{% set version = "1.10.0" %}
{% set name = "scruff" %}
{% set bioc = "3.13" %}

package:
  name: 'bioconductor-{{ name|lower }}'
  version: '{{ version }}'
source:
  url:
    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
  md5: b7b5876be10e87f597631689e20bda8a
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
  noarch: generic
# Suggests: BiocStyle, knitr, rmarkdown, testthat
requirements:
  host:
    - 'bioconductor-annotationdbi >=1.54.0,<1.55.0'
    - 'bioconductor-biocgenerics >=0.38.0,<0.39.0'
    - 'bioconductor-biocparallel >=1.26.0,<1.27.0'
    - 'bioconductor-biostrings >=2.60.0,<2.61.0'
    - 'bioconductor-genomeinfodb >=1.28.0,<1.29.0'
    - 'bioconductor-genomicalignments >=1.28.0,<1.29.0'
    - 'bioconductor-genomicfeatures >=1.44.0,<1.45.0'
    - 'bioconductor-genomicranges >=1.44.0,<1.45.0'
    - 'bioconductor-ggbio >=1.40.0,<1.41.0'
    - 'bioconductor-rsamtools >=2.8.0,<2.9.0'
    - 'bioconductor-rsubread >=2.6.0,<2.7.0'
    - 'bioconductor-rtracklayer >=1.52.0,<1.53.0'
    - 'bioconductor-s4vectors >=0.30.0,<0.31.0'
    - 'bioconductor-shortread >=1.50.0,<1.51.0'
    - 'bioconductor-singlecellexperiment >=1.14.0,<1.15.0'
    - 'bioconductor-summarizedexperiment >=1.22.0,<1.23.0'
    - r-base
    - r-data.table
    - r-ggplot2
    - r-ggthemes
    - r-plyr
    - r-scales
    - r-stringdist
  run:
    - 'bioconductor-annotationdbi >=1.54.0,<1.55.0'
    - 'bioconductor-biocgenerics >=0.38.0,<0.39.0'
    - 'bioconductor-biocparallel >=1.26.0,<1.27.0'
    - 'bioconductor-biostrings >=2.60.0,<2.61.0'
    - 'bioconductor-genomeinfodb >=1.28.0,<1.29.0'
    - 'bioconductor-genomicalignments >=1.28.0,<1.29.0'
    - 'bioconductor-genomicfeatures >=1.44.0,<1.45.0'
    - 'bioconductor-genomicranges >=1.44.0,<1.45.0'
    - 'bioconductor-ggbio >=1.40.0,<1.41.0'
    - 'bioconductor-rsamtools >=2.8.0,<2.9.0'
    - 'bioconductor-rsubread >=2.6.0,<2.7.0'
    - 'bioconductor-rtracklayer >=1.52.0,<1.53.0'
    - 'bioconductor-s4vectors >=0.30.0,<0.31.0'
    - 'bioconductor-shortread >=1.50.0,<1.51.0'
    - 'bioconductor-singlecellexperiment >=1.14.0,<1.15.0'
    - 'bioconductor-summarizedexperiment >=1.22.0,<1.23.0'
    - r-base
    - r-data.table
    - r-ggplot2
    - r-ggthemes
    - r-plyr
    - r-scales
    - r-stringdist
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: 'MIT + file LICENSE'
  summary: 'Single Cell RNA-Seq UMI Filtering Facilitator (scruff)'
  description: 'A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.'
  license_file: LICENSE

