cellgeni / 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)
• --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' (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)
• --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. (default false)
• --ftp_upload: Upload the resulting files to an FTP (default false).
  • Use in combination with --ftp_credenials, --ftp_host and --ftp_path.

Graph

---
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

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nf-irods-to-fastq's Issues

import default workflow from other pipelines

We'd find it very useful if the default workflow was named so it could be imported by other pipelines, also emitting fastqs.
Another default workflow can then call it so it can still be run without a defined entrypoint

nf-irods-to-fastq/main.nf

Line 306 in ec4d9bf

workflow {

Can make a PR for this if helpful

`enabled` option of cramToFastq doesn't work as expected

I've tried to modify enabled part as "${params.publish_fastqs} && ${!params.for_upload} == true" on my side, but it doesn't fix the issue even the expression should return true