From cf805d9ec81a7e36bcf926f453fc7041ce7d39e3 Mon Sep 17 00:00:00 2001 From: Silas Kieser Date: Fri, 28 Jul 2023 14:32:11 +0200 Subject: [PATCH] no temp filtered fasta --- workflow/rules/cobinning.smk | 2 +- workflow/rules/semibin.smk | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/workflow/rules/cobinning.smk b/workflow/rules/cobinning.smk index 5dba9ab3..2c5f5fc0 100644 --- a/workflow/rules/cobinning.smk +++ b/workflow/rules/cobinning.smk @@ -10,7 +10,7 @@ rule filter_contigs: input: get_assembly, output: - temp("Intermediate/cobinning/filtered_contigs/{sample}.fasta"), + "Intermediate/cobinning/filtered_contigs/{sample}.fasta.gz", params: min_length=config["cobining_min_contig_length"], prefix= lambda wc: wc.sample+ config["cobinning_separator"] diff --git a/workflow/rules/semibin.smk b/workflow/rules/semibin.smk index 1780770e..761033c2 100644 --- a/workflow/rules/semibin.smk +++ b/workflow/rules/semibin.smk @@ -82,7 +82,6 @@ def semibin_input(wildcards): assert len(samples_of_bingroup) > 1 mapping = dict( - flag=get_assembly(wildcards), fasta=rules.filter_contigs.output[0].format(**wildcards), bams=expand( "Intermediate/cobinning/{bingroup}/bams/{sample}.sorted.bam",