diff --git a/workflow/rules/novel.smk b/workflow/rules/novel.smk index 7bf8ec4..16182cb 100644 --- a/workflow/rules/novel.smk +++ b/workflow/rules/novel.smk @@ -263,22 +263,7 @@ rule mirdeep2_novel_p2_quantifier: mirna = join(workpath, "novel", "counts", "{sample}_novel_miRNA_expressed.tsv"), params: rname = "novel_quantifier", - fasta = config['references'][genome]['genome'], tmpdir = join(workpath, "novel", "counts", "{sample}"), - # Building miRDeep2 -t species option, - # To get a list of supported species names, - # please run the following command: - # $ miRDeep2.pl -u - # This is not a required option to miRDeep2 - # so if your organism is not on the list, then - # please set the "species" key in the following - # file, config/genome.json, to an empty string. - # This will ensure mirDeep2 is run without this - # option to avoid any errors associated with - # providing an invalid species name. - species_option = lambda _: "-t {0}".format( - config['references'][genome]['species'] - ) if config['references'][genome]['species'] else "", envmodules: config['tools']['bowtie'], container: config['images']['mir-seek'], threads: int(allocated("threads", "mirdeep2_novel_p2_quantifier", cluster)), @@ -299,7 +284,7 @@ rule mirdeep2_novel_p2_quantifier: -p {input.hairpin} \\ -m {input.mature} \\ -r {input.collapsed} \\ - -T {threads} {params.species_option} \\ + -T {threads} # Link novel expression results from # miRDeep2 timestamp directory