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config.yaml
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config.yaml
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## samples information and input files
# prefer to use complete path for all files
samples:
sample01:
lane01:
pe1: '/path/to/sample01_R1.fastq.gz'
pe2: '/path/to/sample01_R2.fastq.gz'
sample02:
lane01:
pe1: '/path/to/sample02_R1.fastq.gz'
pe2: '/path/to/sample02_R2.fastq.gz'
reference: '/path/to/reference.fasta'
# regions to be included in the final filtered bam file
regions: '/path/to/regions.bed'
## conda environment
# unless you'd like to run using your own environment, do not change this
environment: '../envs/fastq2bam.yml'
## threads for overall tasks and for plotting coverage using deeptools
threads: 8
threadsPlotCoverage: 24
## params for trimming reads using fastp
# if clip is true, overlaped paired reads wont be merged
fastpPar: '--cut_mean_quality 24 --cut_tail --trim_front1 10 --detect_adapter_for_pe --merge --dont_eval_duplication --length_required 50'
clip: True
## params for sambamba markdup
# --hash-table-size parameter, the ideal number is depth * insert size
markdupPar: '-r -p --hash-table-size 7000 --overflow-list-size 600000'
## params for samtools view (filtering)
samtoolsFiltPar: '-hb -q 30'