phac-nml/iridanextexample2

Introduction

phac-nml/iridanextexample2 is an example pipeline for integration with IRIDA-Next. It is a successor to the original iridanextexample which replaces nf-validation with nf-schema

1. Read QC (FastQC)
2. Present QC for raw reads (MultiQC)

Usage

Input

First, prepare a samplesheet with your input data that looks as follows:

An example samplesheet, which follows the schema_input.json structure.

sample,fastq_1,fastq_2
SAMPLE1,sample1_R1.fastq.gz,sample1_R2.fastq.gz
SAMPLE2,sample2_R1.fastq.gz,sample2_R2.fastq.gz
SAMPLE3,sample1_R1.fastq.gz,

Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Validation of the samplesheet is performed by nf-schema validateParameters().

Running the pipeline

nextflow run phac-nml/iridanextexample2 \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Output for IRIDA-Next

Output from the pipeline is available in IRIDA-Next users based on the contents of the iridanext.output.json.gz. Files and metadata are passed to the json output file using the nf-iridanext plugin based on the iridanext.config.

Example:

{
    "files": {
        "global": [

        ],
        "samples": {
            "SAMPLE3": [
                {
                    "path": "fastqc/SAMPLE3_fastqc.html"
                }
            ],
            "SAMPLE2": [
                {
                    "path": "fastqc/SAMPLE2_2_fastqc.html"
                },
                {
                    "path": "fastqc/SAMPLE2_1_fastqc.html"
                }
            ],
            "SAMPLE1": [
                {
                    "path": "fastqc/SAMPLE1_2_fastqc.html"
                },
                {
                    "path": "fastqc/SAMPLE1_1_fastqc.html"
                }
            ]
        }
    },
    "metadata": {
        "samples": {
            "SAMPLE3": {
                "id": "SAMPLE3",
                "single_end": "true"
            },
            "SAMPLE2": {
                "id": "SAMPLE2",
                "single_end": "false"
            },
            "SAMPLE1": {
                "id": "SAMPLE1",
                "single_end": "false"
            }
        }
    }
}

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Legal

Copyright 2023 Government of Canada

Licensed under the MIT License (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

https://opensource.org/license/mit/

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.