Example Pipeline for IRIDA Next

This is an example pipeline to be used for integration with IRIDA Next.

Input

The input to the pipeline is a standard sample sheet (passed as --input samplesheet.csv) that looks like:

sample	fastq_1	fastq_2
SampleA	file_1.fastq.gz	file_2.fastq.gz

The structure of this file is defined in assets/schema_input.json. Validation of the sample sheet is performed by nf-validation.

Parameters

The main parameters are --input as defined above and --output for specifying the output results directory. You may wish to provide -profile singularity to specify the use of singularity containers and -r [branch] to specify which GitHub branch you would like to run.

Other parameters (defaults from nf-core) are defined in nextflow_schema.json.

Running

To run the pipeline, please do:

nextflow run phac-nml/fastmatch-in -profile singularity -r main -latest --input assets/samplesheet.csv --outdir results

Where the samplesheet.csv is structured as specified in the Input section.

Output

A JSON file for loading metadata into IRIDA Next is output by this pipeline. The format of this JSON file is specified in our Pipeline Standards for the IRIDA Next JSON. This JSON file is written directly within the --outdir provided to the pipeline with the name iridanext.output.json.gz (ex: [outdir]/iridanext.output.json.gz).

An example of the what the contents of the IRIDA Next JSON file looks like for this particular pipeline is as follows:

{
    "files": {
        "global": [
            {
                "path": "summary/summary.txt.gz"
            }
        ],
        "samples": {
            "SAMPLE1": [
                {
                    "path": "assembly/SAMPLE1.assembly.fa.gz"
                }
            ],
            "SAMPLE2": [
                {
                    "path": "assembly/SAMPLE2.assembly.fa.gz"
                }
            ],
            "SAMPLE3": [
                {
                    "path": "assembly/SAMPLE3.assembly.fa.gz"
                }
            ]
        }
    },
    "metadata": {
        "samples": {
            "SAMPLE1": {
                "reads.1": "sample1_R1.fastq.gz",
                "reads.2": "sample1_R2.fastq.gz"
            },
            "SAMPLE2": {
                "reads.1": "sample2_R1.fastq.gz",
                "reads.2": "sample2_R2.fastq.gz"
            },
            "SAMPLE3": {
                "reads.1": "sample1_R1.fastq.gz",
                "reads.2": "null"
            }
        }
    }
}

Within the files section of this JSON file, all of the output paths are relative to the outdir. Therefore, "path": "assembly/SAMPLE1.assembly.fa.gz" refers to a file located within outdir/assembly/SAMPLE1.assembly.fa.gz.

There is also a pipeline execution summary output file provided (specified in the above JSON as "global": [{"path":"summary/summary.txt.gz"}]). However, there is no formatting specification for this file.

Test profile

To run with the test profile, please do:

nextflow run phac-nml/fastmatch-in -profile docker,test -r main -latest --outdir results

Legal

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.