Commit 54377996 authored by van den Berg's avatar van den Berg
Browse files

Add tests for refFlat file

parent 7da15fdb
......@@ -120,8 +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 = expand("{sample}/coverage/{ref}.coverages.tsv",
sample=settings['samples'], ref=settings['refflat'])
coverage_stats = tuple(expand("{sample}/refFlat_coverage.tsv", sample=settings['samples']))
else:
coverage_stats = tuple()
stats = "stats.json",
......@@ -505,7 +504,7 @@ rule vtools_coverage:
tbi = "{sample}/vcf/{sample}.g.vcf.gz.tbi",
ref = settings.get('refflat', "")
output:
tsv="{sample}/coverage/{ref}.coverages.tsv"
tsv="{sample}/refFlat_coverage.tsv"
singularity: containers["vtools"]
shell: "vtools-gcoverage -I {input.gvcf} -R {input.ref} > {output.tsv}"
......
......@@ -103,3 +103,27 @@
should_exist: false
- path: "micro/vcf/micro.0.vcf.gz.tbi"
should_exist: false
- name: test-integration-refflat
tags:
- integration
command: >
snakemake
--use-singularity
--singularity-prefix /tmp/singularity
--singularity-args ' --cleanenv --bind /tmp'
--jobs 1 -w 120
-r -p -s Snakefile
--config
CONFIG_JSON=tests/data/config/sample_config_refflat.json
stderr:
contains:
- "Job counts"
- "localrule all:"
- "(100%) done"
must_not_contain:
- "rror"
files:
- path: "micro/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"
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment