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Allow prefix in config file #13

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Allow prefix in config file #13

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0d2b481
Allow prefix in config file
endrebak Dec 5, 2019
b36164d
Update config with example prefix
endrebak Dec 5, 2019
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19 changes: 10 additions & 9 deletions Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -19,19 +19,20 @@ def get_region(wildcards):

rule all:
input:
expand("methylation_frequency/{region}_{sample}.tsv",
expand("{prefix}methylation_frequency/{region}_{sample}.tsv",
sample=config["fastq"],
region=config["region"])
region=config["region"],
prefix=config.get("prefix", ""))

rule nanopolish_index:
input:
f5 = get_fast5,
fq = get_fastq,
output:
"indices/index_done_{sample}"
"{prefix}indices/index_done_{sample}"
threads: 10 # Just to ensure that this is not ran in parallel for too many samples
log:
"logs/nanopolish_index/index_{sample}.log"
"{prefix}logs/nanopolish_index/index_{sample}.log"
shell:
"""
nanopolish index -d {input.f5}/ {input.fq} 2> {log}
Expand All @@ -45,12 +46,12 @@ rule call_methylation:
bam = get_bam,
genome = config["genome"],
output:
"methylation_calls/{region}_{sample}.tsv"
"{prefix}methylation_calls/{region}_{sample}.tsv"
threads: 8
params:
region = get_region,
log:
"logs/methylation/methcall_{region}_{sample}.log"
"{prefix}logs/methylation/methcall_{region}_{sample}.log"
shell:
"""
nanopolish call-methylation \
Expand All @@ -63,11 +64,11 @@ rule call_methylation:

rule methylation_frequency:
input:
"methylation_calls/{region}_{sample}.tsv"
"{prefix}methylation_calls/{region}_{sample}.tsv"
output:
"methylation_frequency/{region}_{sample}.tsv"
"{prefix}methylation_frequency/{region}_{sample}.tsv"
log:
"logs/methylation/methfreq_{region}_{sample}.log"
"{prefix}logs/methylation/methfreq_{region}_{sample}.log"
params:
script = os.path.join(workflow.basedir, "scripts/calculate_methylation_frequency.py")
shell:
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3 changes: 3 additions & 0 deletions config_example.yaml
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Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
prefix:
"analysis_name" # or /path/where/you/want/the/results

genome:
/path/to/database/genome.fa.gz

Expand Down