fastq_create_umi_consensus_fgbio

This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads convert them to unmapped BAM file, map them to the reference genome, and finally use the mapped information to group UMIs and generate consensus reads in each group

fgbioumisamblastersamtoolsbwa

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

Description

Input

name

description

pattern

`meta`

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

`reads`

list umi-tagged reads

[ *.{fastq.gz/fq.gz} ]

`fasta_fai_dict`

The reference fasta file, index and dictionary

*.{fa,fasta,fna,fai,dict}

`bwa_index`

The reference genome bwa index files

*.{fa,fasta,fna,amb,ann,bwt,pac,sa}

`groupreadsbyumi_strategy`

Defines the UMI assignment strategy.

`aligner`

The aligner to use for mapping the reads to the reference genome. Options are bwa-mem and bwamem2.

`duplex`

Whether the library contains duplex UMIs.

`min_reads`

One integer (for non-duplex) or a string of up-to three space-separated numbers for duplex sequencing

`min_baseq`

Minimum base quality for bases to be considered in consensus calling.

`max_base_error_rate`

Maximum base error rate for consensus building

Output

name

description

pattern

`ubam`

unmapped bam file

*.bam

`groupbam`

mapped bam file, where reads are grouped by UMI tag

*.bam

`consensusbam`

mapped bam file, where reads are created as consensus of those
belonging to the same UMI group

*.bam

`mappedconsensusbam`

mapped bam file, where reads are created as consensus of those
belonging to the same UMI group and filtered for minimum base quality and maximum error rate

*.bam

fastq_create_umi_consensus_fgbio

Description

Input

`meta`

`reads`

`fasta_fai_dict`

`bwa_index`

`groupreadsbyumi_strategy`

`aligner`

`duplex`

`min_reads`

`min_baseq`

`max_base_error_rate`

Output

`ubam`

`groupbam`

`consensusbam`

`mappedconsensusbam`

included modules and subworkflows

maintainer

get in touch