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lbeltrame
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Feb 27, 2026
| cat("Reading:", input_file, "\n") | ||
| df <- read_tsv(input_file, show_col_types = FALSE) | ||
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| colnames(df) <- c("Sample", "Chromosome", "Start", "End", "Num_Probes", "Segment_Mean") |
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Can you pass the column names directly to read_tsv?
| genomeSize_fga = args$genomeSize_fga | ||
| ) | ||
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| metrics$tai[is.na(metrics$tai)] <- 0 |
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What is this? A data.frame? This is really nit-picking, but if it is so, let's use either tidyverse syntax or the other, not both.
| } | ||
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| // Run CINmetrics if specified | ||
| if (params.compute_cinmetrics) { |
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You use ext.when, so this check is unnecessary.
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Description
This PR integrates the R package CINmetrics in samurai. This addition enables the automated calculation of various Chromosomal Instability (CIN) metrics, providing standardized genomic instability scores directly within the workflow.
PR checklist
nf-core pipelines 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).