Commit e1e83b13 authored by van den Berg's avatar van den Berg
Browse files

Move final functions to separate file

parent 9ab0debe
......@@ -32,19 +32,6 @@ include: "common.smk"
process_config()
def get_readgroup(wildcards):
return config["samples"][wildcards.sample]["read_groups"]
def get_readgroup_per_sample():
for sample in config["samples"]:
for rg in config["samples"][sample]["read_groups"]:
yield rg, sample
def coverage_stats(wildcards):
files = expand("{sample}/coverage/refFlat_coverage.tsv",
sample=config["samples"])
return files if "refflat" in config else []
rule all:
input:
multiqc = "multiqc_report/multiqc_report.html",
......@@ -447,8 +434,7 @@ rule multiqc:
rule merge_stats:
"""Merge all stats of all samples"""
input:
cols = expand("{sample}/{sample}.stats.json",
sample=config['samples']),
cols = expand("{sample}/{sample}.stats.json", sample=config['samples']),
mpy = config["merge_stats"],
insertSize = rules.multiqc.output.insertSize,
AlignmentMetrics = rules.multiqc.output.AlignmentMetrics,
......
......@@ -61,6 +61,12 @@ def process_config():
set_default('py_wordcount', srcdir('src/pywc.py'))
set_default('cutadapt_summary', srcdir('src/cutadapt_summary.py'))
def coverage_stats(wildcards):
files = expand("{sample}/coverage/refFlat_coverage.tsv",
sample=config["samples"])
return files if "refflat" in config else []
def coverage_files(wildcards):
""" Return a list of all coverage files
......
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