From 3b63e6b5ed3a6dd3392a53dbe922b5f6ed21022c Mon Sep 17 00:00:00 2001 From: Jakub Vasicek Date: Wed, 15 Jan 2025 14:20:33 +1100 Subject: [PATCH] bug fix - separator in input file --- Snakefile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Snakefile b/Snakefile index 6c1b401..aa33b6d 100644 --- a/Snakefile +++ b/Snakefile @@ -58,7 +58,7 @@ rule format_input: conda: "condaenv.yaml" shell: "mkdir -p data ; python src/format_input.py -i {input.pep} -f {input.fasta_file} -id {params.id_col} -sc {params.seq_col} " + - ("-s {params.sep} " if (config['sep'] != "\t") else "") + + ("-sep {params.sep} " if (config['sep'] != "\t") else "") + ("-pc {params.prot_col} " if (len(config['prot_col']) > 0) else "") + ("-pos {params.pos_col} " if (len(config['pos_col']) > 0) else "") + "-t {params.max_cores} -removed {output.log} -o {output.pep}" @@ -102,6 +102,7 @@ rule join_output: conda: "condaenv.yaml" shell: "python src/join_reports.py -orig {input.orig} -annot {input.annot} -id {params.id_col} " + + ("-sep {params.sep} " if (config['sep'] != "\t") else "") + ("-pc {params.prot_col} " if (len(config['prot_col']) > 0) else "") + ("-pos {params.pos_col} " if (len(config['pos_col']) > 0) else "") + "-o {output}" \ No newline at end of file