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Add path parameters #206

Merged
merged 1 commit into from
Dec 23, 2022
Merged

Add path parameters #206

merged 1 commit into from
Dec 23, 2022

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sofstam
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@sofstam sofstam commented Dec 23, 2022

Closes #199

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 - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Dec 23, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6ebfdcd

+| ✅ 157 tests passed       |+
!| ❗  28 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • 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 README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • 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_motus.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_motus.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_krakenuniq.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_krakenuniq.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_nopreprocessing.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_nopreprocessing.config: Give any required params for the test so that command line flags are not needed
  • 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_nothing.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_nothing.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_noprofiling.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_noprofiling.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
  • 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in taxprofiler.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2022-12-23 12:47:55

jfy133
jfy133 reviewed Dec 23, 2022
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workflows/taxprofiler.nf
params.shortread_hostremoval_index, params.multiqc_config,
params.shortread_qc_adapterlist
def checkPathParamList = [ params.input, params.genome, params.databases,
params.outdir, params.longread_hostremoval_index
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Suggested change
params.outdir, params.longread_hostremoval_index
params.outdir, params.longread_hostremoval_index,

jfy133
jfy133 approved these changes Dec 23, 2022
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Missing a comma, but I can't commit to your repo, so I'll merge and do a quick fix straight after

@jfy133 jfy133 merged commit 2de0493 into nf-core:dev Dec 23, 2022
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@jfy133 jfy133 jfy133 approved these changes

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Add all file path parameters
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@sofstam @jfy133