Merge pull request #107 from LiuzLab/dockerseparation

Separate R Dockerfile

Dockerfile

@@ -37,37 +37,6 @@ RUN pip3 install --upgrade pip
 RUN pip3 install -r /opt/requirements.txt
 RUN pip3 install bgzip
 
-
-# Install R
-RUN apt-get update
-RUN apt install -y --no-install-recommends software-properties-common dirmngr
-# Add the keys
-RUN apt install wget
-RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
-
-# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
-#RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
-#    apt-key adv --keyserver ha.pool.sks-keyservers.net --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
-#    apt-key adv --keyserver pgp.mit.edu --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
-#    apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
-#    apt-key adv --keyserver keyserver.pgp.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-#RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
-
-RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
-RUN add-apt-repository universe
-RUN apt-get update
-
-RUN apt install -y r-base r-base-core  
-
-# Install R libs
-RUN R -e "install.packages('data.table',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages('dplyr',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages('ontologyIndex',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages('ontologySimilarity',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages('tidyverse',dependencies=TRUE, repos='http://cran.rstudio.com/')"
-
-
-
 # Install bcftools
 RUN wget https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
 RUN mv bcftools-1.20.tar.bz2 /opt/bcftools-1.20.tar.bz2

Dockerfiles/r.Dockerfile

@@ -0,0 +1,5 @@
+FROM rocker/tidyverse
+
+# Install R libs
+RUN R -e "install.packages('ontologyIndex',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('ontologySimilarity',dependencies=TRUE, repos='http://cran.rstudio.com/')"

main.nf

@@ -364,6 +364,8 @@ process GENESYM_TO_PHRANK {
 
 
 process HPO_SIM {
+    container 'zhandongliulab/aim-lite-r'
+
     input:
     path hpo
     path omim_hgmd_phen
@@ -514,28 +516,43 @@ process ANNOTATE_BY_MODULES {
     """
 }
 
-process JOIN_TIER_PHRANK {
+process ANNOTATE_TIER {
+    container 'zhandongliulab/aim-lite-r'
     tag "${scores.simpleName}"
 
     input:
     path scores
     path phrank
-
     path ref_annot_dir
     path ref_var_tier_dir
-    path ref_merge_expand_dir
 
     output:
-    path "${scores.simpleName}_scores.txt.gz", emit: compressed_scores
     path "${scores.simpleName}_Tier.v2.tsv", emit: tier
 
     script:
     """
     mv $scores scores.csv
     VarTierDiseaseDBFalse.R ${params.ref_ver}
+    mv Tier.v2.tsv ${scores.simpleName}_Tier.v2.tsv
+    """
+}
+
+process JOIN_PHRANK {
+    tag "${scores.simpleName}"
+
+    input:
+    path scores
+    path phrank
+    path ref_merge_expand_dir
+
+    output:
+    path "${scores.simpleName}_scores.txt.gz", emit: compressed_scores
+
+    script:
+    """
+    mv $scores scores.csv
     generate_new_matrix_2.py ${params.run_id} ${params.ref_ver}
     mv scores.txt.gz  ${scores.simpleName}_scores.txt.gz
-    mv Tier.v2.tsv ${scores.simpleName}_Tier.v2.tsv
     """
 }
 
@@ -712,19 +729,23 @@ workflow {
         NORMALIZE_VCF.out.vcf,
     )
 
-    JOIN_TIER_PHRANK (
+    ANNOTATE_TIER (
         ANNOTATE_BY_MODULES.out.scores,
         PHRANK_SCORING.out,
-
         file(params.ref_annot_dir),
         file(params.ref_var_tier_dir),
+    )
+
+    JOIN_PHRANK (
+        ANNOTATE_BY_MODULES.out.scores,
+        PHRANK_SCORING.out,
         file(params.ref_merge_expand_dir)
     )
 
     MERGE_SCORES_BY_CHROMOSOME(
         PHRANK_SCORING.out,
-        JOIN_TIER_PHRANK.out.tier.collect(),
-        JOIN_TIER_PHRANK.out.compressed_scores.collect(),
+        ANNOTATE_TIER.out.tier.collect(),
+        JOIN_PHRANK.out.compressed_scores.collect(),
         file(params.ref_annot_dir),
         file(params.ref_mod5_diffusion_dir),
         file(params.ref_merge_expand_dir)