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Added compute_gene_scores nftest and standardized format of module #101

Merged
merged 4 commits into from
Nov 20, 2024
Merged

Added compute_gene_scores nftest and standardized format of module #101

merged 4 commits into from
Nov 20, 2024

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nschcolnicov
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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/nanostring 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 Nov 19, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 27d092f

+| ✅ 199 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-20 13:49:43

atrigila
atrigila requested changes Nov 19, 2024
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conf/test_scores.config Outdated
@@ -24,7 +24,7 @@ params {
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv'
gene_score_yaml = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/gene_score_test.yaml'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv'
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You can add the same params.pipelines_testdata_base_path here, like you did in the line after this one.

modules/local/compute_gene_scores/environment.yml Outdated
channels:
- conda-forge
- bioconda
- defaults
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defaults channel should be removed from the environment.yml.

See:
nf-core/modules#5829

modules/local/compute_gene_scores/environment.yml Outdated
@@ -0,0 +1,16 @@
name: compute_gene_scores
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name is also removed in the new nf-core environment.yml specification convention.

modules/local/compute_gene_scores/main.nf
@@ -1,7 +1,6 @@
process COMPUTE_GENE_SCORES {
label 'process_single'

conda "r-yaml=2.3.7 r-ggplot2=3.4.4 r-dplyr=1.1.4 r-stringr=1.5.0 bioconductor-gsva=1.46.0 bioconductor-singscore=1.18.0 r-factominer=2.8.0 r-tibble=3.2.1 r-matrixstats=1.1.0"
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You removed conda but you didn't add the environment.yml

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Please also test the nf-test with --profile conda

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I also tested with conda, and it worked for some reason, I'll update this

@nschcolnicov nschcolnicov merged commit b2e1d70 into dev Nov 20, 2024
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@atrigila atrigila atrigila approved these changes

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@nschcolnicov @atrigila