Description

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

Input

Name (Type)
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 (file)

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

val_mismatch_parameter (float)

bwa aln compatible allowed-mismatches parameter

val_double_stranded_library (boolean)

If true, --library is set to double_stranded

true|false

val_five_prime_overhang (float)

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

val_three_prime_overhang (float)

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

val_deam_rate_double_stranded (float)

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

val_deam_rate_single_stranded (float)

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

val_indel_rate (float)

-i parameter. Specifies the expected rate of InDels.

Output

Name (Type)
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) ]

included modules and subworkflows
mapad/map samtools/sort samtools/index samtools/stats samtools/idxstats samtools/flagstat bam_sort_stats_samtools
maintainer
Github user jch-13
get in touch
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