From 73b0563067f991ad737581dd7429d8254d27c869 Mon Sep 17 00:00:00 2001 From: Hayden Metsky Date: Tue, 27 Jun 2017 19:03:06 +0000 Subject: [PATCH] Add metagenomics rule to run only kraken --- pipes/rules/metagenomics.rules | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/pipes/rules/metagenomics.rules b/pipes/rules/metagenomics.rules index 874e82f85..555d7392c 100644 --- a/pipes/rules/metagenomics.rules +++ b/pipes/rules/metagenomics.rules @@ -19,6 +19,21 @@ rule all_metagenomics_host_depleted: "{sample}.cleaned.{method}.krona.html"), sample=samples, method=['kraken', 'rna_bwa']) params: LSF='-N' +rule all_kraken: + input: + expand(join(config["data_dir"], config["subdirs"]["metagenomics"], + "{sample}.raw.kraken.report"), sample=samples), + expand(join(config["data_dir"], config["subdirs"]["metagenomics"], + "{sample}.raw.kraken.krona.html"), sample=samples) + params: LSF='-N' + +rule all_kraken_host_depleted: + input: + expand(join(config["data_dir"], config["subdirs"]["metagenomics"], + "{sample}.cleaned.kraken.report"), sample=samples), + expand(join(config["data_dir"], config["subdirs"]["metagenomics"], + "{sample}.cleaned.kraken.krona.html"), sample=samples) + params: LSF='-N' method_props = { 'diamond': {