fastq_align_hisat2
Align reads to a reference genome using hisat2 then sort with samtools
alignsortrnaseqgenomefastqbamsamcram
Input
name
description
pattern
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
Structure: [ val(meta), [ path(reads) ] ]
Reference genome fasta file and its index.
Structure: [ val(meta), path(fasta), path(fai) ]
*.{fasta,fa,fai}Output
name
description
pattern
Unsorted BAM file containing read alignments straight from HISAT2.
Structure: [ val(meta), path(bam) ]
*.bamOptional output FASTQ files containing unaligned reads.
Structure: [ val(meta), [ path(fastq) ] ]
*.fastq.gzFile containing samtools flagstat output.
Structure: [ val(meta), path(flagstat) ]
*.flagstatincluded modules and subworkflows
maintainer
