Merge pull request #240 from Delphine-L/VGP8-update

Vgp8 updateUpdate of Workflow 8 scaffolding with HiC
galaxyproject · Oct 30, 2023 · 41104f0 · 41104f0
2 parents 5ea2daa + 2ae52d9
commit 41104f0
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diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md
@@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+
+## [0.1.1] - 2023-10-26
+
+Added tags for better visibility of outputs in the history, and exposure of the BUSCO lineage parameter
+
 ## [0.1] - 2023-09-27
 
 Creation of the workflow and tests
diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md
@@ -1,6 +1,11 @@
-# Scaffolding HiC
+# Scaffolding with HiC data
 
-Scaffolding using HiC data with YAHS
+This workflow perfoms scaffolding using HiC data with YAHS. It is designed to be run as part of one the VGP analysis trajectories. 
+Example of trajectory : 
+- VGP1 : Kmer profiling 
+- VGP4 : Genome assembly with HiC phasing
+- VGP6 : Purge duplicated haplotigs
+- VGP8 : Scaffolding with HiC
 
 ## Inputs
 

diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml
@@ -16,12 +16,25 @@
       class: File
       location: https://zenodo.org/records/10037496/files/Estimated%20genome%20size%20-%20Parameter%20File.txt?download=1
       filetype: txt
+    Lineage: vertebrata_odb10
     Restriction enzymes: arima2
   outputs:
-    Reconciliated scaffolds:
+    "Reconciliated Scaffolds: gfa":
+      asserts:
+        has_n_lines:
+          n: 169
+    'Reconciliated Scaffolds: fasta':
       asserts:
         has_n_lines:
           n: 168
+    Busco Summary:
+      asserts:
+        has_text:
+          text: "C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354"
+    Assembly Statistics for s2:
+      asserts:
+        has_line:
+          line: "# scaffolds	84"
     Nx Plot:
       asserts:
         has_size: 
@@ -32,15 +45,3 @@
         has_size: 
           value : 893000
           delta: 50000
-    Busco Summary:
-      asserts:
-        has_text:
-          text: "C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354"
-    Yahs scaffolds reconciliated:
-      asserts:
-        has_n_lines:
-          n: 169
-    Assembly Statistics for s2:
-      asserts:
-        has_line:
-          line: "# scaffolds	84"