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Merge branch 'master' into ct-rework-trinity-prep
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tomkinsc committed Aug 10, 2016
2 parents 362d55e + 930999a commit 6d4d4d5
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Showing 2 changed files with 4 additions and 1 deletion.
4 changes: 3 additions & 1 deletion pipes/rules/reports.rules
Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,10 @@ rule fastqc_report:
makedirs(config["reports_dir"])
shutil.rmtree(output[0], ignore_errors=True)
makedirs(os.path.join(config["reports_dir"], 'fastqc'))
shell("/idi/sabeti-scratch/kandersen/bin/fastqc/fastqc -f bam {input} -o {config[reports_dir]}/fastqc")
shell("fastqc -f bam {input} -o {config[reports_dir]}/fastqc")
shell("unzip {config[reports_dir]}/fastqc/{wildcards.sample}_fastqc.zip -d {config[reports_dir]}/fastqc")
os.unlink(output[0]+'.zip')
os.unlink(output[0]+'.html')

rule consolidate_fastqc:
input:
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1 change: 1 addition & 0 deletions requirements-conda.txt
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ diamond=0.7.10=boost1.60_1
kraken-all=0.10.6_eaf8fb68
krona=2.7
last=719
fastqc=0.11.5
mafft=7.221
mummer=3.23
muscle=3.8.1551
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