manifest:
  name: databio/methpl
  version: 1.0.1
  imports:
  - bulker/alpine:default
  - bulker/coreutils:default
  host_commands:
  - cat
  - python
  commands:
  - command: bedGraphToBigWig
    docker_image: quay.io/biocontainers/ucsc-bedgraphtobigwig:357--h35c10e6_3
  - command: bedToBigBed
    docker_image: quay.io/biocontainers/ucsc-bedtobigbed:357--1
    docker_args: -i
  - command: bedtools
    docker_args: -i
    docker_image: quay.io/biocontainers/bedtools:2.29.0--hc088bd4_3
  - command: bigWigCat
    docker_image: quay.io/biocontainers/ucsc-bigwigcat:357--1
    docker_args: -i
  - command: bismark
    docker_image: quay.io/biocontainers/bismark:0.22.1--0
  - command: bissnp
    docker_image: quay.io/biocontainers/bis-snp:1.0.1--2
  - command: bowtie
    docker_image: quay.io/biocontainers/bowtie:1.2.3--py37hc9558a2_0
  - command: bowtie2
    docker_image: quay.io/biocontainers/bowtie2:2.3.5--py37he860b03_0
  - command: bsmap
    docker_image: quay.io/biocontainers/bsmap:2.90--he860b03_2
  - command: deduplicate_bismark
    docker_image: quay.io/biocontainers/bismark:0.22.1--0
  - command: epilog
    docker_image: databio/epilog:latest
  - command: fastqc
    docker_image: quay.io/biocontainers/fastqc:0.11.8--1
  - command: java
    docker_image: openjdk
    docker_args: -i
  - command: macs2
    docker_image: quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0
  - command: perl
    docker_image: perl
    docker_args: -i
  - command: pigz
    docker_image: nsheff/pigz
  - command: preseq
    docker_image: quay.io/biocontainers/preseq:2.0.3--h26b358d_2
  - command: R
    docker_image: databio/rpipe
    docker_command: R
  - command: Rscript
    docker_image: databio/rpipe
  - command: samblaster
    docker_image: quay.io/biocontainers/samblaster:0.1.24--hc9558a2_3
    docker_args: -i
  - command: samtools
    docker_args: -i
    docker_image: quay.io/biocontainers/samtools:1.9--h91753b0_8
  - command: skewer
    docker_image: quay.io/biocontainers/skewer:0.2.2--h2d50403_2
  - command: wigToBigWig
    docker_image: quay.io/biocontainers/ucsc-wigtobigwig:357--h35c10e6_3
    docker_args: -i