manifest:
  name: databio/peppro
  version: 1.1.0
  imports:
  - bulker/alpine:default
  - bulker/coreutils:default
  host_commands:
  - python3
  - perl
  - fqdedup
  commands:
  - command: bedtools
    docker_args: "-i"
    docker_image: quay.io/biocontainers/bedtools:2.31.1--h13024bc_3
  - command: bowtie2
    docker_image: quay.io/biocontainers/bowtie2:2.5.4--he96a11b_7
  - command: cutadapt
    docker_image: quay.io/biocontainers/cutadapt:4.9--py312hf67a6ed_2
  - command: fastp
    docker_image: quay.io/biocontainers/fastp:0.23.4--hadf994f_3
  - command: fastq_pair
    docker_image: quay.io/biocontainers/fastq-pair:1.0--h503566f_6
  - command: fastqc
    docker_image: quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0
  - command: fastx_trimmer
    docker_image: quay.io/biocontainers/fastx_toolkit:0.0.14--he1b5a44_8
  - command: fastx_reverse_complement
    docker_image: quay.io/biocontainers/fastx_toolkit:0.0.14--he1b5a44_8
  - command: flash
    docker_image: databio/flashz
  - command: java
    docker_image: openjdk
    docker_args: "-i"
  - command: bigWigCat
    docker_image: quay.io/biocontainers/ucsc-bigwigcat:377--h0b8a92a_2
  - command: wigToBigWig
    docker_image: quay.io/biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2
  - 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:0.3.1
    docker_command: R
  - command: Rscript
    docker_image: databio/rpipe:0.3.1
  - command: samtools
    docker_args: "-i"
    docker_image: quay.io/biocontainers/samtools:1.23--h96c455f_0
  - command: seqkit
    docker_image: quay.io/biocontainers/seqkit:2.8.2--h9ee0642_1
  - command: seqOutBias
    docker_image: databio/seqoutbias:0.0.1
  - command: seqtk
    docker_image: quay.io/biocontainers/seqtk:1.4--he4a0461_2