fastq_align_mapad

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

sortfastqbammapadalignmap

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

Description

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

Input

name

description

pattern

`ch_reads`

List of input FASTQ file
Structure: [ val(meta), path(reads) ]

`ch_index`

mapAD genome index files
Structure: [ val(meta), path(index) ]

`ch_fasta`

Reference fasta file
Structure: [ val(meta), path(fasta) ]

`val_mismatch_parameter`

bwa aln compatible allowed-mismatches parameter

`val_double_stranded_library`

If true, --library is set to double_stranded

true|false

`val_five_prime_overhang`

5’ overhang parameter (global overhang parameter
if val_double_stranded_library is set to true)

`val_three_prime_overhang`

3’ overhang parameter (ignored if
val_double_stranded_library is set to true)

`val_deam_rate_double_stranded`

-d parameter. Specifies the expected deamination
rate in double-stranded stems of the reads.

`val_deam_rate_single_stranded`

-s parameter. Specifies the expected deamination
rate in single-stranded overhangs of the reads.

`val_indel_rate`

-i parameter. Specifies the expected rate of InDels.

Output

name

description

pattern

`bam_unsorted`

BAM file produced by mapAD
Structure: [ val(meta), path(bam) ]

`bam`

BAM file sorted by samtools
Structure: [ val(meta), path(bam) ]

`bai`

BAI index of the sorted BAM file
Structure: [ val(meta), path(bai) ]

`csi`

CSI index of the sorted BAM file
Structure: [ val(meta), path(csi) ]

`stats`

File containing samtools stats output
Structure: [ val(meta), path(stats) ]

`flagstat`

File containing samtools flagstat output
Structure: [ val(meta), path(flagstat) ]

`idxstats`

File containing samtools idxstats output
Structure: [ val(meta), path(idxstats) ]

`versions`

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