make sure your code lints (nf-core lint .).
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github-actions bot commented Jun 15, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d67fbbd

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

❗ 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 2022-06-17 07:09:05

@lassefolkersen
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Ok, I think this is ready for review now. Intended behaviour:

  • if csv file has 0 or 1 lines. Full stop, no matter what. That can never be productive (and would skip subsequent checks anyway, because they get read as empty, [BUG] Sarek-dev skips directly to multiqc after interval split #589 ).
  • if csv file has >1 lines, check for presence of fields patient and sample, full stop if not present.
  • remaining checks are unaltered - e.g. if fastq_1 is present, and that file is not there it will check and stop (but that was already part of the code)

FriederikeHanssen
FriederikeHanssen approved these changes Jun 17, 2022
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Nice! Thanks for adding this. Just something small, I would propose renaming to "numberOfLinesInSampleSheet" or maybe at least num .

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@FriederikeHanssen
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Do you think it would be possible to add a check that each header field is one of (patient, sample, status, gender, lane, fastq1, fastq2, bam, bai, table, cram, crai, vcf)? (I think those are all but I would need to double check)

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asp8200 commented Jun 17, 2022 •
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Do you think it would be possible to add a check that each header field is one of (patient, sample, status, gender, lane, fastq1, fastq2, bam, bai, table, cram, crai, vcf)? (I think those are all but I would need to double check)

I was thinking along the same lines. Could we do something like

accepted_headers = ['patient', 'sample', 'status', 'gender', 'lane', 'fastq1', 'fastq2', 'bam', 'bai', 'table', 'cram', 'crai', 'vcf']

for each header_field in headers:
    if header_field not in accepted_headers then throw error

@lassefolkersen
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Do you think it would be possible to add a check that each header field is one of (patient, sample, status, gender, lane, fastq1, fastq2, bam, bai, table, cram, crai, vcf)? (I think those are all but I would need to double check)

I was thinking along the same lines. Could we do something like

accepted_headers = ['patient', 'sample', 'status', 'gender', 'lane', 'fastq1', 'fastq2', 'bam', 'bai', 'table', 'cram', 'crai', 'vcf']

for each header_field in headers:
    if header_field not in accepted_headers then throw error

No, I don't like that solution. Because if you then do -step variant_calling (a bam/cram as input) or -step annotation(a vcf as input), then all those accepted_headers, except for patient and sample are not required anymore. So it would effectively hinder the ability to enter Sarek at a later stage.

So any solution has to be conditional on -step.

@FriederikeHanssen
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No, I don't like that solution. Because if you then do -step variant_calling (a bam/cram as input) or -step annotation(a vcf as input), then all those accepted_headers, except for patient and sample are not required anymore. So it would effectively hinder the ability to enter Sarek at a later stage.

I am not sure I follow. The way I understand Anders proposal, it would mean that a header could just not be mysillyheaderfield but we would at least check that it is in general part of correct list and then throw an error

Unknown header field. Accepted columns are:

. I agree it wouldn't check at all that the combination are proper, i.e. --step annotation should only have patient,sample,vcf but would at least prevent typos and so on, but i don't get why it wouldn't advance

@FriederikeHanssen
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No, I don't like that solution. Because if you then do -step variant_calling (a bam/cram as input) or -step annotation(a vcf as input), then all those accepted_headers, except for patient and sample are not required anymore. So it would effectively hinder the ability to enter Sarek at a later stage.

I am not sure I follow. The way I understand Anders proposal, it would mean that a header could just not be mysillyheaderfield but we would at least check that it is in general part of correct list and then throw an error

Unknown header field. Accepted columns are:

. I agree it wouldn't check at all that the combination are proper, i.e. --step annotation should only have patient,sample,vcf but would at least prevent typos and so on, but i don't get why it wouldn't advance

But either way we can save this for the next PR :)

@FriederikeHanssen FriederikeHanssen merged commit 0473d6f into nf-core:dev Jun 17, 2022
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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

@asp8200 asp8200 Awaiting requested review from asp8200

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@lassefolkersen @FriederikeHanssen @asp8200