-
Notifications
You must be signed in to change notification settings - Fork 0
/
config.yaml
35 lines (30 loc) · 1.29 KB
/
config.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
30
31
32
33
34
35
# Coverage analysis of DNASeq data
# Input reads must be paired-end and must end with "_R1.fastq.gz" or "_R2.fastq.gz"
# Input directory of all fastq.gz files
fastq_input_dir: "input/fastq_files"
# Base pair resolution used for coverage bar charts. Charts for all resolutions will be created
coverage_resolutions: [1000, 100000]
# Coverage analysis will be applied on all references in this list
references:
xylella:
genome: "reference/GCF_000007245.1_ASM724v1_genomic.fna"
annotation: "reference/GCF_000007245.1_ASM724v1_genomic.gff"
gff_features: ["gene", "CDS", "rRNA", "tRNA"]
bradyrhizobium:
genome: "reference/contamination/GCF_002831585.1_ASM283158v1_genomic.fna"
annotation: "reference/contamination/GCF_002831585.1_genomic.gff"
gff_features: ["CDS", "rRNA", "tRNA"]
variovorax:
genome: "reference/contamination/GCF_033807855.1_ASM3380785v1_genomic.fna"
annotation: "reference/contamination/GCF_033807855.1_genomic.gff"
gff_features: ["CDS"]
# Will only be used in when using Snakemake on computing cluster or when using limited memory settings (--resources mem_mb=<max_ram_usage_in_mb>)
memory_usage_in_mb:
fastp: 3000
sortmerna: 5000
bowtie2_index: 1500
bowtie2_mapping: 2000
samtools_sort: 3000
featureCounts: 1000
bedgraph_coverage: 1000
sushi: 2000