retrieve_mapped¶
Purpose¶
This component retrieves the mapping reads of a previous bowtie mapping process. The procedure is carried out with samtools and aims to retrieve the reads that map to target reference.
Note
- samtools documentation can be found here.
Input/Output type¶
- Input type:
bam
- Output type:
FastQ
Note
This process has the bowtie2
process as a dependency.
Parameters¶
None
Published results¶
results/mapping/retrieve_mapped
: Contains the resultingFastQ
files.
Published reports¶
None.
Default directives¶
remove_host
:cpus
: 2memory
: 5GB (dynamically increased on retry)container
: flowcraft/bowtie2_samtoolsversion
: 1.0.0-1