feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input.

workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /PretextMap_Generation.ga
+  testParameterFiles:
+  - /PretextMap_Generation-tests.yml
+  authors:
+  - name: Patrik Smeds
+    orcid: 0000-0001-6228-2785
+  - name: Delphine Lariviere
+    orcid: 0000-0001-6421-3484

workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/CHANGELOG.md

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+# Changelog
+
+## [1.0] 2024-11-12
+
+- Creation of a workflow for the generation of Hi-C Maps with coverage, gaps and Telomere Tracks

workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml

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+- doc: Test outline for PretextMap-Generation-from-2-haplotypes
+  job:
+    Haplotype 1:
+      class: File
+      location: https://zenodo.org/records/14230702/files/Haplotype%201.fasta
+      filetype: fasta
+    Haplotype 2:
+      class: File
+      location: https://zenodo.org/records/14230702/files/Haplotype%202.fasta
+      filetype: fasta
+    Hi-C reads - forward:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: HiC forward reads
+        location: https://zenodo.org/records/14230702/files/HiC%20forward.fastqsanger.gz
+    Hi-C reads - reverse:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: HI-C reverse reads
+        location: https://zenodo.org/records/14230702/files/HiC%20reverse.fastqsanger.gz
+    PacBio reads:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: PacBio reads.fastq.gz
+        location: https://zenodo.org/records/14230702/files/PacBio%20reads.fastq.gz
+    Do you want to add suffixes to the scaffold names?: true
+    Haplotype 1 suffix: hap1
+    Haplotype 2 suffix: hap2
+    Do you want to trim the Hi-C data?: true
+    Telomere repeat to suit species: CCCTAA
+  outputs:
+    Merged Haplotypes:
+      asserts:
+        has_text:
+          text: ">scaffold_10.hap1"
+        has_text:
+          text: ">scaffold_10.hap2"
+    Gaps Bed:
+      asserts:
+        has_text:
+          text: "scaffold_10.hap1	34145604	34145804"
+        has_text:
+          text: "scaffold_10.hap2	137138839	137139039"
+    Seqtk-telo Output:
+      asserts:
+        has_text:
+          text: "scaffold_10.hap2	0	11012	139653677"
+    Gaps Bedgraph:
+      asserts:
+        has_text:
+          text: "scaffold_10.hap2	137138839	137139039	200"
+    BigWig Coverage:
+      asserts:
+        has_size:
+          value : 112000
+          delta: 4000
+    Telomeres Bedgraph:
+      asserts:
+        has_text:
+          text: "scaffold_10.hap2	0	11012	11012"
+    Trimmed Hi-C Forward Reads:
+      asserts:
+        has_size:
+          value : 13900000
+          delta: 2000000
+    Trimmed Hi-C Reverse Reads:
+      asserts:
+        has_size:
+          value : 14300000
+          delta: 2000000
+    Merged Hi-C Alignments:
+      asserts:
+        has_size:
+          value : 4600000
+          delta: 1000000
+    Pretext All tracks:
+      asserts:
+        has_size:
+          value : 946900
+          delta: 40000
+