manifest:
  name: databio/pepatac
  version: 1.1.4
  imports:
  - bulker/alpine:default
  - bulker/coreutils:default
  host_commands:
  - python3
  - perl
  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:2.31.1--h13024bc_3
  - command: bowtie2
    docker_image: quay.io/biocontainers/bowtie2:2.5.5--ha27dd3b_0
  - command: bwa
    docker_image: quay.io/biocontainers/bwa:0.7.17--h7132678_9
  - command: fastqc
    docker_image: quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0
  - command: findPeaks
    docker_image: quay.io/biocontainers/homer:4.11--pl5321h9f5acd7_7
  - command: findMotifsGenome.pl
    docker_image: quay.io/biocontainers/homer:4.11--pl5321h9f5acd7_7
  - command: fseq
    docker_image: quay.io/biocontainers/fseq:1.84--py35pl5.22.0_0
  - command: Genrich
    docker_image: quay.io/biocontainers/genrich:0.6.1--h7132678_2
  - command: hmmratac
    docker_image: quay.io/biocontainers/hmmratac:1.2.10--hdfd78af_1
  - command: java
    docker_image: eclipse-temurin:21-jre
    docker_args: "-i"
  - command: macs3
    docker_image: quay.io/biocontainers/macs3:3.0.3--py310h397c9d8_0
  - command: picard
    docker_image: quay.io/biocontainers/picard:2.27.5--hdfd78af_0
  - command: pigz
    docker_image: nsheff/pigz
  - command: preseq
    docker_image: quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3
  - command: R
    docker_image: databio/rpipe:0.4.0
    docker_command: R
  - command: Rscript
    docker_image: databio/rpipe:0.4.0
  - command: samblaster
    docker_image: quay.io/biocontainers/samblaster:0.1.26--h9f5acd7_2
    docker_args: "-i"
  - command: samtools
    docker_args: "-i"
    docker_image: quay.io/biocontainers/samtools:1.23--h96c455f_0
  - command: seqOutBias
    docker_image: databio/seqoutbias:0.0.1
  - command: skewer
    docker_image: quay.io/biocontainers/skewer:0.2.2--hc9558a2_3
  - command: trimmomatic
    docker_image: quay.io/biocontainers/trimmomatic:0.39--hdfd78af_2
  - command: gtars
    docker_image: quay.io/biocontainers/rust-gtars:0.9.0--ha3ccbb0_0