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feat add drop AE #34

Merged
merged 9 commits into from
Aug 7, 2023
Merged

feat add drop AE #34

merged 9 commits into from
Aug 7, 2023

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Lucpen
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@Lucpen Lucpen commented Jul 28, 2023 •
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PR checklist

  • Add drop AE
  • 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
  • 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 Jul 28, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e2df270

+| ✅ 142 tests passed       |+
#| ❔ 139 tests were ignored |#
!| ❗  18 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 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 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 output.md: Write this documentation describing your workflow's output
  • 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 tomte.nf: Add all file path parameters for the pipeline to the list below
  • 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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-07 15:50:06

@Lucpen Lucpen marked this pull request as ready for review August 6, 2023 05:51
@Lucpen Lucpen requested a review from jemten August 6, 2023 13:44
@Lucpen Lucpen added the Ready for review Ready for review label Aug 6, 2023
@Lucpen Lucpen changed the title feat trial add drop AE feat add drop AE Aug 7, 2023
jemten
jemten approved these changes Aug 7, 2023
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Looks good

subworkflows/local/analyse_transcripts.nf Outdated Show resolved Hide resolved
modules/local/drop_config_runAE.nf Outdated
Comment on lines 5 to 14
//conda "bioconda::drop=1.3.3"
//container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
// 'https://depot.galaxyproject.org/singularity/drop:1.3.3--pyhdfd78af_0' :
// 'biocontainers/drop:1.3.3--pyhdfd78af_0' }"

//containerOptions {
// (workflow.containerEngine == 'singularity') ?
// "--writable" :
// "--privileged"
// }
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Do we need this?

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Not for the time being, I will remove it and if we decide to go that way later on, add it once again

Lucpen and others added 2 commits August 7, 2023 17:42
@Lucpen @jemten
Update subworkflows/local/analyse_transcripts.nf
bdecbe8 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
fix remove commented part
e2df270
@Lucpen Lucpen merged commit f48060e into master Aug 7, 2023
7 checks passed
@Lucpen Lucpen deleted the add_AE_part2 branch August 7, 2023 16:48
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@jemten jemten jemten approved these changes

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@Lucpen @jemten