Commit aa37905b authored by van den Berg's avatar van den Berg
Browse files

Remove explicit path from params for linting

parent f1f323f5
......@@ -391,13 +391,11 @@ rule fastqc_raw:
input:
r1 = lambda wc: (config['samples'][wc.sample]['read_groups'][wc.read_group]['R1']),
r2 = lambda wc: (config['samples'][wc.sample]['read_groups'][wc.read_group]['R2']),
params:
folder = "{sample}/pre_process/raw-{sample}-{read_group}"
output:
done = "{sample}/pre_process/raw-{sample}-{read_group}/.done"
log: "log/{sample}/fastqc_raw.{read_group}.log"
container: containers["fastqc"]
shell: "fastqc --threads 4 --nogroup -o {params.folder} "
shell: "fastqc --threads 4 --nogroup -o $(dirname {output.done}) "
"{input.r1} {input.r2} 2> {log} && "
"touch {output.done}"
......@@ -406,13 +404,11 @@ rule fastqc_postqc:
input:
r1 = rules.cutadapt.output.r1,
r2 = rules.cutadapt.output.r2
params:
folder = "{sample}/pre_process/trimmed-{sample}-{read_group}"
output:
done = "{sample}/pre_process/trimmed-{sample}-{read_group}/.done"
log: "log/{sample}/fastqc_postqc.{read_group}.log"
container: containers["fastqc"]
shell: "fastqc --threads 4 --nogroup -o {params.folder} "
shell: "fastqc --threads 4 --nogroup -o $(dirname {output.done}) "
"{input.r1} {input.r2} 2> {log} && "
"touch {output.done}"
......@@ -492,7 +488,7 @@ rule multiple_metrics:
bam = rules.markdup.output.bam,
ref = config["reference"],
params:
prefix = "{sample}/bams/{sample}",
prefix = lambda wildcards, output: output.alignment[:-26]
output:
alignment = "{sample}/bams/{sample}.alignment_summary_metrics",
insertMetrics = "{sample}/bams/{sample}.insert_size_metrics"
......
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