From 3f7825f89a245f8325136cd1d816d6f219e30502 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 27 Oct 2023 12:34:08 +0200
Subject: [PATCH] Update labels, minor description fixes

---
 .../Purgedups-VGP6/Purgedups-WF6-tests.yml                | 1 -
 workflows/VGP-assembly-v2/Purgedups-VGP6/Purgedups-WF6.ga | 8 ++++----
 workflows/VGP-assembly-v2/Purgedups-VGP6/README.md        | 6 +++---
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/workflows/VGP-assembly-v2/Purgedups-VGP6/Purgedups-WF6-tests.yml b/workflows/VGP-assembly-v2/Purgedups-VGP6/Purgedups-WF6-tests.yml
index c6f298744..1e7bd5a15 100644
--- 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://www.dropbox.com/scl/fi/lurqcq79www0e1g4e3qo3/Pacbio-Reads-Collection-Trimmed_yeast_reads_sub1.fastq.gz.fastq.gz?rlkey=nfbvfr0jcpknj66mp2fb0xsv2&dl=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
index 419e1a354..2e5cda674 100644
--- 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
index 046309ee8..b2d6c9577 100644
--- 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
\ No newline at end of file
+7. QC: Size plot for both assemblies