Precision Oncology data workflow
CADD downloads:
- wget -c https://krishna.gs.washington.edu/download/CADD/v1.5/GRCh38/whole_genome_SNVs.tsv.gz
- wget -c https://krishna.gs.washington.edu/download/CADD/v1.5/GRCh38/whole_genome_SNVs.tsv.gz.tbi
- wget -c https://krishna.gs.washington.edu/download/CADD/v1.5/GRCh38/InDels.tsv.gz
- wget -c https://krishna.gs.washington.edu/download/CADD/v1.5/GRCh38/InDels.tsv.gz.tbi
Manifest file:
$ cat manifest.tsv
tow19 tow19_normal 0 190719_A00421_0090_BHKNYWDMXX_S1 /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/bwa-nf/test-data/16239X1_190719_A00421_0090_BHKNYWDMXX_S1_L002_R1_001.fastq.gz /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/bwa-nf/test-data/16239X1_190719_A00421_0090_BHKNYWDMXX_S1_L002_R2_001.fastq.gz
tow19 tow19_tumor 1 190628_A00421_0082_AHKTTKDMXX_S19 /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/bwa-nf/test-data/16201X1_190628_A00421_0082_AHKTTKDMXX_S19_L001_R1_001.fastq.gz /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/bwa-nf/test-data/16201X1_190628_A00421_0082_AHKTTKDMXX_S19_L001_R2_001.fastq.gz
tow19 tow19_tumor 1 190628_A00421_0082_AHKTTKDMXX_S20 /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/bwa-nf/test-data/16201X2_190628_A00421_0082_AHKTTKDMXX_S20_L001_R1_001.fastq.gz /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/bwa-nf/test-data/16201X2_190628_A00421_0082_AHKTTKDMXX_S20_L001_R2_001.fastq.gz
Usage:
nextflow run main.nf -c nextflow.config -resume -profile redwood -qs 100 \
--project tow19 --manifest manifest.tsv \
--fasta /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/assets/broad_bundle_hg38/Homo_sapiens_assembly38.fasta \
--caddsnv /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/assets/GRCh38/cadd/whole_genome_SNVs.tsv.gz \
--caddindel /uufs/chpc.utah.edu/common/HIPAA/u6022494/work/assets/GRCh38/cadd/InDels.tsv.gz