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Add new modules #1

Merged
merged 7 commits into from
Nov 1, 2021
Merged

Add new modules #1

merged 7 commits into from
Nov 1, 2021

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daichengxin
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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/quantms 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).
  • 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 Oct 28, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit de8d3f1

+| ✅ 137 tests passed       |+
!| ❗  24 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • 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 nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 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 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 quantms.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in check_samplesheet.py: Update the script to check the samplesheet
  • pipeline_todos - TODO string in check_samplesheet.py: Update the check_samplesheet function
  • pipeline_todos - TODO string in check_samplesheet.py: Update the column names for the input samplesheet
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-01 07:45:30

@daichengxin daichengxin reopened this Oct 28, 2021
@daichengxin daichengxin changed the title Add sdrf and thermorawfileparser modules Add new modules Oct 30, 2021
@ypriverol ypriverol self-requested a review October 30, 2021 10:48
ypriverol
ypriverol requested changes Oct 30, 2021
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@ypriverol ypriverol requested a review from jpfeuffer October 30, 2021 17:31
@jpfeuffer
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Wow that was quick. Great work. I will need some time to go over everything.

@daichengxin
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I am also learning DSL2, and many codes may be optimized and corrected.

@ypriverol ypriverol self-requested a review October 31, 2021 11:39
@ypriverol ypriverol merged commit 9a8ca28 into bigbio:dev Nov 1, 2021
ypriverol pushed a commit that referenced this pull request Nov 13, 2021
@daichengxin
Merge pull request #1 from bigbio/dev
6988fbc 
u
jpfeuffer pushed a commit that referenced this pull request Mar 27, 2022
@daichengxin
Merge pull request #1 from bigbio/dev
bd2adf2 
pull
ypriverol pushed a commit that referenced this pull request Aug 3, 2022
@WangHong007
Merge pull request #1 from daichengxin/dev
b70e851 
pull fixed
ypriverol pushed a commit that referenced this pull request Sep 23, 2022
@fabianegli
Merge pull request #1 from fabianegli/debug-multi-command-failure
ef667b1 
split command on multiple lines
ypriverol added a commit that referenced this pull request Oct 27, 2023
@ypriverol
Merge pull request #1 from bigbio/dev
30708dc 
small changes.
@NikoHensley NikoHensley mentioned this pull request Oct 18, 2024
Open
ypriverol added a commit that referenced this pull request Oct 20, 2024
@ypriverol
Merge pull request #1 from daichengxin/dev
2274b60 
fixed version
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@ypriverol ypriverol ypriverol approved these changes

@jpfeuffer jpfeuffer Awaiting requested review from jpfeuffer

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@daichengxin @jpfeuffer @ypriverol