addition of a workflow for purging duplicates in a single haplotype

workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2024-02-07
+
+### Added
+
+- Workflow for purging duplication in contigs in single haplotype

workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b-tests.yml

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+- doc: Test outline for Purging-duplicates-one-haplotype-VGP6b
+  job:
+    Genomescope model parameters:
+      class: File
+      location: https://www.dropbox.com/scl/fi/6a6b9xc6jih3rtfrfy7ch/Genomescope-model-parameters.tabular?rlkey=2d86kp0wsdlzk5bxzvs36ry4a&dl=1
+      filetype: tabular
+    Assembly to purge:
+      class: File
+      location: https://www.dropbox.com/scl/fi/7hbeju59zkbc5d28lpp19/hap1.fasta?rlkey=xii6j4iq0y48f5qulu0nti8uu&dl=1
+      filetype: fasta
+    Meryl Database:
+      class: File
+      location: https://www.dropbox.com/scl/fi/gpkhbn9onssi5z776kwzy/Meryl-Database.meryldb?rlkey=2ozjdiego6ew9nwaxjgmw3a79&dl=1
+      filetype: meryldb
+    Estimated genome size - Parameter File:
+      class: File
+      location: https://www.dropbox.com/scl/fi/s1jieqs34p5ol3xjcez39/Estimated-genome-size-Parameter-File.expression.json?rlkey=bamnfmxo7mqk7y3gq59v5rrzb&dl=1
+      filetype: expression.json
+    Assembly to leave alone (need this for merqury):
+      class: File
+      location: https://www.dropbox.com/scl/fi/xz7v21ora7n86iisopr8i/hap2.fasta?rlkey=91vdm0bes0a77kaz17rwv759y&dl=1
+      filetype: fasta
+    Pacbio Reads Collection - Trimmed:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: yeast_reads_sub1.fastq.gz
+        location: https://www.dropbox.com/scl/fi/1xmp7kajhdp5cnm4nc8qj/Trimmed_yeast_reads_sub1.fastq.gz?rlkey=q7e54x26fm6fp732kp2lz6bxf&dl=1
+    Name of un-altered assembly: Hap2
+    Name of purged assembly: Hap1
+  outputs:
+    Removed haplotigs:
+      asserts:
+        has_n_lines:
+          n: 14
+    Purged assembly:
+      asserts:
+        has_n_lines:
+          n: 158
+    Purged assembly (GFA):
+     asserts:
+        has_n_lines:
+          n: 160
+    Assembly statistics:
+      asserts:
+        has_text:
+          text: "Average contig length	23,851.86	24,476.28"
+    Cutoffs:
+      asserts:
+        has_text:
+          text: "1       15      15      16      16      48"
+    'Busco on Purged Primary assembly: short summary':
+      asserts:
+        has_text:
+          text: "C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354"
+    Purged assembly statistics:
+      asserts:
+        has_text:
+          text: "# scaffolds	79"
+    Nx Plot:
+      asserts:
+        has_size:
+          value : 57000
+          delta: 5000
+    Size Plot:
+      asserts:
+        has_size:
+          value : 84000
+          delta: 5000
+    'Merqury on Phased assemblies: stats':
+      element_tests:
+        output_merqury.completeness:
+          asserts:
+            has_text:
+              text: "both    all     1244957 1300032 95.7636"