From 4fd3fed98a3b61f945c46566b3d864a5617c7750 Mon Sep 17 00:00:00 2001 From: Mattias Date: Mon, 1 Oct 2018 16:26:22 +0200 Subject: [PATCH] Add ITS region conditional in config --- Snakefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Snakefile b/Snakefile index b1bf380..0817cfb 100644 --- a/Snakefile +++ b/Snakefile @@ -301,7 +301,7 @@ if config['its'] == True: input: fasta="{project}/mergepairs/{data}.fasta" output: - fasta=temporary("{project}/itsx/{data}.ITS2.fasta") + fasta="{project}/itsx/{data}.ITS1.fasta" if config['its_region'] == 'ITS1' else "{project}/itsx/{data}.ITS2.fasta" if config['its_region'] == 'ITS2' else "{project}/itsx/{data}.full.fasta" params: basename="{project}/itsx/{data}", dir="{project}/itsx" @@ -315,7 +315,7 @@ if config['its'] == True: # Combine per sample files to a single project file rule mergefiles: input: - fasta = expand(PROJECT + "itsx/{data}.ITS2.fasta", data=config["data"]) if config['its'] \ + fasta = expand(rules.extract_its.output, data=config["data"], project=config['project']) if config['its'] \ else expand(PROJECT + "mergepairs/{data}.fasta", data=config["data"]), output: fasta=temporary("{project}/mergefiles/{project}.fasta")