samtools/samtools_collate
collate
counts
bam
sam
cram
Description
Shuffles and groups reads in SAM/BAM/CRAM files together by their names.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | The input BAM file. |
--reference | file | Reference sequence FASTA FILE. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | The output filename. |
Options
Name | Type & Properties | Description |
|---|---|---|
--uncompressed -u | boolean_true | Output uncompressed BAM. |
--fast -f | boolean_true | Fast mode, only primary alignments. |
--working_reads -r | integer | Working reads stored (for use with -f). |
--compression -l | integer | Compression level. |
--nb_tmp_files -n | integer | Number of temporary files. |
--tmp_prefix -T | string | Write temporary files to PREFIX.nnnn.bam. |
--no_pg | boolean_true | Do not add a PG line. |
--input_fmt_option | string | Specify a single input file format option in the form of OPTION or OPTION=VALUE. |
--output_fmt | 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. |
Run this component
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 Relationships
Used by
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Current component
samtools/samtools_collatebiobox v0.3.0
Uses
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