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Hotfix for mm10 Kraken #58

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merged 2 commits into from
Dec 6, 2023
Merged

Hotfix for mm10 Kraken #58

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6d31557
Update mm10.biowulf.json
dnousome Oct 30, 2023
65d8b04
fix: ignore track and browser reformat
dnousome Nov 1, 2023
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2 changes: 1 addition & 1 deletion config/genomes/mm10.biowulf.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"references": {
"FASTQ_SCREEN_CONFIG": "resources/fastq_screen.biowulf.conf",
"KRAKENBACDB": "/data/CCBR_Pipeliner/Exome-seek/hg38/kraken/20180907_standard_kraken2",
"KRAKENBACDB": "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/kraken/20180907_standard_kraken2",
"trimmomatic.adapters": "resources/adapters.fa",
"SNPEFF_GENOME": "GRCm38.86",
"SNPEFF_CONFIG": "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/snpEff/4.3t/snpEff.config",
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2 changes: 1 addition & 1 deletion workflow/scripts/reformat_bed.py
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Expand Up @@ -29,7 +29,7 @@
### Step through each line of input
for line in inputFile:
### Skip comments
if not line.startswith("#"):
if not line.startswith("#") and not line.startswith("track") and not line.startswith("browser"):
curr_cols=line.strip().split("\t")
if (len(curr_cols) < 3):
sys.exit("Targets BED file must contain at least three columns: chr, start, end")
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