Workflow build files

gatk4-mutect2-tumor-only-cwl/Dockerfile

@@ -1,17 +1,24 @@
-FROM quay.io/ncigdc/bio-alpine:py36-8dee591
+ARG REGISTRY=docker.osdc.io
+FROM ${REGISTRY}/ncigdc/bio-alpine:cwltool3 as builder
 
 ARG WORKFLOW
 
-COPY ./${WORKFLOW} /opt
-# TODO: Copy additional directories as needed
+COPY ./${WORKFLOW} /opt 
 COPY ./tools /tools
-COPY ./utils-cwl /utils-cwl
 COPY ./subworkflows /subworkflows
+COPY ./utils-cwl /utils-cwl
+
+WORKDIR /opt
+
+RUN just validate && just pack 
+
+FROM ${REGISTRY}/ncigdc/bio-alpine:just
 
-RUN make -C /opt init-pip
+COPY --from=builder /opt/cwl.json /opt/cwl.json
+COPY --from=builder /opt/justfile /opt/justfile
 
 WORKDIR /opt
 
-ENTRYPOINT ["make"]
+ENTRYPOINT ["just"]
 
-CMD ["pack"]
+CMD ["_print-cwl"]

gatk4-mutect2-tumor-only-cwl/dockers.json

@@ -0,0 +1,3 @@
+{
+        "docker_repository": "docker.osdc.io/ncigdc"
+}

gatk4-mutect2-tumor-only-cwl/justfile

@@ -0,0 +1,50 @@
+ENTRY_CWL := "gpas_gatk4.2.4.1_mutect2_tumor_only_workflow.cwl"
+
+# Pack and apply Jinja templating. Creates cwl.json file
+# Should be runnable in built docker container
+pack:
+    #!/bin/sh
+    if [ ! -f cwl.json ]; then
+        just _validate_entry
+        just _cwltool-pack > tmp.json
+        just _jinja tmp.json > cwl.json
+        rm tmp.json
+    fi
+    just _print-cwl
+
+# Ensures CWL entrypoint script exists
+_validate_entry:
+    #!/bin/sh
+    if [ ! -f {{ENTRY_CWL}} ]; then
+        echo "No entry CWL file found!"
+        echo {{ENTRY_CWL}}
+        exit 1;
+    fi
+
+# Prints cwl.json if exists
+_print-cwl:
+    @cat cwl.json
+
+# Packs CWL workflow into single json file
+_cwltool-pack: _validate_entry
+	python3 -m cwltool --pack {{ENTRY_CWL}}
+
+# Apply template to JSON from dockers.json, errors on missing keys
+_jinja JSON:
+    jinja -u 'strict' -d dockers.json {{JSON}}
+
+# Validates CWL workflow
+validate: _validate_entry
+	python3 -m cwltool --validate {{ENTRY_CWL}}
+
+# Formats and prints all Dockers used in workflow
+get-dockers:
+  just pack | grep dockerPull | cut -f2- -d ":" | sort | uniq | sed "s/\"//g"
+
+# Prints all dockerPull declarations in unformatted workflow
+get-dockers-template:
+  just _cwltool-pack | grep dockerPull | cut -f2- -d ":" | sort | uniq | sed "s/\"//g"
+
+# Print template input file for workflow
+inputs:
+  python3 -m cwltool --make-template {{ENTRY_CWL}}

gatk4-pon-cwl/Dockerfile

@@ -1,17 +1,24 @@
-FROM quay.io/ncigdc/bio-alpine:py36-8dee591
+ARG REGISTRY=docker.osdc.io
+FROM ${REGISTRY}/ncigdc/bio-alpine:cwltool3 as builder
 
 ARG WORKFLOW
 
-COPY ./${WORKFLOW} /opt
-# TODO: Copy additional directories as needed
+COPY ./${WORKFLOW} /opt 
 COPY ./tools /tools
-COPY ./utils-cwl /utils-cwl
 COPY ./subworkflows /subworkflows
+COPY ./utils-cwl /utils-cwl
+
+WORKDIR /opt
+
+RUN just validate && just pack 
+
+FROM ${REGISTRY}/ncigdc/bio-alpine:just
 
-RUN make -C /opt init-pip
+COPY --from=builder /opt/cwl.json /opt/cwl.json
+COPY --from=builder /opt/justfile /opt/justfile
 
 WORKDIR /opt
 
-ENTRYPOINT ["make"]
+ENTRYPOINT ["just"]
 
-CMD ["pack"]
+CMD ["_print-cwl"]

gatk4-pon-cwl/dockers.json

@@ -0,0 +1,3 @@
+{
+        "docker_repository": "docker.osdc.io/ncigdc"
+}

gatk4-pon-cwl/justfile

@@ -0,0 +1,50 @@
+ENTRY_CWL := "gpas_gatk4.2.4.1_mutect2_pon_workflow.cwl"
+
+# Pack and apply Jinja templating. Creates cwl.json file
+# Should be runnable in built docker container
+pack:
+    #!/bin/sh
+    if [ ! -f cwl.json ]; then
+        just _validate_entry
+        just _cwltool-pack > tmp.json
+        just _jinja tmp.json > cwl.json
+        rm tmp.json
+    fi
+    just _print-cwl
+
+# Ensures CWL entrypoint script exists
+_validate_entry:
+    #!/bin/sh
+    if [ ! -f {{ENTRY_CWL}} ]; then
+        echo "No entry CWL file found!"
+        echo {{ENTRY_CWL}}
+        exit 1;
+    fi
+
+# Prints cwl.json if exists
+_print-cwl:
+    @cat cwl.json
+
+# Packs CWL workflow into single json file
+_cwltool-pack: _validate_entry
+	python3 -m cwltool --pack {{ENTRY_CWL}}
+
+# Apply template to JSON from dockers.json, errors on missing keys
+_jinja JSON:
+    jinja -u 'strict' -d dockers.json {{JSON}}
+
+# Validates CWL workflow
+validate: _validate_entry
+	python3 -m cwltool --validate {{ENTRY_CWL}}
+
+# Formats and prints all Dockers used in workflow
+get-dockers:
+  just pack | grep dockerPull | cut -f2- -d ":" | sort | uniq | sed "s/\"//g"
+
+# Prints all dockerPull declarations in unformatted workflow
+get-dockers-template:
+  just _cwltool-pack | grep dockerPull | cut -f2- -d ":" | sort | uniq | sed "s/\"//g"
+
+# Print template input file for workflow
+inputs:
+  python3 -m cwltool --make-template {{ENTRY_CWL}}