databio/peppro:1.0.1

Raw Manifest

manifest:
  name: databio/peppro
  version: 1.0.1
  imports:
  - bulker/alpine:default
  - bulker/coreutils:default
  host_commands:
  - python3
  commands:
  - command: bedtools
    docker_args: -i
    docker_image: quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2
  - command: bigWigCat
    docker_image: quay.io/biocontainers/ucsc-bigwigcat:377--ha8a8165_3
    docker_args: -i
  - command: bowtie2
    docker_image: quay.io/biocontainers/bowtie2:2.4.4--py38he5f0661_1
  - command: cutadapt
    docker_image: quay.io/biocontainers/cutadapt:3.5--py38h4a8c8d9_0
  - command: fastp
    docker_image: quay.io/biocontainers/fastp:0.23.2--h79da9fb_0
  - command: fastq_pair
    docker_image: quay.io/biocontainers/fastq-pair:1.0--h1b792b2_2
  - command: fastqc
    docker_image: quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1
  - command: flash
    docker_image: databio/flashz
  - command: gt
    docker_image: quay.io/biocontainers/genometools-genometools:1.6.2--py38h3356801_0
  - command: java
    docker_image: openjdk
    docker_args: -i
  - command: perl
    docker_image: perl
    docker_args: -i
  - command: picard
    docker_image: quay.io/biocontainers/picard:2.26.10--hdfd78af_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
    docker_command: R
  - command: Rscript
    docker_image: databio/rpipe
  - command: samtools
    docker_args: -i
    docker_image: quay.io/biocontainers/samtools:1.14--hb421002_0
  - command: seqkit
    docker_image: quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0
  - command: seqOutBias
    docker_image: databio/seqoutbias:0.0.1
  - command: seqtk
    docker_args: -i
    docker_image: quay.io/biocontainers/seqtk:1.3--h5bf99c6_3
  - command: wigToBigWig
    docker_image: quay.io/biocontainers/ucsc-wigtobigwig:377--ha8a8165_3
    docker_args: -i