name: cellranger_mkgtf
namespace: reference
scope: "public"
description: Make a GTF file - filter by a specific attribute.
authors:
  - __merge__: /src/authors/jakub_majercik.yaml
    roles: [ author ]
arguments:
  # inputs
  - type: file
    name: --input_gtf
    required: true
    description: Reference GTF annotation.
    example: transcriptome_annotation.gtf.gz
  - type: file
    name: --output_gtf
    direction: output
    required: true
    description: Output GTF file.
    example: output.gtf.gz
  - type: string
    name: --attribute
    required: true
    description: Key-value pair in attributes field to be kept in the GTF file of the format attribute:attribute_value.
    example: [gene_type:transcribed_unprocessed_pseudogene,gene_type:miRNA]
    multiple: true
resources:
  - type: bash_script
    path: script.sh
test_resources:
  - type: python_script
    path: test.py
  - path: /resources_test/reference_gencodev41_chr1
engines:
  - type: docker
    image: ghcr.io/data-intuitive/cellranger:9.0
    setup:
      - type: docker
        run: |
          DEBIAN_FRONTEND=noninteractive apt update && \
          apt upgrade -y && apt install -y pigz procps && rm -rf /var/lib/apt/lists/*
    __merge__: [ /src/base/requirements/python_test_setup.yaml, . ]
runners:
  - type: executable
  - type: nextflow
    directives:
      label: [ midmem, lowcpu ]