From 3ac804285ab66dd31b064c085d69d72272842b3e Mon Sep 17 00:00:00 2001 From: Cedric Midoux <cedric.midoux@inra.fr> Date: Mon, 3 Feb 2020 14:35:12 +0100 Subject: [PATCH] checkm --- catalogue.smk | 6 +++--- global.smk | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/catalogue.smk b/catalogue.smk index 61c1289..7e67aa5 100644 --- a/catalogue.smk +++ b/catalogue.smk @@ -167,9 +167,9 @@ rule checkm: input: "work/metabat/{sample}/{sample}.unbinned.fa" output: - "work/checkm/{sample}/checkm.log" + "work/checkm/{sample}/lineage.ms" threads: - 8 + 4 params: input = lambda wildcards, input: os.path.dirname(str(input)), output = lambda wildcards, output: os.path.dirname(str(output)) @@ -180,7 +180,7 @@ rule checkm: "lineage_wf " "-t {threads} " "-x fa " - "{params.output} " "{params.input} " + "{params.output} " " ; " "conda deactivate" diff --git a/global.smk b/global.smk index 68c0b4a..03b1de5 100644 --- a/global.smk +++ b/global.smk @@ -17,6 +17,7 @@ rule all: "report/contigs_coassembly-taxNames.tsv", "report/genes_coassembly-taxNames.tsv", "work/metabat/coassembly.done", + "work/checkm/coassembly/lineage.ms", #catalogue "report/quast_results/report.html", expand("report/count-contigs-catalogue-{sample}.tsv", sample=config["SAMPLES"]), -- GitLab