Permalink
Cannot retrieve contributors at this time
Name already in use
A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
nascONT-seq-pipeline/example_config.yaml
Go to fileThis commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
executable file
36 lines (27 sloc)
851 Bytes
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
--- | |
## Pipeline-specific parameters | |
# samples with .fastq.gz extenssion must be placed in the RawData folder | |
sampleID: "example" | |
# kit and cell parameters | |
flowcell: FLO-MIN106 | |
kit: SQK-DCS109 | |
#threads | |
threads : 20 | |
#junction bonus | |
junc_bonus : 19 | |
#gap opening costs | |
gap_open_cost : 12 | |
#minimum MAPQ | |
MAPQ : 0 | |
#guppy | |
guppy: "/project/owlmayer/Applications/14_MinION/Guppy324/bin/guppy_basecaller" | |
#minimap2 | |
minimap2 : "/project/owlmayer/Applications/minimap2/./minimap2" | |
# hmmer folder, NOT THE APPLICATION | |
hmmer : "/project/owlmayer/Applications/hmmer-3.3/bin/" | |
#maskTypes | |
maskRrna : "/project/owlmayer/Applications/18_MinIon_cDNA/maskRrna.txt" | |
#maskTypes | |
maskRegions : "/project/owlmayer/Applications/18_MinIon_cDNA/maskRegion.txt" | |
#featureCounts | |
featureCounts : "/project/owlmayer/Applications/subread-2.0.0-Linux-x86_64/bin/./featureCounts" |