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Add nanopore reads input #24

Merged
merged 4 commits into from
Mar 18, 2022
Merged

Add nanopore reads input #24

merged 4 commits into from
Mar 18, 2022

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ljmesi
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@ljmesi ljmesi commented Mar 18, 2022

Add reading Oxford Nanopore fastq reads from samplesheet

Fixes #23

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 `).
  • 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).

@ljmesi ljmesi requested a review from jfy133 March 18, 2022 10:05
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github-actions bot commented Mar 18, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 2e1b6c5

+| ✅ 139 tests passed       |+
!| ❗  20 tests had warnings |!
-| ❌   6 tests failed       |-

❌ Test failures:

  • schema_params - Param databases from nextflow config not found in nextflow_schema.json
  • schema_params - Param fastp_clip_merge from nextflow config not found in nextflow_schema.json
  • schema_params - Param fastp_exclude_unmerged from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_malt from nextflow config not found in nextflow_schema.json
  • schema_params - Param malt_mode from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_kraken2 from nextflow config not found in nextflow_schema.json

❗ 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: Update the example "typical command" below used to run the pipeline
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 taxprofiler.nf: Add all file path parameters for the pipeline to the list below
  • 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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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_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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

✅ Tests passed:

Run details

  • nf-core/tools version 2.3
  • Run at 2022-03-18 10:06:30

jfy133
jfy133 approved these changes Mar 18, 2022
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Reviewed from my phone because I locked up my laptop with the new test data, but LGTM

@ljmesi ljmesi marked this pull request as ready for review March 18, 2022 11:14
@jfy133 jfy133 merged commit 45428c2 into nf-core:dev Mar 18, 2022
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YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install yamllint
  • Fix the markdown errors
    • Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml
    • Fix any reported errors in your YAML files

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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@jfy133 jfy133 jfy133 approved these changes

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Taxprofiler can take Nanopore reads (fastq.gz) as input through sample sheet
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@ljmesi @jfy133