Merge pull request galaxyproject#224 from Delphine-L/VGP8

Addition of workflow Vgp8 : scaffolding with HiC data

workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  primaryDescriptorPath: /Scaffolding-HiC-VGP8.ga
+  subclass: Galaxy
+  testParameterFiles:
+  - /Scaffolding-HiC-VGP8-tests.yml

workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.1] - 2023-09-27
+
+Creation of the workflow and tests

workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/README.md

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+# Scaffolding HiC
+
+Scaffolding using HiC data with YAHS
+
+## Inputs
+
+1. Scaffolded assembly [fasta]
+2. Concatenated HiC forward reads [fastq]
+3. Concatenated HiC reverse reads [fastq]
+4. Restriction enzyme sequence [txt]
+5. Estimated genome size [txt]
+
+### Outputs
+
+1. Scaffolds in [fasta] and [gfa] format
+2. QC: Assembly statistics
+3. QC: Nx plot
+4. QC: Size plot
+5. QC: BUSCO report
+6. QC: Pretext Maps before and after scaffolding

workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml

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+- doc: Test outline for Scaffolding-HiC-VGP8
+  job:
+    input GFA:
+      class: File
+      location: https://zenodo.org/records/10037496/files/input%20GFA.gfa1?download=1
+      filetype: gfa1
+    HiC Forward reads:
+      class: File
+      location: https://zenodo.org/records/10037496/files/HiC%20Forward%20reads.fastqsanger.gz?download=1
+      filetype: fastqsanger.gz
+    HiC reverse reads:
+      class: File
+      location: https://zenodo.org/records/10037496/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
+      filetype: fastqsanger.gz
+    Estimated genome size - Parameter File:
+      class: File
+      location: https://zenodo.org/records/10037496/files/Estimated%20genome%20size%20-%20Parameter%20File.txt?download=1
+      filetype: txt
+    Restriction enzymes: arima2
+  outputs:
+    Reconciliated scaffolds:
+      asserts:
+        has_n_lines:
+          n: 168
+    Nx Plot:
+      asserts:
+        has_size: 
+          value : 47000
+          delta: 5000
+    Pretext Map After HiC scaffolding:
+      asserts:
+        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"