no temp filtered fasta

metagenome-atlas · Jul 28, 2023 · cf805d9 · cf805d9
1 parent f866e84
commit cf805d9
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git 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
@@ -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",