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biocorecrg / master_of_pores

Nextflow pipeline for analysis of direct RNA Nanopore reads
https://biocorecrg.github.io/master_of_pores/
MIT License
88 stars 16 forks source link

Can't select genome instead of transcriptome #115

Open melispyilmaz opened 1 year ago

melispyilmaz commented 1 year ago

Hi, When I try to run MOP2 with "genome" as the reference type instead of "transcriptome" it doesn't create results. But it seems to be running (with the reference genome I provide) using "transcriptome" as the ref_type it seems to be working. The log file doesn't state any errors, in fact, it doesn't provide any lines after:

----------------------CHECK TOOLS ----------------------------- basecalling : guppy

demultiplexing will be skipped mapping : minimap2 filtering : nanoq counting : nanocount discovery will be skipped

[-        ] process > flow1:GUPPY_BASECALL:baseCall           - [-        ] process > flow1:NANOQ_FILTER:filter               - [-        ] process > preprocess_flow:MinIONQC                - [-        ] process > preprocess_flow:MINIMAP2:map            - [-        ] process > preprocess_flow:SAMTOOLS_CAT:catAln     - [-        ] process > preprocess_flow:SAMTOOLS_SORT:sortAln   - [-        ] process > preprocess_flow:SAMTOOLS_INDEX:indexBam - [-        ] process > preprocess_flow:checkRef                -