bbmap/bbmap_bbsplit

Description

Split sequencing reads by mapping them to multiple references simultaneously.

Type

bash_script

License

Links

Repository

Documentation

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
index: "$id.$key.index.BBSplit_index"  
fastq_1: "$id.$key.fastq_1.fastq"  
fastq_2: "$id.$key.fastq_2.fastq"  
sam2bam: "$id.$key.sam2bam.sh"  
scafstats: "$id.$key.scafstats.txt"  
refstats: "$id.$key.refstats.txt"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.1 \  
  -main-script target/nextflow/bbmap/bbmap_bbsplit/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--id	string	Sample ID
--paired	boolean_true	Paired fastq files or not?
--input	file multiple	Input fastq files, either one or two (paired), separated by ";".
--ref	file multiple	Reference FASTA files, separated by ";". The primary reference should be specified first.
--only_build_index	boolean_true	If set, only builds the index. Otherwise, mapping is performed.
--build	file	Index to be used for mapping.
--qin	string	Set to 33 or 64 to specify input quality value ASCII offset. Automatically detected if not specified.
--interleaved	boolean_true	True forces paired/interleaved input; false forces single-ended mapping. If not specified, interleaved status will be autodetected from read names.
--maxindel	integer	Don't look for indels longer than this. Lower is faster. Set to >=100k for RNA-seq.
--minratio	double	Fraction of max alignment score required to keep a site. Higher is faster.
--minhits	integer	Minimum number of seed hits required for candidate sites. Higher is faster.
--ambiguous	string	Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations). * best Use the first best site (Default) * toss Consider unmapped * random Select one top-scoring site randomly * all Retain all top-scoring sites. Does not work yet with SAM output
--ambiguous2	string	Set behavior only for reads that map ambiguously to multiple different references. Normal 'ambiguous=' controls behavior on all ambiguous reads; Ambiguous2 excludes reads that map ambiguously within a single reference. * best Use the first best site (Default) * toss Consider unmapped * all Write a copy to the output for each reference to which it maps * split Write a copy to the AMBIGUOUS_ output for each reference to which it maps
--qtrim	string	Quality-trim ends to Q5 before mapping. Options are 'l' (left), 'r' (right), and 'lr' (both).
--untrim	boolean_true	Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings.

Name

Type & Properties

--id

string

--paired

boolean_true

--input

file

multiple

--ref

file

multiple

--only_build_index

boolean_true

--build

file

--qin

string

--interleaved

boolean_true

--maxindel

integer

--minratio

double

--minhits

integer

--ambiguous

string

--ambiguous2

string

--qtrim

string

--untrim

boolean_true

Output

Name	Type & Properties	Description
--index	file output	Location to write the index.
--fastq_1	file output	Output file for read 1.
--fastq_2	file output	Output file for read 2.
--sam2bam --bs	file output	Write a shell script to 'file' that will turn the sam output into a sorted, indexed bam file.
--scafstats	file output	Write statistics on how many reads mapped to which scaffold to this file.
--refstats	file output	Write statistics on how many reads were assigned to which reference to this file. Unmapped reads whose mate mapped to a reference are considered assigned and will be counted.
--nzo	boolean_true	Only print lines with nonzero coverage.
--bbmap_args	string	Additional arguments from BBMap to pass to BBSplit.

Name

Type & Properties

--index

file

output

--fastq_1

file

output

--fastq_2

file

output

--sam2bam

--bs

file

output

--scafstats

file

output

--refstats

file

output

--nzo

boolean_true

--bbmap_args

string