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 runs all workflows
• modules/metatable.nf - a collection of processes that help getting IRODS metadata for samples listed in --findmeta <samples.csv> file
• modules/getfiles.nf - a collection of processes that help loading the data (.cram or .bam files) from IRODS and converting them to .fastq.gz files
• modules/upload2ftp.nf - a collection of processes that help uploading a list of .fastq.gz files to FTP server (specified in nextflow.config)
• nextflow.config - the configuration script that controls the cluster scheduler, process and container
• bin/parser.py - script that parses metadata from imeta ls output and saves it in .json format
• bin/combine_meta.py - script that combines all metadata in .json format and saves it to .tsv file
• examples/samples.csv - an example samples.csv file, contains one colum with sample names (no header is required)
• examples/run.sh - an example run script that executes the pipeline.

Pipeline Arguments

• --findmeta: specify a .csv file with sample names to run a metadata search
• --cram2fastq: if specified the script runs conversion of cram files that are found on findmeta step
• --meta: this argument spicifies the .tsv with cram files (potentially from findmeta step) to run cram2fastq conversion
• --publish_dir: path to put the output filess of the pipeline. (default 'results')
• --index_format: index-format formula for samtools, only if you really know what you're doing (default "i*i*")
• --toftp: upload the resulting files to the ArrayExpress FTP server (default false).
  • Use in combination with --ftp_credenials, --ftp_host and --ftp_path
• --fastqfiles: this argument spicifies the .fastq.gz files (potentially from cram2fastq step) to upload them to the ArrayExpress ftp server

Examples of use

1. Run a metadata search for a specified list of samples:

nextflow run main.nf --findmeta ./examples/samples.csv

2. Download cram files (specified in metadata.tsv) from IRODS and convert them to fastq

nextflow run main.nf --cram2fastq --meta metadata/metadata.tsv

3. Upload fastq files to ftp server (you to set up the ftp server in nextflow.config):

nextflow run main.nf --toftp --fastqfiles ./results/

4. Combine several steps to run them together

nextflow run main.nf --findmeta ./examples/samples.csv --cram2fastq --toftp

Graph

---
title: Nextflow pipeline for retrieving CRAM files stored in IRODS and convert them to FASTQ
---
flowchart TB
    subgraph findmeta["Find CRAM metadata"]
    direction LR
      v0([findCrams])
      v1([getMetadata])
      v2([parseMetadata])
      v3([combineMetadata])
    end
    subgraph downloadcrams["Covert CRAMS --> FASTQ"]
    direction LR
        v4([downloadCram])
        v5([cramToFastq])
        v6([calculateReadLength])
        v7([checkATAC])
        v8([renameATAC])
        v9([saveMetaToJson])
        v10([updateMetadata])
    end
    subgraph uploadtoftp["Upload data to FTP"]
    direction LR
      v11([concatFastqs])
      v12([uploadFTP])
    end
    v0 --> v1 --> v2 --> v3
    v4 --> v5 --> v6 --> v7{10X ATAC}
    v11 --> v12
    v7 --YES--> v8
    v8 --> v9
    v7 --NO--> v9
    v9 --> v10
    findmeta -.-> downloadcrams -.-> uploadtoftp

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