Align reads to a reference genome using hisat2 then sort with samtools
meta
Groovy Map containing sample information e.g. [ id:‘test’ ]
reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
index
HISAT2 genome index file
*.ht2
splicesites
Splices sites in gtf file
*.{txt}
fasta
Reference genome fasta file
*.{fasta,fa}
bam
Output BAM file containing read alignments
*.{bam}
summary
Aligment log
*.log
fastq
Optional output FASTQ file containing unaligned reads
.fastq.gz
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
bai
BAM/CRAM/SAM index file
*.{bai,crai,sai}
crai
stats
File containing samtools stats output
*.{stats}
flagstat
File containing samtools flagstat output
*.{flagstat}
idxstats
File containing samtools idxstats output
*.{idxstats}
versions
File containing software versions
versions.yml
