diff --git a/workflow/rules/altsplicing.smk b/workflow/rules/altsplicing.smk index 1071359..22bcc5a 100644 --- a/workflow/rules/altsplicing.smk +++ b/workflow/rules/altsplicing.smk @@ -9,9 +9,9 @@ rule spladder: log: "logs/{sample}/spladder/{group}_build.log" params: - confidence = "--confidence {config[altsplicing][confidence]}", - iteration = "--iterations {config[altsplicing][iterations]}", - edgelimit = "--ase-edge-limit {config[altsplicing][edgelimit]}", + confidence=f"""--confidence {config["altsplicing"]["confidence"]}""", + iteration=f"""--iterations {config["altsplicing"]["iterations"]}""", + edgelimit=f"""--ase-edge-limit {config["altsplicing"]["edgelimit"]}""" shell: """ spladder build -b {input.bam} \ @@ -23,7 +23,7 @@ rule spladder: {params.edgelimit} \ --qmode all > {log} 2>&1 """ - + rule splicing_to_vcf: input: "results/{sample}/rnaseq/altsplicing/spladder/{group}"