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nascONT-seq-pipeline/example_config.yaml
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| --- | |
| ## 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" |