Description

Align reads to a reference genome using hisat2 then sort with samtools

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

index (file)

HISAT2 genome index file

*.ht2

splicesites (file)

Splices sites in gtf file

*.{txt}

fasta (file)

Reference genome fasta file

*.{fasta,fa}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

bam (file)

Output BAM file containing read alignments

*.{bam}

summary (file)

Aligment log

*.log

fastq (file)

Optional output FASTQ file containing unaligned reads

.fastq.gz

bam (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

bai (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

crai (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

stats (file)

File containing samtools stats output

*.{stats}

flagstat (file)

File containing samtools flagstat output

*.{flagstat}

idxstats (file)

File containing samtools idxstats output

*.{idxstats}

versions (file)

File containing software versions

versions.yml
included in
rnadnavar rnaseq
author
Github user priyanka-surana
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