Merge pull request galaxyproject#245 from Delphine-L/VGP5

Addition of Vgp5 : Assembly with Hifi and parental data

workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  primaryDescriptorPath: /Assembly-Hifi-Trio-phasing-VGP5.ga
+  subclass: Galaxy
+  testParameterFiles:
+  - /Assembly-Hifi-Trio-phasing-VGP5-tests.yml

workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml

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+- doc: Test outline for Assembly-Hifi-Trio-phasing-VGP5
+  job:
+    'Meryl Database : Child':
+      class: File
+      location: https://zenodo.org/records/10056319/files/Meryl%20Database%20-%20Child.meryldb?download=1
+      filetype: meryldb
+    'Hapmer Database : Paternal':
+      class: File
+      location: https://zenodo.org/records/10056319/files/Hapmer%20Database%20-%20Paternal.meryldb?download=1
+      filetype: meryldb
+    'Hapmer Database : Maternal':
+      class: File
+      location: https://zenodo.org/records/10056319/files/Hapmer%20Database%20-%20Maternal.meryldb?download=1
+      filetype: meryldb
+    Genomescope Summary:
+      class: File
+      location: https://zenodo.org/records/10056319/files/Genomescope%20Summary.txt?download=1
+      filetype: txt
+    'Pacbio Reads Collection : child':
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: yeast_reads_sub1.fastq.gz
+        location: https://zenodo.org/records/10056319/files/Pacbio%20Reads%20Collection.fastq.gz?download=1
+    Paternal Illumina reads (hap1):
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: hap1_2.fq
+        location: https://zenodo.org/records/10056319/files/Sub_hap1_2.fastqsanger?download=1
+      - class: File
+        identifier: hap1_1.fq
+        location: https://zenodo.org/records/10056319/files/Sub_hap1_1.fastqsanger?download=1
+    Maternal Illumina reads (hap2):
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: hap2_2.fq
+        location: https://zenodo.org/records/10056319/files/Sub_hap2_2.fastqsanger?download=1
+      - class: File
+        identifier: hap2_1.fq
+        location: https://zenodo.org/records/10056319/files/Sub_hap2_1.fastqsanger?download=1
+    SAK input file (Optional): null
+    Bits for bloom filter: 32
+    Name for Haplotype 1: Hap1
+    Name for Haplotype 2: Hap2
+  outputs:
+    Estimated Genome size: 2288021 
+    Assembly statistics for Hap1 and Hap2:
+      asserts:
+        has_line:
+          line: "# contigs	86	79"
+    usable hap1 gfa:
+      asserts:
+        has_n_lines:
+          n: 177
+    Hifiasm Trio hap1:
+      asserts:
+        has_n_lines:
+          n: 172
+    Busco Summary Hap1:
+      asserts:
+        has_text:
+          text: "C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354"
+    Nx Plot:
+      asserts:
+        has_size: 
+          value : 57000
+          delta: 5000
+
+
+