BAM files should be indexed. Run as indicated below. $ nextflow run tron-bioinformatics/tronflow-hla-hd --help N E X T F L O W ~ version 19.07.0 Launching `main.nf ...
This pipeline aligns paired and single end FASTQ files with BWA aln and mem algorithms and with BWA mem 2. For RNA-seq STAR is also supported. To increase sensitivity of novel junctions use --star_two ...
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