Commit 333a02ca authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Updating Snakefile

parent 42f4e382
......@@ -23,12 +23,14 @@ if TEST:
SAMPLES = [w.replace('.fastq.gz', '') for w in SAMPLES]
SAMPLES_LONG = [os.path.basename(w).replace('.fastq.gz', '') for w in SAMPLES_LONG]
SAMPLES_MERGE = [w.replace('_R1', '').replace('_R2', '') for w in SAMPLES]
list(set(SAMPLES_MERGE))
else:
SAMPLES_LONG = glob.glob('data/fastq/*.fastq.gz')
SAMPLES = [w.replace('lane[123]+_', '') for w in SAMPLES_LONG]
SAMPLES = [w.replace('_[ATCG]+_.*.fastq.gz', '') for w in SAMPLES]
SAMPLES_LONG = [os.path.basename(w).replace('.fastq.gz', '') for w in SAMPLES_LONG]
SAMPLES_MERGE = [w.replace('_R1', '').replace('_R2', '') for w in SAMPLES]
SAMPLES_MERGE = list(set(SAMPLES_MERGE))
fastqc_html_reports = expand('reports/fastqc/{sample}_fastqc.html', sample = SAMPLES_LONG)
......
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