-
Notifications
You must be signed in to change notification settings - Fork 0
/
config_Fibs.yaml
executable file
·29 lines (24 loc) · 1.44 KB
/
config_Fibs.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
# general settings
settings:
mapper: ["bwa"]
threads: 1
seqdir: "path to fibs fastqs"
resdir: "paths to output dir"
javaopts: "-Xmx5g -Djava.io.tmpdir=`pwd`/tmp"
# information on folder/file structure for the samples
sampleinfo:
file: "sampleinfo_fibs.csv"
outfmt: "{sample}{extension}"
mergefmt: "{experiment}/{sample}/{sample}"
# genome and other reference files, where symlinks will be created
ref:
genome: "indexfiles/human_g1k_v37_decoy.fasta"
mills: "indexfiles/Mills_and_1000G_gold_standard.indels.b37.vcf"
kgindels: "indexfiles/1000G_phase1.indels.b37.vcf"
bundle:
genome: "human_g1k_v37_decoy.fasta"
mills: "Mills_and_1000G_gold_standard.indels.b37.vcf"
kgindels: "1000G_phase1.indels.b37.vcf"
multiqc:
bwa_targets: [".reAligned.bwa.qualimap/genome_results.txt",".reAligned.bwa.qualimap/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt",".reAligned.bwa.qualimap/raw_data_qualimapReport/coverage_histogram.txt",".reAligned.bwa.qualimap/raw_data_qualimapReport/insert_size_histogram.txt",".merged.bwa.flagstat",".fixed.bwa.flagstat"]
bowtie2_targets: [".reAligned.bowtie2.qualimap/genome_results.txt",".reAligned.bowtie2.qualimap/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt",".reAligned.bowtie2.qualimap/raw_data_qualimapReport/coverage_histogram.txt",".reAligned.bowtie2.qualimap/raw_data_qualimapReport/insert_size_histogram.txt",".merged.bowtie2.flagstat",".fixed.bowtie2.flagstat"]