databio/pepatac:1.0.10

Raw Manifest

manifest:
  name: databio/pepatac
  version: 1.0.10
  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:2.29.2--hc088bd4_0
  - command: bigWigCat
    docker_image: quay.io/biocontainers/ucsc-bigwigcat:357--1
    docker_args: -i
  - command: bowtie2
    docker_image: quay.io/biocontainers/bowtie2:2.4.1--py37h8270d21_3
  - command: bwa
    docker_image: quay.io/biocontainers/bwa:0.7.8--hed695b0_5
  - command: fastqc
    docker_image: quay.io/biocontainers/fastqc:0.11.9--0
  - command: findMotifsGenome.pl
    docker_image: quay.io/biocontainers/homer:4.11--pl526hc9558a2_3
  - command: findPeaks
    docker_image: quay.io/biocontainers/homer:4.11--pl526hc9558a2_3
  - command: fseq
    docker_image: quay.io/biocontainers/fseq:1.84--py35pl5.22.0_0
  - command: Genrich
    docker_image: quay.io/biocontainers/genrich:0.6--hed695b0_0
  - command: hmmratac
    docker_image: quay.io/biocontainers/hmmratac:1.2.10--0
  - command: java
    docker_image: openjdk
    docker_args: -i
  - command: macs2
    docker_image: quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0
  - command: picard
    docker_image: quay.io/biocontainers/picard:2.23.3--0
  - 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:0.3.0
    docker_command: R
  - command: Rscript
    docker_image: databio/rpipe:0.3.0
  - command: samblaster
    docker_image: quay.io/biocontainers/samblaster:0.1.26--hc9558a2_0
    docker_args: -i
  - command: samtools
    docker_args: -i
    docker_image: quay.io/biocontainers/samtools:1.9--h91753b0_8
  - command: seqOutBias
    docker_image: databio/seqoutbias:0.0.1
  - command: skewer
    docker_image: quay.io/biocontainers/skewer:0.2.2--h2d50403_2
  - command: trimmomatic
    docker_image: quay.io/biocontainers/trimmomatic:0.35--6
  - command: wigToBigWig
    docker_image: quay.io/biocontainers/ucsc-wigtobigwig:357--h35c10e6_3
    docker_args: -i