Merge pull request #74 from simleo/wf_specific_ci

Workflow-specific CI workflows

workflows/computational-chemistry/fragment-based-docking-scoring/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.1.1] 2021-12-06
 
 ### Fixed

workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring.ga

@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "Fragment-based virtual screening using rDock for docking and SuCOS for pose scoring",
-    "release": "0.1.1",
+    "release": "0.1.2",
     "steps": {
         "0": {
             "annotation": "Number of docking poses to generate per input compound",

workflows/computational-chemistry/gromacs-dctmd/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.1.1] 2021-12-06
 
 ### Fixed

workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "dcTMD calculations with GROMACS",
-    "release": "0.1.1",
+    "release": "0.1.2",
     "steps": {
         "0": {
             "annotation": "List of atom indices (separated with spaces) which make up the protein pull group",

workflows/computational-chemistry/gromacs-mmgbsa/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.1.1] 2021-12-06
 
 ### Fixed

workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "MMGBSA calculations with GROMACS",
-    "release": "0.1.1",
+    "release": "0.1.2",
     "steps": {
         "0": {
             "annotation": "Size of the MMGBSA ensemble",

workflows/computational-chemistry/protein-ligand-complex-parameterization/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.1.1] 2021-12-06
 
 ### Fixed

workflows/computational-chemistry/protein-ligand-complex-parameterization/protein-ligand-complex-parameterization.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "Create GRO and TOP complex files",
-    "release": "0.1.1",
+    "release": "0.1.2",
     "steps": {
         "0": {
             "annotation": "pH for protonating the ligand. Set to -1.0 to skip.",

workflows/data-fetching/parallel-accession-download/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.1.1] 2021-07-23
 
 ### Added

workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga

@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.1.1",
+    "release": "0.1.2",
     "name": "Parallel Accession Download",
     "steps": {
         "0": {

workflows/gen_crates.py

@@ -54,8 +54,8 @@
 except ImportError:
     from yaml import Loader
 
-OWNER = "galaxyproject"
-REPO = "iwc"
+THIS_DIR = Path(__file__).absolute().parent
+
 GH_WORKFLOW = "workflow_test.yml"
 TARGET_OWNER = "iwc-workflows"
 GH_API_URL = "https://api.github.com"
@@ -75,6 +75,7 @@
 DOCKSTORE_CFG_VERSION = "1.2"
 LM_URL = "https://api.lifemonitor.eu"
 LM_API_KEY = os.getenv("LM_API_KEY")
+CI_WORKFLOW = THIS_DIR / "wftest.yml"
 
 
 class HubClient:
@@ -229,7 +230,7 @@ def get_workflow_name(repo_dir):
     return f"{repo_dir.name}/{wf_entry['name']}"
 
 
-def make_crate(crate_dir, target_owner, resource, planemo_version):
+def make_crate(crate_dir, target_owner, planemo_version):
     wf_id = get_wf_id(crate_dir)
     planemo_id, planemo_source = get_planemo_id(crate_dir, wf_id)
     crate = ROCrate(gen_preview=False)
@@ -254,6 +255,7 @@ def make_crate(crate_dir, target_owner, resource, planemo_version):
     if readme_source.is_file():
         crate.add_file(readme_source, "README.md")
     suite = crate.add_test_suite(identifier="#test1")
+    resource = f"repos/{target_owner}/{crate_dir.name}/actions/workflows/{CI_WORKFLOW.name}"
     crate.add_test_instance(suite, GH_API_URL, resource=resource,
                             service="github", identifier="test1_1")
     crate.add_test_definition(suite, source=planemo_source,
@@ -343,13 +345,15 @@ def main(args):
     args.hub_url = args.hub_url.rstrip("/")
     if args.upload_to_hub or args.upload_to_lm:
         client = HubClient(base_url=args.hub_url)
-    resource = f"repos/{args.owner}/{args.repo}/actions/workflows/{args.workflow}"
     for repo in find_repos(args.root, exclude=args.exclude):
         print(f"processing {repo}")
         if args.no_overwrite and (repo / "ro-crate-metadata.json").is_file():
             print("  crate exists, not overwriting")
         else:
-            make_crate(repo, args.target_owner, resource, args.planemo_version)
+            target_ci_workflow = repo / ".github" / "workflows" / CI_WORKFLOW.name
+            target_ci_workflow.parent.mkdir(parents=True, exist_ok=True)
+            shutil.copyfile(CI_WORKFLOW, target_ci_workflow)
+            make_crate(repo, args.target_owner, args.planemo_version)
         if args.zip_dir:
             # if args.no_overwrite, zip existing crates
             path = zip_dir / f"{repo.name}.crate"
@@ -390,10 +394,6 @@ def main(args):
                         nargs="*", default=[os.getcwd()])
     parser.add_argument("--exclude", metavar="PATH", nargs="*", default=(),
                         help="paths to exclude while searching for workflow repos")
-    parser.add_argument("--owner", metavar="STRING", default=OWNER,
-                        help="owner of the github workflow that runs the tests")
-    parser.add_argument("--repo", metavar="STRING", default=REPO,
-                        help="repository that contains the github workflow")
     parser.add_argument("--workflow", metavar="STRING", default=GH_WORKFLOW,
                         help="github workflow file name (basename)")
     parser.add_argument("--target-owner", metavar="STRING", default=TARGET_OWNER,

workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.2.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.2.1] 2021-07-23
 
 ### Added

workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: consensus construction",
-    "release": "0.2.1",
+    "release": "0.2.2",
     "steps": {
         "0": {
             "annotation": "Collection of VCFs produced by upstream workflows for variation analysis",

workflows/sars-cov-2-variant-calling/sars-cov-2-ont-artic-variant-calling/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.3.1] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.3] 2021-09-22
 
 ### Changed
@@ -24,12 +29,10 @@ statistics are calculated:
 
   * the tool can now emit variant calls at complex sites with > 1 lengths of
     both the REF and the ALT allele, which were previously dropped
-
   * the workflow became more complex; to account for shortcomings of medaka
     tools annotate, the variant call statistics of regular variants and of
     primer binding site variants have to be determined in separate runs of the
     tool
-
   * All key INFO fields (DP, DP4, AF) will change slightly in this version of
     the workflow
 
@@ -38,7 +41,6 @@ which have been introduced into version 0.3 of the PE Illumina worflow for
 amplicon data before:
 
 - Update ivar trim to version 1.3.1
-
 - Run ivar trim as the last mapped reads processing step before variant
   calling, i.e., after left-alignment of indels
 
@@ -47,7 +49,6 @@ and:
 - Rename the output of the ivar trim step to "Fully processed reads for
   variant calling (primer-trimmed, realigned reads)" like the corresponding
   output of the PE Illumina workflow
-
 - Fix a typo in the allowed input formats for the collection of sequenced
   reads, which caused fastqsanger.gz data to undergo an implicit and
   unnecessary decompression step.

workflows/sars-cov-2-variant-calling/sars-cov-2-ont-artic-variant-calling/ont-artic-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis of ARTIC ONT data",
-    "release": "0.3",
+    "release": "0.3.1",
     "steps": {
         "0": {
             "annotation": "ONT reads from ARTIC assay with fastqsanger encoding",

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.2.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.2.1] 2021-11-04
 
 ### Added

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis.ga

@@ -8,7 +8,7 @@
             "name": "Peter van Heusden"
         }
     ],
-    "release": "0.2.1",
+    "release": "0.2.2",
     "format-version": "0.1",
     "license": "MIT",
     "name": "SARS-CoV-2 Illumina Amplicon pipeline - iVar based",

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.4.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.4.1] 2021-07-23
 
 ### Added

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis on ARTIC PE data",
-    "release": "0.4.1",
+    "release": "0.4.2",
     "steps": {
         "0": {
             "annotation": "Illumina reads from ARTIC assay with fastqsanger encoding",

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.2.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.2.1] 2021-07-23
 
 ### Added

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis on WGS PE data",
-    "release": "0.2.1",
+    "release": "0.2.2",
     "steps": {
         "0": {
             "annotation": "Illumina reads with fastqsanger encoding",

workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.3] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.1.2] 2021-07-23
 
 ### Added

workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis on WGS SE data",
-    "release": "0.1.2",
+    "release": "0.1.3",
     "steps": {
         "0": {
             "annotation": "Illumina reads with fastqsanger encoding",

workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.2] 2021-12-13
+
+### Added
+- Added GitHub Actions workflow. No functional changes.
+
 ## [0.1.1] 2021-07-23
 
 ### Added

workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis reporting",
-    "release": "0.1.1",
+    "release": "0.1.2",
     "steps": {
         "0": {
             "annotation": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the report.",

workflows/wftest.yml

@@ -0,0 +1,24 @@
+name: Periodic workflow test
+on:
+  schedule:
+    - cron: '0 3 * * *'
+  workflow_dispatch:
+jobs:
+  setup:
+    name: Setup cache
+    uses: galaxyproject/iwc/.github/workflows/setup.yml@main
+    with:
+      python-version-list: "[\"3.7\"]"
+      galaxy-fork: galaxyproject
+      galaxy-branch: master
+  test:
+    name: Test workflow
+    needs: setup
+    uses: galaxyproject/iwc/.github/workflows/test_workflows.yml@main
+    with:
+      galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }}
+      python-version-list: "[\"3.7\"]"
+      galaxy-fork: galaxyproject
+      galaxy-branch: master
+      repository-list: '.'
+      check-outputs: true