environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: nf-core-smrnaseq-1.0.0
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
 ## conda-forge packages
  - conda-forge::r-base=3.6.1
  - conda-forge::openjdk=11.0.1 # Needed for FastQC - conda build hangs without this
  - conda-forge::r-statmod=1.4.32
  - conda-forge::r-data.table=1.12.2
  - conda-forge::r-gplots=3.0.1.1
  - conda-forge::r-r.methodss3=1.7.1
  - conda-forge::r-markdown=1.0
  - conda-forge::matplotlib=3.0.3 # Current 3.1.0 build incompatible with multiqc=1.7

  ## bioconda packages
  - fastqc=0.11.8
  - trim-galore=0.6.3
  - samtools=1.9
  - bowtie=1.2.2
  - multiqc=1.7
  - mirtop=0.4.22
  - seqcluster=1.2.5
  - htseq=0.11.2
  - fastx_toolkit=0.0.14
  - seqkit=0.10.1
  - mirtrace=1.0.0
  - bioconductor-edger=3.26.5
  - bioconductor-limma=3.40.2