manifest:
  name: databio/refgenie
  version: 1.1.1
  description: 'Containerized tools for building refgenie reference assets. Self-contained:
    activate this crate alone. Image pins are synced quarterly from bulker/biobase
    by update_refgenie_crate.py.'
  imports:
  - bulker/coreutils:default
  commands:
  - command: bedtools
    docker_image: quay.io/biocontainers/bedtools:2.31.1--h13024bc_3
  - command: bgzip
    docker_image: quay.io/biocontainers/htslib:1.24--ha79157c_0
  - command: bismark_genome_preparation
    docker_image: quay.io/biocontainers/bismark:3.1.0--hfa8f182_0
  - command: bowtie-build
    docker_image: quay.io/biocontainers/bowtie:1.3.1--hb82490e_11
  - command: bowtie2-build
    docker_image: quay.io/biocontainers/bowtie2:2.5.5--ha27dd3b_0
  - command: bwa
    docker_image: quay.io/biocontainers/bwa:0.7.19--h577a1d6_1
  - command: epilog
    docker_image: databio/epilog:latest
  - command: gt
    docker_image: quay.io/biocontainers/genometools-genometools:1.6.6--py311h21ec246_1
  - command: hisat2-build
    docker_image: quay.io/biocontainers/hisat2:2.2.2--h503566f_0
  - command: kallisto
    docker_image: quay.io/biocontainers/kallisto:0.52.0--h13ff97a_0
  - command: mashmap
    docker_image: quay.io/biocontainers/mashmap:3.1.3--pl5321hb4818e0_2
  - command: pigz
    docker_image: nsheff/pigz
    docker_command: pigz
    docker_args: -i
  - command: salmon
    docker_image: quay.io/biocontainers/salmon:2.3.4--hfa8f182_0
  - command: samtools
    docker_image: quay.io/biocontainers/samtools:1.24--h9dcdb79_1
    docker_args: -i
  - command: STAR
    docker_image: quay.io/biocontainers/star:2.7.11b--h5ca1c30_8
  - command: tabix
    docker_image: quay.io/biocontainers/htslib:1.24--ha79157c_0