Commit ae68936e authored by van den Berg's avatar van den Berg
Browse files

Add localrules if rules take less then 5 seconds

parent 8a6c6da6
......@@ -25,6 +25,14 @@ include: "common.smk"
process_config()
localrules:
collectstats,
create_markdup_tmp,
cutadapt_summary,
merge_stats,
multiqc,
stats_tsv
rule all:
input:
multiqc = "multiqc_report/multiqc_report.html",
......@@ -331,7 +339,7 @@ rule vtools_coverage:
"vtools-gcoverage -I {input.gvcf} "
"-R {input.ref} > {output} 2> {log}"
rule collect_cutadapt_summary:
rule cutadapt_summary:
"""Colect cutadapt summary from each readgroup per sample """
input:
cutadapt = sample_cutadapt_files,
......@@ -339,7 +347,7 @@ rule collect_cutadapt_summary:
output:
"{sample}/cutadapt.json"
log:
"log/{sample}/collect_cutadapt_summary.log"
"log/{sample}/cutadapt_summary.log"
container:
containers["python3"]
shell:
......@@ -350,7 +358,7 @@ rule collectstats:
"""Collect all stats for a particular sample"""
input:
cov = rules.covstats.output.covj if "targetsfile" in config else [],
cutadapt = rules.collect_cutadapt_summary.output,
cutadapt = rules.cutadapt_summary.output,
colpy = config["collect_stats"]
output:
"{sample}/{sample}.stats.json"
......
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