Commit 1723beab authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Updating Snakefile

parent 72293a69
......@@ -23,6 +23,8 @@ SAMPLES_LONG = [os.path.basename(w).replace('.fastq.gz', '') for w in SAMPLES_LO
SAMPLES_MERGE = [w.replace('_R1', '').replace('_R2', '') for w in SAMPLES]
SAMPLES_MERGE = list(set(SAMPLES_MERGE))
SAMPLES_DICT = dict(zip(SAMPLES, SAMPLES_LONG))
print(SAMPLES)
print(SAMPLES_LONG)
......@@ -50,10 +52,10 @@ rule fastqc_reports:
rule trim_fastq:
input:
'data/fastq/{sample}.fastq.gz'
lambda wildcards: expand('data/fastq/{sample_long}.fastq.gz', sample_long=SAMPLES_DICT[wildcards.sample])
output:
temp('{sample}_trimmed.fq.gz'),
temp('{sample}.fastq.gz_trimming_report.txt')
fq='data/fastq/{sample}_trimmed.fq.gz',
txt='data/fastq/{sample}.fastq.gz_trimming_report.txt'
log:
"logs/trim_fastq/{sample}.log"
shell:
......@@ -63,7 +65,7 @@ rule trim_fastq:
rule fastqc_reports_trimmed:
input:
'{sample}_trimmed.fq.gz'
'data/fastq/{sample}_trimmed.fq.gz'
output:
temp('reports/fastqc/{sample}_trimmed_fastqc.html')
params:
......@@ -87,7 +89,7 @@ rule bismark_prepare_genome:
rule bismark:
input:
'{sample}_trimmed.fq.gz',
'data/fastq/{sample}_trimmed.fq.gz',
'genome/Bisulfite_Genome'
output:
temp('data/bismark/raw/{sample}_trimmed_bismark_bt2.bam') ## CHECK BISMARK OUTPUT
......
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