This Nextflow pipeline pulls samples from iRODS and converts them to FASTQ files.
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.
--meta
: A metadata CSV with the sample IDs, and possibly other iRODS parameters. Header relevant, as specifies iRODS metadata field names (required)--publish_dir
: Path to put the output filess of the pipeline. (default'results'
)--type
: Other potential arguments, though not mandatory. If ATAC, set this to 'ATAC' (defaultnull
)--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 (defaulttrue
)--find_crams_only
: For advanced CRAM list manipulation. Only return the found SAMPLE,CRAM list, e.g. for manual curation/manipulation (defaultfalse
)--cram_list
: Accept SAMPLE,CRAM list on input (defaultnull
)--merge
: Concatenate FASTQ files for samples with multiple lanes or sample numbers. Only one R1, R2 (and optionally R3) will be generated per each sample. (defaultfalse
)--ftp_upload
: Upload the resulting files to an FTP (defaultfalse
).- Use in combination with
--ftp_credenials
,--ftp_host
and--ftp_path
.
- Use in combination with
---
title: Nextflow pipeline for retrieving CRAM files stored in IRODS and convert them to FASTQ
---
flowchart LR
subgraph "find and pull CRAM files"
v0([findCrams])
v1([combineCramLists])
v2([downloadCram])
v3([renameCram])
end
v4(((cramToFastq)))
subgraph "optional steps"
v5([merge])
v6([uploadFTP])
end
v0 --> v1
v1 --> v2
v2 --> v3
v3 --> v4
v4 --> v5
v5 --> v6