Merge branch 'VGP6' of https://github.com/Delphine-L/iwc into VGP6

Delphine-L · Oct 27, 2023 · bfee856 · bfee856
2 parents 51bf602 + 3f7825f
commit bfee856
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diff --git a/workflows/VGP-assembly-v2/Purgedups-VGP6/Purgedups-WF6-tests.yml b/workflows/VGP-assembly-v2/Purgedups-VGP6/Purgedups-WF6-tests.yml
@@ -28,7 +28,6 @@
         identifier: yeast_reads_sub1.fastq.gz
         location: https://zenodo.org/records/10047837/files/Pacbio%20Reads%20Collection%20-%20Trimmed_yeast_reads_sub1.fastq.gz.fastq.gz?download=1
     Busco Lineage: vertebrata_odb10
-    SAK input file (Optional): null
     Name of primary assembly: Primary
     Name of alternate assembly: Alternate
   outputs:

diff --git a/workflows/VGP-assembly-v2/Purgedups-VGP6/Purgedups-WF6.ga b/workflows/VGP-assembly-v2/Purgedups-VGP6/Purgedups-WF6.ga
@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "",
+    "annotation": "Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)",
     "creator": [
         {
             "class": "Organization",
@@ -15,7 +15,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.1",
-    "name": "Purgedups-WF6",
+    "name": "Purge Duplicate Contigs - WF6",
     "steps": {
         "0": {
             "annotation": "",
@@ -221,10 +221,10 @@
             "inputs": [
                 {
                     "description": "",
-                    "name": "SAK input file (Optional)"
+                    "name": "SAK input file"
                 }
             ],
-            "label": "SAK input file (Optional)",
+            "label": "SAK input file",
             "name": "Input dataset",
             "outputs": [],
             "position": {

diff --git a/workflows/VGP-assembly-v2/Purgedups-VGP6/README.md b/workflows/VGP-assembly-v2/Purgedups-VGP6/README.md
@@ -1,7 +1,7 @@
-# Purgedups 
+# Purge Duplicate Contigs
 
 Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication)
-This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging step (Workflow 3, 4, or 5)
+This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)
 
 ## Inputs
 
@@ -23,4 +23,4 @@ This workflow is the 6th workflow of the VGP pipeline. It is meant to be run aft
 4. QC: Merqury report for both assemblies
 5. QC: Assembly statistics for both assemblies
 6. QC: Nx plot for both assemblies
-7. QC: Size plot for both assemblies
+7. QC: Size plot for both assemblies