Merge pull request #27 from UCSC-Treehouse/issue-25-add-jfkm-pipeline

Add JFKM Pipeline

Makefile

@@ -90,6 +90,19 @@ variants:
 			/inputs/sample.bam \
 			/outputs
 
+jfkm:
+	echo "Running Jellyfish - Km pipeline on $(R1) and $(R2)"
+	mkdir -p outputs/jfkm
+	docker run --rm \
+	       -v $(shell pwd)/samples:/data/samples \
+	       -v $(shell pwd)/outputs/jfkm:/data/outputs \
+               jpfeil/jfkm:0.1.0 \
+                        --CPU `nproc` \
+                        --FLT3-ITD \
+                        --left-fq $(R1) \
+                        --right-fq $(R2) \
+                        --output-dir outputs
+
 verify:
 	echo "Verifying md5 of output of TEST file"
 	tar -xOzvf outputs/expression/TEST_R1merged.tar.gz TEST_R1merged/RSEM/rsem_genes.results | md5sum -c md5/expression.md5

fabfile.py

@@ -478,6 +478,32 @@ def process(manifest="manifest.tsv", base=".", checksum_only="False"):
         with open("{}/methods.json".format(dest), "w") as f:
             f.write(json.dumps(methods, indent=4))
 
+        # Calculate jfkm
+        methods["start"] = datetime.datetime.utcnow().isoformat()
+        with settings(warn_only=True):
+            result = run("cd /mnt && make jfkm")
+            if result.failed:
+                _log_error("{} Failed jfkm: {}".format(sample_id, result))
+                continue
+
+        # Update methods.json and copy output back
+        dest = "{}/jpfeil-jfkm-0.1.0-26350e0".format(output)
+        local("mkdir -p {}".format(dest))
+        methods["inputs"] = fastqs
+        methods["outputs"] = [
+            os.path.relpath(p, base) for p in get("/mnt/outputs/jfkm/*", dest)]
+        methods["end"] = datetime.datetime.utcnow().isoformat()
+        methods["pipeline"] = {
+            "source": "https://github.com/UCSC-Treehouse/jfkm",
+            "docker": {
+                "url": "https://cloud.docker.com/repository/docker/jpfeil/jfkm",
+                "version": "0.1.0",
+                "hash": "sha256:26350e02608115341fe8e735ef6d08216e71d962b176eb53b9a7bc54ef715c10" # NOQA
+            }
+        }
+        with open("{}/methods.json".format(dest), "w") as f:
+            f.write(json.dumps(methods, indent=4))
+
         # Calculate variants
         methods["start"] = datetime.datetime.utcnow().isoformat()
         with settings(warn_only=True):