Commit 8354e946 authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Bugfix to snakemake workflow

parent f56d8719
......@@ -29,8 +29,7 @@ SAMPLES_MERGE = list(set(SAMPLES_MERGE))
SAMPLES_DICT = dict(zip(SAMPLES, SAMPLES_LONG))
print(SAMPLES)
print(SAMPLES_LONG)
print(SAMPLES_DICT)
fastqc_html_reports = expand('reports/fastqc/{sample}_fastqc.html', sample = SAMPLES_LONG)
......@@ -133,8 +132,8 @@ rule multiqc:
input:
fastqc_html_reports,
expand('data/bismark/methyl/{sample}_trimmed_bismark_bt2.deduplicated.bismark.cov.gz', sample = SAMPLES),
expand('data/fastq/{sample}_trimmed.fq.gz', sample = SAMPLES),
expand('data/fastq/{sample}.fastq.gz_trimming_report.txt', sample = SAMPLES)
expand('data/fastq/{sample}_trimmed.fq.gz', sample = SAMPLES_LONG),
expand('data/fastq/{sample}.fastq.gz_trimming_report.txt', sample = SAMPLES_LONG)
output:
'reports/multiqc/multiqc_report.html'
singularity:
......
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