BCCDC-PHL / mlst-nf

The pipeline currently creates one output directory per sample and publishes all outputs there. eg:

    
           publishDir "${params.outdir}/${sample_id}", mode: 'copy', pattern: "${sample_id}_mlst.json"

When combining this pipeline with others, it may be useful to encapsulate the outputs from this pipeline in a sub-directory that is named with the pipeline name and version.

So by default we would create outputs of this structure:

.
├── sample-01
│   ├── sample-01_alleles.csv
│   └── sample-01_sequence_type.csv
├── sample-02
│   ├── sample-02_alleles.csv
│   └── sample-02_sequence_type.csv
└── sample-03
    ├── sample-03_alleles.csv
    └── sample-03_sequence_type.csv

...but when running with a --versioned_outdir flag , we would produce:

.
├── sample-01
│   └── mlst-nf-v0.1-output
│       ├── sample-01_alleles.csv
│       └── sample-01_sequence_type.csv
├── sample-02
│   └── mlst-nf-v0.1-output
│       ├── sample-01_alleles.csv
│       └── sample-01_sequence_type.csv
└── sample-03
    └── mlst-nf-v0.1-output
        ├── sample-01_alleles.csv
        └── sample-01_sequence_type.csv

...then a subsequent analysis could produce similar outputs alongside:

.
├── sample-01
│   ├── mlst-nf-v0.1-output
│   │   └── sample-01_mlst.csv
│   └── routine-assembly-v0.2-output
│       ├── sample-01_bakta.gbk
│       └── sample-01_unicycler.fa
├── sample-02
│   ├── mlst-nf-v0.1-output
│   │   └── sample-02_mlst.csv
│   └── routine-assembly-v0.2-output
│       ├── sample-02_bakta.gbk
│       └── sample-02_unicycler.fa
└── sample-03
    ├── mlst-nf-v0.1-output
    │   └── sample-03_mlst.csv
    └── routine-assembly-v0.2-output
        ├── sample-03_bakta.gbk
        └── sample-03_unicycler.fa

Add optional versioned output directory