Commit 763610b4 authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Bugfix to snakemake workflow

parent 8354e946
......@@ -98,11 +98,13 @@ rule bismark:
gn='genome/Bisulfite_Genome'
output:
temp('data/bismark/raw/{sample}_trimmed_bismark_bt2.bam') ## CHECK BISMARK OUTPUT
params:
basename=expand('data/bismark/raw/{sample_short}_trimmed_bismark_bt2', sample_short=wildcards.sample)
singularity:
"docker://dmccarthy/embo-singlecellomics-methylation_2019-05_heidelberg:0.4"
shell:
'bismark --non_directional --genome genome -o data/bismark/raw '
'{input.fq}'
'--basename {params.basename} {input.fq}'
rule bismark_dedup:
......
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