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Refactoring of code to remove it from main and more #213

Merged
merged 30 commits into from
Nov 15, 2024
Merged

Refactoring of code to remove it from main and more #213

merged 30 commits into from
Nov 15, 2024

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JoseEspinosa
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@JoseEspinosa JoseEspinosa commented Nov 14, 2024 •
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This PR contains:

  • Refactor main to move code to the post-processing subworkflow.
  • Change wave images pointing to oras to point to https.
  • Adapt modules to the nf-core folder structure.

Closes #183

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Nov 14, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 12e3525

+| ✅ 205 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-14 12:53:28

@JoseEspinosa JoseEspinosa marked this pull request as ready for review November 14, 2024 14:56
luisas
luisas approved these changes Nov 15, 2024
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LGTM - just left a minor comment!

modules/local/run_alphafold2_pred/main.nf
@@ -30,11 +30,11 @@ process RUN_ALPHAFOLD2_PRED {

output:
path ("${fasta.baseName}*")
tuple val(meta), path ("${meta.id}_alphafold2.pdb"), emit: main_pdb
tuple val(meta), path ("${meta.id}_alphafold2.pdb") , emit: top_ranked_pdb
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should we use here the prefix instead of meta id directly? So that the user could customize

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Good spot! However I am not sure if we are using it to create the reports, will check and if not will update in a new PR 😄

modules/local/run_alphafold2_pred/main.nf
@@ -30,11 +30,11 @@ process RUN_ALPHAFOLD2_PRED {

output:
path ("${fasta.baseName}*")
tuple val(meta), path ("${meta.id}_alphafold2.pdb"), emit: main_pdb
tuple val(meta), path ("${meta.id}_alphafold2.pdb") , emit: top_ranked_pdb
tuple val(meta), path ("${fasta.baseName}/ranked*pdb"), emit: pdb
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same here?

modules/local/run_alphafold2/main.nf
@@ -29,7 +29,7 @@ process RUN_ALPHAFOLD2 {

output:
path ("${fasta.baseName}*")
tuple val(meta), path ("${meta.id}_alphafold2.pdb"), emit: main_pdb
tuple val(meta), path ("${meta.id}_alphafold2.pdb") , emit: top_ranked_pdb
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same

@JoseEspinosa JoseEspinosa merged commit 19ed119 into nf-core:dev Nov 15, 2024
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@luisas luisas luisas approved these changes

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@JoseEspinosa @luisas