Merge pull request #14 from msk-access/hotfix/athena_toil_updates

Hotfix/athena toil updates
msk-access · May 18, 2023 · f5d93e4 · f5d93e4
2 parents d1a6362 + 64685ca
commit f5d93e4
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Showing 7 changed files with 25 additions and 4 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,6 +1,8 @@
 [submodule "cwl-commandlinetools"]
 	path = cwl-commandlinetools
 	url = https://github.com/msk-access/cwl-commandlinetools.git
+	branch = hotfix/athena_inputs
 [submodule "cwl_subworkflows"]
 	path = cwl_subworkflows
 	url = https://github.com/msk-access/cwl_subworkflows.git
+	branch = hotfix/athena
diff --git a/cwl-commandlinetools b/cwl-commandlinetools
diff --git a/cwl_subworkflows b/cwl_subworkflows
diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl
@@ -192,7 +192,7 @@ inputs:
     'sbg:x': 386.90625
     'sbg:y': 2449.734375
   - id: output
-    type: string?
+    type: 'string[]?'
     'sbg:exposed': true
   - id: omaf
     type: boolean?

diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,7 @@
 coloredlogs==15.0.1
 pytest==7.2.0
 setuptools==65.4.1
-cwltool==3.1.20220628170238
+cwltool==3.1.20230425144158
+toil[cwl] @ git+https://github.com/DataBiosphere/toil.git
 pytest-runner==6.0.0
 tox==3.27.1
diff --git a/requirements_voyager.txt b/requirements_voyager.txt
@@ -0,0 +1,7 @@
+coloredlogs==15.0.1
+pytest==7.2.0
+setuptools==65.4.1
+cwltool==3.1.20230425144158
+git+https://github.com/mskcc/[email protected]#egg=toil[cwl]
+pytest-runner==6.0.0
+tox==3.27.1
diff --git a/tox.ini b/tox.ini
@@ -22,3 +22,14 @@ passenv = {gh-actions,pytest}
 deps = -r ./requirements.txt
 # run the tests
 commands = pytest
+
+[testenv-voyager]
+
+passenv = {gh-actions,pytest}
+# allowlist_externals= /bin/bash
+# install data 
+# commands_pre = bash install_data.sh
+# install testing framework
+deps = -r ./requirements_voyager.txt
+# run the tests
+commands = pytest