Commit 595d0c7a authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Fixing bugs in Snakefile

parent 3d503651
......@@ -62,6 +62,8 @@ rule trim_fastq:
txt='data/fastq/{sample}.fastq.gz_trimming_report.txt'
log:
"logs/trim_fastq/{sample}.log"
singularity:
"docker://dmccarthy/embo-singlecellomics-methylation_2019-05_heidelberg:0.4"
shell:
'trim_galore --gzip --non_directional --rrbs '
'{input} '
......@@ -77,7 +79,7 @@ rule fastqc_reports_trimmed:
singularity:
"docker://dmccarthy/embo-singlecellomics-methylation_2019-05_heidelberg:0.4"
shell:
'/Users/davis/src/FastQC.app/Contents/MacOS/fastqc -o {params.output_dir} {input}'
'fastqc -o {params.output_dir} {input}'
rule bismark_prepare_genome:
......
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