fastq_align_dna

Align fastq files to a reference genome

fastqbamsortbwamembwamem2dragmapsnapaligner

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

Description

Align fastq files to a reference genome

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.

`meta2`

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

`index`

Aligner genome index files

Directory containing aligner index

`meta3`

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

`fasta`

Reference genome in fasta format

*.{fa, fasta, fna}

`aligner`

Aligner to use for alignment

`sort_bam`

sort output

Output

name

description

pattern

`meta`

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

`bam`

BAM file

*.bam

`bam_index`

BAM index (currently only for snapaligner)

*.{bai, csi}

`report`

Alignment report (currently only for dragmap)

*.txt

`versions`

File containing software versions

versions.yml