umi_tools/umi_tools_prepareforrsem

umi_tools

rsem

bam

sam

Description

Make the output from umi-tools dedup or group compatible with RSEM

Type

bash_script

License

MIT

Keywords

umi_tools

rsem

bam

sam

Links

Repository

Documentation

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bam"  
log: "$id.$key.log"  
error: "$id.$key.error"  
id: "run"  
publish_dir: "output/"  
EOM

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

Input

Name	Type & Properties	Description
--input -I --stdin	file required

Name

Type & Properties

--input

-I

--stdin

file

required

Output

Name	Type & Properties	Description
--output -S --stdout	file output
--log -L	file output	File with logging information [default = stdout].
--error -E	file output	File with error information [default = stderr].
--log2stderr	boolean_true	Send logging information to stderr [default = False].
--temp_dir	string	Directory for temporary files. If not set, the bash environmental variable TMPDIR is used.
--compresslevel	integer	Level of Gzip compression to use. Default (6) matchesGNU gzip rather than python gzip default (which is 9).

Name

Type & Properties

--output

-S

--stdout

file

output

--log

-L

file

output

--error

-E

file

output

--log2stderr

boolean_true

--temp_dir

string

--compresslevel

integer

Options

Name	Type & Properties	Description
--tags	string	Comma-seperated list of tags to transfer from read1 to read2 (Default: 'UG,BX')
--sam	boolean_true	Input and output SAM rather than BAM.
--timeit	string	Store timeing information in file [none].
--timeit_name	string	Name in timing file for this class of jobs [all].
--timeit_header	boolean_true	Add header for timing information [none].
--verbose -v	integer	Loglevel [1]. The higher, the more output.
--random_seed	integer	Random seed to initialize number generator with [none].

Name

Type & Properties

--tags

string

--sam

boolean_true

--timeit

string

--timeit_name

string

--timeit_header

boolean_true

--verbose

-v

integer

--random_seed

integer