subworkflows/fastq_align_bwaaln

Align FASTQ files against reference genome with the bwa aln short-read aligner producing a sorted and indexed BAM files

bwaalnfastabwaalignmap

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

Description

Align FASTQ files against reference genome with the bwa aln short-read aligner producing a sorted and indexed BAM files

Input

Name (Type)

Description

Pattern

`ch_reads`

Structure: [ val(meta), path(fastq) ]
One or two FASTQ files for single or paired end data respectively.
Note: the subworkflow adds a new meta ID meta.id_index that must
be used in prefix to ensure unique file names. See the associated
nextflow.config file.

`ch_index`

Structure: [ val(meta), path(index) ]
A directory containing bwa aln reference indices as from bwa index
Contains files ending in extensions such as .amb, .ann, .bwt etc.

Output

Name (Type)

Description

Pattern

`bam`

Structure: [ val(meta), path(bam) ]
Sorted BAM/CRAM/SAM file
Note: the subworkflow adds a new meta ID meta.id_index that must
be used in prefix to ensure unique file names. See the associated
nextflow.config file.

`bai`

Structure: [ val(meta), path(bai) ]
BAM/CRAM/SAM samtools index file

`csi`

Structure: [ val(meta), path(csi) ]
BAM/CRAM/SAM samtools index file for larger references

`versions`

Files containing software versions
Structure: [ path(versions.yml) ]

subworkflows/fastq_align_bwaaln

Description

Input

`ch_reads`

`ch_index`

Output

`bam`

`bai`

`csi`

`versions`

included in

included modules and subworkflows

maintainer

get in touch