mapping/samtools_sort

Description

Sort and (optionally) index alignments.

Reads are sorted by leftmost coordinates, or by read name when --sort_by_read_names is used.

An appropriate @HD-SO sort order header tag will be added or an existing one updated if necessary.

Note that to generate an index file (by specifying --output_bai), the default coordinate sort must be used.
Thus the --sort_by_read_names and --sort_by <TAG> options are incompatible with --output_bai.

Type

python_script

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_bam: "$id.$key.output_bam.bam"  
output_bai: "$id.$key.output_bai.bai"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.3 \  
  -main-script target/nextflow/mapping/samtools_sort/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required	Path to the SAM/BAM/CRAM files containing the mapped reads.

Name

Type & Properties

--input

file

required

Output

Name	Type & Properties	Description
--output_bam	file required output	Filename to output the counts to.
--output_bai	file output	BAI-format index for BAM file.
--output_format	string	The output format. By default, samtools tries to select a format based on the -o filename extension; if output is to standard output or no format can be deduced, bam is selected.
--compression	integer	Compression level, from 0 (uncompressed) to 9 (best

Name

Type & Properties

--output_bam

file

required

output

--output_bai

file

output

--output_format

string

--compression

integer

Arguments

Name	Type & Properties	Description
--minimizer_cluster	boolean_true	Sort unmapped reads (those in chromosome "*") by their sequence minimiser (Schleimer et al., 2003; Roberts et al., 2004), also reverse complementing as appropriate. This has the effect of collating some similar data together, improving the compressibility of the unmapped sequence. The minimiser kmer size is adjusted using the -K option. Note data compressed in this manner may need to be name collated prior to conversion back to fastq. Mapped sequences are sorted by chromosome and position.
--minimizer_kmer	integer	Sets the kmer size to be used in the -M option.
--sort_by_read_names	boolean_true	Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates.
--sort_by	string	Sort first by this value in the alignment tag, then by position or name (if also using -n).
--no_pg	boolean_true	Do not add a @PG line to the header of the output file.

Name

Type & Properties

--minimizer_cluster

boolean_true

--minimizer_kmer

integer

--sort_by_read_names

boolean_true

--sort_by

string

--no_pg

boolean_true