Issue 106 #114
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Issue 106 #114
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@apeltzer @atrigila We wont be migrating these modules to nf-core for now, as I was told they weren't good candidates since they aren't based on a tool but on a single script which is only hosted in the pipeline. |
atrigila
reviewed
Nov 28, 2024
| @@ -21,7 +21,7 @@ process COMPUTE_GENE_SCORES { | |||
| def args = task.ext.args ?: '' | |||
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| """ | |||
| compute_gene_scores.R $geneset_yaml $counts $args | |||
| compute_gene_scores.R $gene_score_yaml $normalized_counts $args | |||
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Something like this can make it easier to read in the log :)
Suggested change
| compute_gene_scores.R $gene_score_yaml $normalized_counts $args | |
| compute_gene_scores.R \\ | |
| $gene_score_yaml \\ | |
| $args \\ | |
| $normalized_counts |
| @@ -20,7 +19,7 @@ process CREATE_GENE_HEATMAP { | |||
| def args = task.ext.args ?: '' | |||
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| """ | |||
| compute_gene_heatmap.R $annotated_counts $counts $heatmap_genes_to_filter $args | |||
| compute_gene_heatmap.R $annotated_endo_data $normalized_counts $heatmap_genes_to_filter $args | |||
There was a problem hiding this comment.
Something like this can make it easier to read in the log :)
Suggested change
| compute_gene_heatmap.R $annotated_endo_data $normalized_counts $heatmap_genes_to_filter $args | |
| compute_gene_heatmap.R \\ | |
| $annotated_endo_data \\ | |
| $normalized_counts \\ | |
| $args \\ | |
| $heatmap_genes_to_filter |
| // | ||
| // MODULE: Compute gene-count heatmap for MultiQC report based on annotated (ENDO) counts | ||
| // | ||
| if(!params.skip_heatmap){ |
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I think we can't have params inside subworkflows now. They should be only in the main workflow. There was a guideline somewhere written by Ben but I can't find it now.
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Makes sense, if this was an nf-core subworkflow this would be an issue. I don't think we will be migrating this subworkflow anytime soon, but since I already formatted it all, Ill do this too.
Closed
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@atrigila all set 😄 |
atrigila
approved these changes
Nov 28, 2024
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).