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DSL2: Pull input files from reference sheet columns #1018

Merged
merged 11 commits into from
Oct 27, 2023
Merged

DSL2: Pull input files from reference sheet columns #1018

merged 11 commits into from
Oct 27, 2023

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scarlhoff
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@scarlhoff scarlhoff commented Jul 28, 2023 •
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This PR edits the input of files to be through the reference indexing subworkflow both for single and multiple references.

Adds input for these files:

  • HapMap file for angsd contamination estimation
  • SNP bed file and masked fasta for pmdtools
  • SNP bed for genotyping
  • SNP eigenstrat file for pileupcaller
  • SNP bed for sexdeterrmine
  • SNP bed for qualimap
  • Analysis file for bedtools

This closes #988.

@scarlhoff scarlhoff linked an issue Jul 28, 2023 that may be closed by this pull request
DSL2: Add popgen input files to reference sheet #988
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github-actions bot commented Jul 28, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6e2abeb

+| ✅ 159 tests passed       |+
!| ❗  20 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_humanbam.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_humanbam.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowEager.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • schema_description - No description provided in schema for parameter: skip_qualimap
  • schema_description - No description provided in schema for parameter: skip_damage_calculation

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-20 09:09:59

@scarlhoff scarlhoff marked this pull request as ready for review October 6, 2023 13:48
@scarlhoff scarlhoff requested a review from a team October 10, 2023 08:04
TCLamnidis
TCLamnidis approved these changes Oct 13, 2023
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LGTM!

jfy133
jfy133 approved these changes Oct 13, 2023
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Tired look says this is OK, although we really need much more extensive tests (leave one out like things) as this is a bit of a monster, but well done @scarlhoff for taking this one on!!!

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@scarlhoff scarlhoff requested a review from jfy133 October 20, 2023 09:08
jfy133
jfy133 reviewed Oct 25, 2023
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jfy133
jfy133 approved these changes Oct 25, 2023
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One tiny syntax improvement but not necessary otherwise OK for me 👌

We must make sure to test the crap out of this (tbh we should already add nf-test...)

@scarlhoff scarlhoff merged commit 6cb0c30 into nf-core:dev Oct 27, 2023
18 checks passed
@scarlhoff scarlhoff deleted the dsl2_ref_sheet branch October 27, 2023 08:27
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@TCLamnidis TCLamnidis TCLamnidis approved these changes

@jfy133 jfy133 jfy133 approved these changes

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DSL2: Add popgen input files to reference sheet
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@scarlhoff @jfy133 @TCLamnidis