Merge pull request nf-core#10 from tiagochst/bioconda

Bioconda

Dockerfile

@@ -1,8 +1,8 @@
 FROM nfcore/base
 MAINTAINER Phil Ewels <phil.ewels@scilifelab.se>
 LABEL authors="phil.ewels@scilifelab.se" \
-    description="Docker image containing all requirements for the nfcore/ChIPseq pipeline"
+      description="Docker image containing all requirements for the nfcore/ChIPseq pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nfcore-chipseq-1.4dev/bin:$PATH
+ENV PATH /opt/conda/envs/nfcore-chipseq-1.4dev/bin:$PATH

environment.yml

@@ -10,6 +10,7 @@ dependencies:
   - fastqc=0.11.7
   - trim-galore=0.4.5
   - bwa=0.7.17
+  - conda-forge::gawk=4.2.1 
   - conda-forge::r-markdown=0.8
   - bioconda::r-spp=1.15.2
   - bedtools=2.27.1
@@ -28,6 +29,7 @@ dependencies:
   - conda-forge::r-ggplot2=2.2.1
   - conda-forge::r-knitr=1.20
   - conda-forge::r-rmysql=0.10.13
+  - conda-forge::r-doparallel=1.0.11
   - bioconda::bioconductor-bsgenome=1.46.0
   - bioconda::bioconductor-rsamtools=1.30.0
   - bioconda::bioconductor-shortread=1.36.0
@@ -41,4 +43,5 @@ dependencies:
   - bioconda::bioconductor-org.hs.eg.db=3.5.0
   - bioconda::bioconductor-bsgenome.mmusculus.ucsc.mm10=1.4.0
   - bioconda::bioconductor-org.mm.eg.db=3.5.0
-  - bioconda::r-spp=1.15.2
+  - deeptools=3.0.2
+  - bioconda::r-spp=1.15.2

main.nf

@@ -597,7 +597,7 @@ process deepTools {
         bamCoverage \\
            -b $bam \\
            --extendReads ${params.extendReadsLen} \\
-           --normalizeUsingRPKM \\
+           --normalizeUsing RPKM \\
            -o ${bam}.bw
         """
     } else {
@@ -619,7 +619,7 @@ process deepTools {
             bamCoverage \\
               -b \$bamfile \\
               --extendReads ${params.extendReadsLen} \\
-              --normalizeUsingRPKM \\
+              --normalizeUsing RPKM \\
               -o \${bamfile}.bw
         done