Description
Shuffles and groups reads in SAM/BAM/CRAM files together by their names.
Type
bash_script
License
MIT/Expat
Keywords
Contributors
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output"
working_reads: [ 10000 ]
compression: [ 1 ]
nb_tmp_files: [ 64 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.3.0 \
-main-script target/nextflow/samtools/samtools_collate/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--input | file required |
--reference | file |
Name | Type & Properties |
|---|---|
--output -o | file required output |
Name | Type & Properties |
|---|---|
--uncompressed -u | boolean_true |
--fast -f | boolean_true |
--working_reads -r | integer |
--compression -l | integer |
--nb_tmp_files -n | integer |
--tmp_prefix -T | string |
--no_pg | boolean_true |
--input_fmt_option | string |
--output_fmt | string |
--output_fmt_option | string |