Align fastq files to a reference genome
ch_reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
Structure: [ val(meta), [ path(reads) ] ]
ch_aligner_index
Directory containing the aligner genome index files.
Structure: [ val(meta2), path(index) ]
ch_fasta
Reference genome in fasta format.
Structure: [ val(meta3), path(fasta) ]
*.{fa, fasta, fna}
aligner
Aligner to use for alignment
sort
sort output
bam
BAM file.
Structure: [ val(meta), path(bam) ]
*.bam
bam_index
BAM index (only produced by some aligners).
Structure: [ val(meta), path(bai/csi) ]
*.{bai, csi}
reports
Alignment report (currently only for dragmap).
Structure: [ val(meta), path(log) ]
