fastq_align_hisat2

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

alignsortrnaseqgenomefastqbamsamcram

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fastq_align_hisat2

Description

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

Input

name

description

pattern

`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}

Output

name

description

pattern

`meta`

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

`bam`

Output BAM file containing read alignments

*.{bam}

`summary`

Alignment log

*.log

`fastq`

Optional output FASTQ file containing unaligned reads

.fastq.gz

`bam`

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

`bai`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`crai`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`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