samtools/samtools_sort

sort

bam

sam

cram

Description

Sort SAM/BAM/CRAM file.

Type

bash_script

License

MIT/Expat

Keywords

sort

bam

sam

cram

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bam"  
compression: [ 0 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/samtools/samtools_sort/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	SAM/BAM/CRAM input file.

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Write final output to file.
--output_fmt -O	string	Specify output format (SAM, BAM, CRAM).
--output_fmt_option	string	Specify a single output file format option in the form of OPTION or OPTION=VALUE.
--reference	file	Reference sequence FASTA FILE.
--write_index	boolean_true	Automatically index the output files.
--prefix -T	string	Write temporary files to PREFIX.nnnn.bam.
--no_PG	boolean_true	Do not add a PG line.
--template_coordinate	boolean_true	Sort by template-coordinate.
--input_fmt_option	string	Specify a single input file format option in the form of OPTION or OPTION=VALUE.

Name

Type & Properties

--output

file

required

output

--output_fmt

-O

string

--output_fmt_option

string

--reference

file

--write_index

boolean_true

--prefix

-T

string

--no_PG

boolean_true

--template_coordinate

boolean_true

--input_fmt_option

string

Options

Name	Type & Properties	Description
--compression -l	integer	Set compression level, from 0 (uncompressed) to 9 (best).
--uncompressed -u	boolean_true	Output uncompressed data (equivalent to --compression 0).
--minimiser -M	boolean_true	Use minimiser for clustering unaligned/unplaced reads.
--not_reverse -R	boolean_true	Do not use reverse strand (only compatible with --minimiser)
--kmer_size -K	integer	Kmer size to use for minimiser.
--order -I	file	Order minimisers by their position in FILE FASTA.
--window -w	integer	Window size for minimiser INDEXING VIA --order REF.FA.
--homopolymers -H	boolean_true	Squash homopolymers when computing minimiser.
--natural_sort -n	boolean_true	Sort by read name (natural): cannot be used with samtools index.
--ascii_sort -N	boolean_true	Sort by read name (ASCII): cannot be used with samtools index.
--tag -t	string	Sort by value of TAG. Uses position as secondary index (or read name if --natural_sort is set).

Name

Type & Properties

--compression

-l

integer

--uncompressed

-u

boolean_true

--minimiser

-M

boolean_true

--not_reverse

-R

boolean_true

--kmer_size

-K

integer

--order

-I

file

--window

-w

integer

--homopolymers

-H

boolean_true

--natural_sort

-n

boolean_true

--ascii_sort

-N

boolean_true

--tag

-t

string