vjbaskar / nf-irods-to-fastq

Get CRAMs from iRODS and convert them to fastq

nf-irods-to-fastq

This Nextflow pipeline pulls samples from iRODS and converts them to fastq files.

Contents of Repo:

• main.nf - the Nextflow pipeline that pulls the samples and converts them.
• nextflow.config - the configuration script that controls the cluster scheduler, process and container.
• examples/samples.csv - an example samples.csv file, contains one colum with sample names (header 'sample' is required).
• examples/run.sh - an example run script that executes the pipeline.

Pipeline Arguments:

• --meta = A metadata CSV with the sample IDs, and possibly other iRODS parameters. Header relevant, as specifies iRODS metadata field names (required)
• --type = Other potential arguments, though not mandatory. If ATAC, set this to 'ATAC' (default null)
• --index_format = index-format formula for samtools, only if you really know what you're doing (default "i*i*")
• --publish_fastqs = Whether to publish fastqs - other workflows using this may not want to (default true)
• --find_crams_only = For advanced CRAM list manipulation. Only return the found SAMPLE,CRAM list, e.g. for manual curation/manipulation (default false)
• --cram_list = Accept SAMPLE,CRAM list on input (default null)