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target-DNAseq/config/default.yml
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# | |
# The action section | |
# | |
# clean - whether or not to skip the prinseq cleaning step (see below). | |
# snv - whether or not to perform SNV analysis. | |
# cnv - whether or not to perform CNV analysis. | |
# container - whether or not to create a RDS container. | |
# | |
action: | |
clean: True | |
snv: True | |
cnv: True | |
container: True | |
# | |
# The samplesheet section | |
# | |
# file - The path to the SampleSheet text file. Set to None if no samplesheet is available | |
# index - The name of the Column that should be used as index | |
# case - The name of the Column containing the case identifier to which the index belongs to | |
# | |
samplesheet: | |
file: 'SampleSheet.txt' | |
index: 'Sample' | |
case: 'Case' | |
# | |
# The data section | |
# | |
# Contains named dictionaries with input sequencing files: | |
# r1 - The fastq file containing R1. | |
# r2 - The fastq file containing R2. | |
# | |
data: | |
sample1: | |
r1: '' | |
r2: '' | |
# | |
# The reference section | |
# | |
# URL - The URL from where the reference genome can be downloaded. Wildcards are allowed in curly brackets | |
# organism - Wildcard for the reference organism | |
# release - Wildcard for the reference release | |
# file - Wildcard(s) for the reference files that should be merged into the final reference transcriptome | |
# target - The path to a bed file with coordinates of the target regions | |
# | |
reference: | |
annotation_URL: 'ftp.ebi.ac.uk/pub/databases/gencode/Gencode_{organism}/release_{release}/gencode.v{release}.{file}.fa.gz' | |
genome_URL: 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_{organism}/release_{release}/{assembly}.primary_assembly.genome.fa.gz' | |
organism: 'mouse' | |
release: 'M17' | |
assembly: 'GRCm38' | |
file: | |
- basic_annotation | |
target: 'path/to/target_regions.bed' | |
# | |
# The directory section | |
# | |
# ref - directory name for reference files | |
# fastq - directory name for fastq files | |
# bam - directory name for STAR alignments | |
# cnv - directory name for Copy Number Variation analysis | |
# snv - directory name for Sequence Nucleotide Variation analysis | |
# tables - directory name for aggregated tables | |
# log - directory name for program logs | |
# R - directory name for Rdata objects | |
# | |
dirs: | |
ref: 'ref' | |
fastq: 'fastq' | |
bam: 'bam' | |
cnv: 'cnv' | |
snv: 'snv' | |
tables: 'tables' | |
log: 'log' | |
R: 'rds' | |
# | |
# The debug section | |
# | |
debug: False |