revert changes for the three workflows failing

galaxyproject · Nov 22, 2023 · 1df11b7 · 1df11b7
1 parent 6fb518a
commit 1df11b7
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Showing 12 changed files with 104 additions and 245 deletions.
diff --git a/...lows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/.dockstore.yml b/...lows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/.dockstore.yml
@@ -1,11 +1,7 @@
 version: 1.2
 workflows:
 - name: 'SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE'
-  subclass: Galaxy
-  publish: true
   primaryDescriptorPath: /pe-wgs-ivar-analysis.ga
+  subclass: Galaxy
   testParameterFiles:
-  - /pe-wgs-ivar-analysis-tests.yml
-  authors:
-  - name: Peter van Heusden
-    orcid: 0000-0001-6553-5274
+  - /pe-wgs-ivar-analysis-test.yml
diff --git a/...s-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/CHANGELOG.md b/...s-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/CHANGELOG.md
@@ -3,6 +3,7 @@
 ## [0.2.4] 2023-11-20
 
 - Fix author in dockstore
+- Import and export in galaxy to get fixed changeset
 
 ## [0.2.3] 2022-05-25
 

diff --git a/...r-analysis/pe-wgs-ivar-analysis-tests.yml → ...ar-analysis/pe-wgs-ivar-analysis-test.yml b/...r-analysis/pe-wgs-ivar-analysis-tests.yml → ...ar-analysis/pe-wgs-ivar-analysis-test.yml
diff --git a/...-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis.ga b/...-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis.ga
diff --git a/...ws/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/.dockstore.yml b/...ws/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/.dockstore.yml
@@ -1,11 +1,7 @@
 version: 1.2
 workflows:
 - name: 'COVID-19-PE-ARTIC-ILLUMINA'
-  subclass: Galaxy
-  publish: true
   primaryDescriptorPath: /pe-artic-variation.ga
+  subclass: Galaxy
   testParameterFiles:
-  - /pe-artic-variation-tests.yml
-  authors:
-  - name: Wolfgang Maier
-    orcid: 0000-0002-9464-6640
+  - /pe-artic-variation-test.yml
diff --git a/...cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md b/...cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md
@@ -1,10 +1,5 @@
 # Changelog
 
-## [0.5.1] 2023-11-20
-
-- Fix author in dockstore
-- Use zenodo link instead of googleapis for fastq
-
 ## [0.5] - 2022-02-08
 
 ### Fixed

diff --git a/...iant-calling/pe-artic-variation-tests.yml → ...riant-calling/pe-artic-variation-test.yml b/...iant-calling/pe-artic-variation-tests.yml → ...riant-calling/pe-artic-variation-test.yml
@@ -22,10 +22,12 @@
           elements:
           - identifier: forward
             class: File
-            location: "https://zenodo.org/records/10174466/files/SRR11578257_R1.fastq.gz?download=1"
+            location: "https://storage.googleapis.com/nih-sequence-read-archive/sra-src/SRR11578257/VIC818_R1.fq.gz"
+            filetype: fastqsanger.gz
           - identifier: reverse
             class: File
-            location: "https://zenodo.org/records/10174466/files/SRR11578257_R2.fastq.gz?download=1"
+            location: "https://storage.googleapis.com/nih-sequence-read-archive/sra-src/SRR11578257/VIC818_R2.fq.gz"
+            filetype: fastqsanger.gz
   outputs:
     annotated_softfiltered_variants:
       attributes: {}

diff --git a/...-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga b/...-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": "0.5.1",
+    "release": "0.5",
     "steps": {
         "0": {
             "annotation": "Illumina reads from ARTIC assay with fastqsanger encoding",

diff --git a/...lows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/.dockstore.yml b/...lows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/.dockstore.yml
@@ -1,11 +1,7 @@
 version: 1.2
 workflows:
 - name: 'COVID-19-SE-WGS-ILLUMINA'
-  subclass: Galaxy
-  publish: true
   primaryDescriptorPath: /se-wgs-variation.ga
+  subclass: Galaxy
   testParameterFiles:
-  - /se-wgs-variation-tests.yml
-  authors:
-  - name: Wolfgang Maier
-    orcid: 0000-0002-9464-6640
+  - /se-wgs-variation-test.yml
diff --git a/...s-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/CHANGELOG.md b/...s-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/CHANGELOG.md
@@ -1,9 +1,5 @@
 # Changelog
 
-## [0.1.4] 2023-11-20
-
-- Fix author in dockstore
-
 ## [0.1.3] 2021-12-13
 
 ### Added

diff --git a/...ariant-calling/se-wgs-variation-tests.yml → ...variant-calling/se-wgs-variation-test.yml b/...ariant-calling/se-wgs-variation-tests.yml → ...variant-calling/se-wgs-variation-test.yml
diff --git a/...sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation.ga b/...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": "0.1.4",
+    "release": "0.1.3",
     "steps": {
         "0": {
             "annotation": "Illumina reads with fastqsanger encoding",