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Remove duplicated code in cell type module #685

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Feb 5, 2024
Merged

Remove duplicated code in cell type module #685

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24 changes: 0 additions & 24 deletions modules/classify-celltypes.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -129,30 +129,6 @@ workflow annotate_celltypes {
take: sce_files_channel // channel of meta, unfiltered_sce, filtered_sce, processed_sce
main:

// read in sample metadata and make a list of cell line samples; these won't be cell typed
cell_line_samples = Channel.fromPath(params.sample_metafile)
.splitCsv(header: true, sep: '\t')
.map{
[
sample_id: it.scpca_sample_id,
is_cell_line: Utils.parseNA(it.is_cell_line).toBoolean() // FALSE -> false, NA -> false, TRUE -> true
]
}
.filter{it.is_cell_line}
.map{it.sample_id}
.toList()

// branch to cell type the non-cell line libraries only
sce_files_channel_branched = sce_files_channel
.branch{
cell_line: it[0]["sample_id"].split(",").collect{it in cell_line_samples.getVal()}.every()
// only run cell typing on tissue samples
tissue: true
}

// get just the meta and processed sce from the tissue (not cell line) samples
processed_sce_channel = sce_files_channel_branched.tissue.map{[it[0], it[3]]}

// read in sample metadata and make a list of cell line samples; these won't be cell typed
cell_line_samples = Channel.fromPath(params.sample_metafile)
.splitCsv(header: true, sep: '\t')
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