Merge pull request #84 from rabix/bugfix/samplesheet_input_and_nf_core

NF schema is built only if it's missing
rabix · Jun 3, 2024 · e9eb2da · e9eb2da
2 parents 09e8e35 + 45a1689
commit e9eb2da
Show file tree

Hide file tree

Showing 55 changed files with 4 additions and 3 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
diff --git a/.gitignore b/.gitignore
diff --git a/LICENSE b/LICENSE
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/Readme.md b/Readme.md
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
 ruamel.yaml >= 0.16
 sevenbridges-python >= 2.0
 nf-core==2.1
-wrabbit==0.1.2
+wrabbit==0.1.3
 cwlformat
 packaging
diff --git a/sbpack/__init__.py b/sbpack/__init__.py
diff --git a/sbpack/lib.py b/sbpack/lib.py
diff --git a/sbpack/noncwl/Readme.md b/sbpack/noncwl/Readme.md
diff --git a/sbpack/noncwl/__init__.py b/sbpack/noncwl/__init__.py
diff --git a/sbpack/noncwl/constants.py b/sbpack/noncwl/constants.py
diff --git a/sbpack/noncwl/copy_app.py b/sbpack/noncwl/copy_app.py
diff --git a/sbpack/noncwl/manifest.py b/sbpack/noncwl/manifest.py
diff --git a/sbpack/noncwl/nextflow.py b/sbpack/noncwl/nextflow.py
@@ -250,7 +250,8 @@ def main():
     else:
         # build schema
         # Do this only if the nextflow_schema.json is missing
-        nf_wrapper.nf_schema_build()
+        if not nf_wrapper.nf_schema_path:
+            nf_wrapper.nf_schema_build()
 
         # Create app
         nf_wrapper.generate_sb_app(

diff --git a/sbpack/noncwl/utils.py b/sbpack/noncwl/utils.py
diff --git a/sbpack/noncwl/wdl.py b/sbpack/noncwl/wdl.py
diff --git a/sbpack/pack.py b/sbpack/pack.py
diff --git a/sbpack/schemadef.py b/sbpack/schemadef.py
diff --git a/sbpack/unpack.py b/sbpack/unpack.py
diff --git a/sbpack/version.py b/sbpack/version.py
@@ -1 +1 @@
-__version__ = "2024.5.21rc1"
+__version__ = "2024.6.3rc1"
diff --git a/setup.py b/setup.py
diff --git a/test-requirements.txt b/test-requirements.txt
diff --git a/tests/lib.js b/tests/lib.js
diff --git a/tests/remote-cwl/tool1.cwl b/tests/remote-cwl/tool1.cwl
diff --git a/tests/remote-cwl/tool2.cwl b/tests/remote-cwl/tool2.cwl
diff --git a/tests/remote-cwl/wf1.cwl b/tests/remote-cwl/wf1.cwl
diff --git a/tests/test_localpack.py b/tests/test_localpack.py
diff --git a/tests/test_packing.py b/tests/test_packing.py
diff --git a/tests/test_pulling.py b/tests/test_pulling.py
diff --git a/tests/test_schemadefs.py b/tests/test_schemadefs.py
diff --git a/tests/test_validation_battery.py b/tests/test_validation_battery.py
diff --git a/tests/tools/clt1.cwl b/tests/tools/clt1.cwl
diff --git a/tests/tools/clt2.cwl b/tests/tools/clt2.cwl
diff --git a/tests/tools/clt3.cwl b/tests/tools/clt3.cwl
diff --git a/tests/types/array.yml b/tests/types/array.yml
diff --git a/tests/types/recursive.yml b/tests/types/recursive.yml
diff --git a/tests/types/singletype.yml b/tests/types/singletype.yml
diff --git a/tests/types/singletype2.yml b/tests/types/singletype2.yml
diff --git a/tests/types/testtypes.yml b/tests/types/testtypes.yml
diff --git a/tests/wf2.cwl b/tests/wf2.cwl
diff --git a/tests/workflows/count-lines16-wf.cwl b/tests/workflows/count-lines16-wf.cwl
diff --git a/tests/workflows/import-in-type.cwl b/tests/workflows/import-in-type.cwl
diff --git a/tests/workflows/scatter-wf4.cwl b/tests/workflows/scatter-wf4.cwl
diff --git a/tests/workflows/type-import.yaml b/tests/workflows/type-import.yaml
diff --git a/tests/workflows/wf-with-git.cwl b/tests/workflows/wf-with-git.cwl
diff --git a/tests/workflows/wf1.cwl b/tests/workflows/wf1.cwl
diff --git a/tests/workflows/wf2.cwl b/tests/workflows/wf2.cwl
diff --git a/tests/workflows/wf3.cwl b/tests/workflows/wf3.cwl
diff --git a/tests/workflows/wf4.cwl b/tests/workflows/wf4.cwl
diff --git a/tests/workflows/wf5.cwl b/tests/workflows/wf5.cwl
diff --git a/tests/workflows/wf6.cwl b/tests/workflows/wf6.cwl
diff --git a/tests/workflows/wf6.json b/tests/workflows/wf6.json
diff --git a/tests/workflows/wf6_with_ids.json b/tests/workflows/wf6_with_ids.json
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		__version__ = "2024.5.21rc1"
		__version__ = "2024.6.3rc1"