Profiles

Extending profiles:

Similarly to the pipelines, the profiles are YAML files in a python module (it is requires a __init__.py file in the folder containing the files). In order to be parsed correctly, the profile YAML file needs to have a specific structure:

info:
   description: Test Profile
   date:        23/11/2020
genome_build: hg38
files:
   genome_fa:    /abs/path/to/fasta.fa
   genome_fa_gz: /abs/path/to/fasta.fa.gz
   dummy_file:   /home/docs/checkouts/readthedocs.org/user_builds/bio-pype/checkouts/latest/test/data/files/dummy_file.txt

programs:
   samtools_0:
      namespace: path@samtools
      version: 0.1.19
   samtools_1:
      namespace: path@samtools
      version: 1.2
   bwa:
      namespace: path@bwa
      version: 0.7.10
   star:
      namespace: path@star
      version: 2.5.1b
   alpine_3:
      namespace: path@alpine
      version: latest

info:
   description: Test Profile with Docker Namespace
   date:        23/11/2020
genome_build: hg38
files:
   genome_fa:    /abs/path/to/fasta.fa
   genome_fa_gz: /abs/path/to/fasta.fa.gz
   dummy_file:   /home/docs/checkouts/readthedocs.org/user_builds/bio-pype/checkouts/latest/test/data/files/dummy_file.txt

programs:
   samtools_0:
      namespace: path@samtools
      version: 0.1.19
   samtools_1:
      namespace: docker@biocontainers/samtools
      version: v1.7.0_cv4
   bwa:
      namespace: docker@biocontainers/bwa
      version: v0.7.15_cv4
   star:
      namespace: path@star
      version: 2.5.1b
   alpine_3:
      namespace: docker@alpine
      version: latest