convert2bam.nf

This workflow is used to convert one or multiple files in the CRAM format to the BAM format (see here)

Dependencies

Samtools

Docker image

The best way of running this pipeline is by using the following Docker image: https://hub.docker.com/r/elowy01/samtools

Nextflow configuration file

The configuration file that can be used with this pipeline can be found here

Nextflow workflow

This workflow is implemented in the script named convert2bam.nf

Usage

nextflow -C convert2bam.config run convert2bam.nf --input '*.cram'

Parameters

--input

Used to specify the directory containing the CRAM files.
Note: The single quotes are necessary

Output

The BAM files resulting after converting the CRAM files can be found in a directory named:
converted_bam/