Commit 6ba8b697 authored by Sander Bollen's avatar Sander Bollen
Browse files

add stats to tsv in pipeline

parent d74bc3be
......@@ -28,6 +28,7 @@ colpy = fsrc_dir("src", "collect_stats.py")
mpy = fsrc_dir("src", "merge_stats.py")
seq = fsrc_dir("src", "seqtk.sh")
fqpy = fsrc_dir("src", "fastqc_stats.py")
tsvpy = fsrc_dir("src", "stats_to_tsv.py")
if FASTQ_COUNT is None:
fqc = "python {0}".format(fsrc_dir("src", "fastq-count.py"))
......@@ -585,13 +586,24 @@ rule merge_stats:
shell: "python {input.mpy} --vcfstats {input.vstat} {input.cols} > {output.stats}"
rule stats_tsv:
"""Convert stats.json to tsv"""
input:
stats=out_path("stats.json"),
sc=tsvpy
output:
stats=out_path("stats.tsv")
conda: "envs/collectstats.yml"
shell: "python {input.sc} -i {input.stats} > {output.stats}"
rule multiqc:
"""
Create multiQC report
Depends on stats.json to forcefully run at end of pipeline
Depends on stats.tsv to forcefully run at end of pipeline
"""
input:
stats=out_path("stats.json")
stats=out_path("stats.tsv")
params:
odir=out_path("."),
rdir=out_path("multiqc_report")
......
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