Merge d2a51d8 into 2ea1b25

.travis.yml

@@ -38,9 +38,11 @@ jobs:
     - env: CI_TARGET=integration_tests
     - env: CI_TARGET=skylab_bulk_rna
     - env: CI_TARGET=DVGLx
+    - env: CI_TARGET=viral_assemble
   allow_failures:
     - env: CI_TARGET=skylab_bulk_rna
     - env: CI_TARGET=DVGLx
+    - env: CI_TARGET=viral_assemble
   fast_finish: true
 
 # bash -c "while true ; do sleep 60; docker service ls; done" &

Makefile

@@ -25,6 +25,9 @@ skylab_bulk_rna:
 DVGLx:
 	prove -v tests/applied/DVGLx.t
 
+viral_assemble:
+	prove -v tests/applied/viral_assemble.t
+
 ci_housekeeping: sopretty check_check check doc
 
 ci_unit_tests: unit_tests
@@ -79,4 +82,4 @@ doc:
 
 docs: doc
 
-.PHONY: check check_check sopretty pretty test qtest docker doc docs pypi_test pypi bdist ci_housekeeping unit_tests integration_tests skylab_bulk_rna DVGLx
+.PHONY: check check_check sopretty pretty test qtest docker doc docs pypi_test pypi bdist ci_housekeeping unit_tests integration_tests skylab_bulk_rna DVGLx viral_assemble

WDL/runtime/task.py

@@ -509,7 +509,7 @@ def chown(self, logger: logging.Logger, client: docker.DockerClient) -> None:
                 if t_delta >= 60:
                     logger.warning(
                         _(
-                            "post-task chown was slow (symptomatic of excessive file count and/or IOPS saturation)",
+                            "post-task chown was slow (indicative of excessive file count and/or IOPS exhaustion)",
                             seconds=int(t_delta),
                         )
                     )

tests/applied/viral_assemble.t

@@ -0,0 +1,25 @@
+#!/bin/bash
+set -eo pipefail
+
+cd "$(dirname $0)/../.."
+SOURCE_DIR="$(pwd)"
+
+DN=$(mktemp -d --tmpdir miniwdl_runner_tests_XXXXXX)
+cd $DN
+echo "$DN"
+
+git clone --depth=1 https://github.com/broadinstitute/viral-pipelines.git
+cd viral-pipelines
+
+export PYTHONPATH="$SOURCE_DIR:$PYTHONPATH"
+miniwdl="python3 -m WDL"
+
+BASH_TAP_ROOT="$SOURCE_DIR/tests/bash-tap"
+source $SOURCE_DIR/tests/bash-tap/bash-tap-bootstrap
+plan tests 1
+set +e
+
+$miniwdl run pipes/WDL/workflows/assemble_denovo_with_deplete.wdl \
+    --path pipes/WDL/tasks --dir "$DN" --verbose \
+    -i test/input/WDL/test_inputs-assemble_denovo_with_deplete-local.json
+is "$?" "0" "pipeline success"