Merge pull request #5 from dbmi-bgm/annotation

CNVs annot

VERSION

@@ -1 +1 @@
-v1.0.0
+v1.1.0

descriptions/driver_catalog.cwl

@@ -0,0 +1,56 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+requirements:
+  - class: InlineJavascriptRequirement
+
+hints:
+  - class: DockerRequirement
+    dockerPull: ACCOUNT/genomic_ranges:VERSION
+
+baseCommand: [driver_catalog.sh]
+
+inputs:
+  - id: ascat
+    type: File
+    inputBinding:
+        prefix: "--ascat"
+    doc: tsv file containing ASCAT CNVs
+
+  - id: gene_panel
+    type: File
+    inputBinding:
+        prefix: "--gene_panel"
+    doc: tsv configuration file of which genes to add to the driver catalog from Hartwig Medical Foundation
+
+  - id: cgap_genes
+    type: File
+    inputBinding:
+        prefix: "--cgap_genes"
+    doc: tsv file of genes available on CGAP
+
+  - id: ascat_objects
+    type: File
+    inputBinding:
+        prefix: "--ascat_objects"
+    doc: ascat objects from the CGAP SV somatic pipeline (ASCAT)
+
+  - id: output
+    type: string
+    inputBinding:
+        prefix: "--output"
+    default: putative_drivers_CNV_ASCAT.tsv
+    doc: output file name
+
+outputs:
+  - id: putative_drivers_tsv
+    type: File
+    outputBinding:
+      glob: $(inputs.output).gz
+    doc: tsv file containing reported putative drivers
+
+doc: |
+  run driver_catalog.sh

dockerfiles/genomic_ranges/Dockerfile

@@ -0,0 +1,48 @@
+#######################################################################
+#     Basic image
+#######################################################################
+FROM cgap/cgap-ubuntu2004-py-38:0.0.1
+MAINTAINER Michele Berselli ([email protected]), Dominika Maziec ([email protected])
+
+#######################################################################
+#     General updates & installing necessary Linux components
+#       - tabix brings in bgzip and tabix
+#       - locales for UTF-8
+#######################################################################
+RUN apt-get update && apt-get install -y \
+    locales \
+    tabix 
+
+#######################################################################
+#     Software
+#######################################################################
+## Install R
+RUN apt-get install -y --no-install-recommends r-base
+RUN apt-get install -y --no-install-recommends r-cran-tidyverse r-cran-optparse r-cran-biocmanager
+
+## Install GenomicRanges
+RUN R -e "BiocManager::install('GenomicRanges')"
+
+#######################################################################
+#     Setting working env
+#######################################################################
+WORKDIR /usr/local/bin
+
+#######################################################################
+#     Scripts
+#######################################################################
+## driver_catalog.sh
+COPY scripts/driver_catalog.sh .
+RUN chmod +x driver_catalog.sh
+
+## postprocess_ascat.R
+COPY scripts/postprocess_ascat.R .
+
+#######################################################################
+#     Setting env variables
+#######################################################################
+## Supporting UTF-8
+RUN locale-gen "en_US.UTF-8" && update-locale LC_ALL="en_US.UTF-8"
+ENV LC_ALL=en_US.UTF-8
+
+CMD ["bash"]

dockerfiles/genomic_ranges/scripts/driver_catalog.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+WORKDIR="/usr/local/bin"
+
+while [ "$1" != "" ]; do
+    case $1 in
+    --ascat)
+        shift
+        ascat=$1
+        ;;
+    --gene_panel)
+        shift
+        gene_panel=$1
+        ;;
+    --cgap_genes)
+        shift
+        cgap_genes=$1
+        ;;
+    --ascat_objects)
+        shift
+        ascat_objects=$1
+        ;;
+    --output)
+        shift
+        output=$1
+        ;;
+    esac
+    shift
+done
+
+
+Rscript $WORKDIR/postprocess_ascat.R --ascat $ascat --ascat_objects $ascat_objects --gene_panel $gene_panel --cgap_genes $cgap_genes --output $output || exit 1
+gzip $output  || exit 1