Commit 0102bc14 authored by van den Berg's avatar van den Berg
Browse files

Move refflat results to the coverage folder

parent 54377996
......@@ -120,7 +120,7 @@ def metrics(do_metrics=True):
fqcp = expand("{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R1_fastqc.zip",
sample=settings['samples']),
if "refflat" in settings:
coverage_stats = tuple(expand("{sample}/refFlat_coverage.tsv", sample=settings['samples']))
coverage_stats = tuple(expand("{sample}/coverage/refFlat_coverage.tsv", sample=settings['samples']))
else:
coverage_stats = tuple()
stats = "stats.json",
......@@ -504,7 +504,7 @@ rule vtools_coverage:
tbi = "{sample}/vcf/{sample}.g.vcf.gz.tbi",
ref = settings.get('refflat', "")
output:
tsv="{sample}/refFlat_coverage.tsv"
tsv="{sample}/coverage/refFlat_coverage.tsv"
singularity: containers["vtools"]
shell: "vtools-gcoverage -I {input.gvcf} -R {input.ref} > {output.tsv}"
......
......@@ -124,6 +124,6 @@
must_not_contain:
- "rror"
files:
- path: "micro/refFlat_coverage.tsv"
- path: "micro/coverage/refFlat_coverage.tsv"
contains:
- "1\tMIR12136\t133.0\t99.0\t133.0\t99.0\t100.0\t100.0\t100.0\t100.0\t100.0\t100.0\t100.0\t100.0\t100.0\t100.0\tNR_162149"
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