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fix(dram): pass boolean string to FORMAT_KEGG_DB skip_gene_ko_link
The companion fix for the bash condition in format_kegg_db.nf requires that skip_gene_ko_link be the string "true" or "false" rather than the integer 1 or 0. In bash: `if [ "0" ]` -> true (non-empty string) `if [ "false" ]` -> true (still non-empty - also wrong) The correct pattern used in format_kegg_db.nf is: `if [ "${skip_gene_ko_link}" = "true" ]` which requires this value to be exactly the string "true" or "false". Changed `params.skip_gene_ko_link ? 1 : 0` to `params.skip_gene_ko_link ? "true" : "false"`.
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workflows/dram.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -203,7 +203,7 @@ workflow DRAM {
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gene_ko_link_f = params.gene_ko_link_loc && file(params.gene_ko_link_loc).exists() ? file(params.gene_ko_link_loc) : default_sheet
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kegg_download_date = params.kegg_download_date ? params.kegg_download_date : "''"
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skip_gene_ko_link = params.skip_gene_ko_link ? 1 : 0
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skip_gene_ko_link = params.skip_gene_ko_link ? "true" : "false"
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FORMAT_KEGG_DB( kegg_pep_f, gene_ko_link_f, kegg_download_date, skip_gene_ko_link )
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} else if (params.merge_annotations){

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