Merge pull request #854 from Delphine-L/vgp1

VGP 1 - Add Rdeval, hetorozygous coverage, and estimated genome size outputs

Author: Delphine-L

workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+
+## [0.2] - 2025-05-16
+
+### Changes
+- Add RDeval to evaluate PacBio HiFi reads quality
+- Now compute the homozygous read coverage and the estimated genome size in this workflow
+
 ## [0.1.9] - 2024-12-17
 ### Added
 - Annotation for workflow describing its function

workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/README.md

@@ -1,16 +1,18 @@
 # VGP Workflow #1
 
-This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.
+This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality. It also provides statistics on the PacBio Hifi reads. 
 
 ### Inputs
 
--   A collection of Hifi long reads in FASTQ format
--   *k*-mer length
--   Ploidy
+1. The name of the species being assembled
+2. The Name of the assembly
+3. A collection of Hifi long reads in FASTQ format
+4. *k*-mer length
+5. Ploidy
 
 ### Outputs
 
--   Meryl Database of kmer counts
+-   Meryl Database of *k*-mer counts
 -   GenomeScope
     -   Linear plot
     -   Log plot
@@ -19,5 +21,9 @@ This workflow produces a Meryl database and Genomescope outputs that will be use
     -   Summary
     -   Model
     -   Model parameteres
+- RDeval for PacBio Hifi Reads QC
+    -   Reads statistics
+    -   HTML report
+  
 
  ![image](https://github.com/galaxyproject/iwc/assets/4291636/565238fc-f8a9-46ac-8b31-6276410fa436)

workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml

@@ -1,46 +1,44 @@
 - doc: Test outline for kmer-profiling-hifi-VGP1.ga
   job:
+    Species Name: Test Species
+    Assembly Name: testSpe1
     Collection of Pacbio Data:
       class: Collection
       collection_type: list
       elements:
       - class: File
         identifier: pacbio_reads
-        location: https://zenodo.org/record/6603774/files/child.fastq?download=1
+        location: https://zenodo.org/record/6098306/files/HiFi_synthetic_50x_01.fasta
         filetype: fastqsanger
-    'K-mer length ': 8
-    Ploidy: 1
+    'K-mer length': 21
+    Ploidy: 2
   outputs:
     GenomeScope linear plot:
-      file: test-data/GenomeScope_Linear_plot.png
-      compare: sim_size
-      delta: 10000
+      asserts:
+        has_size:
+            value: 182100
+            delta: 10000
     GenomeScope log plot:
-      file: test-data/GenomeScope_Log_plot.png
-      compare: sim_size
-      delta: 10000
-    GenomeScope transformed linear plot:
-      file: test-data/GenomeScope_Transformed_linear_plot.png
-      compare: sim_size
-      delta: 10000
-    GenomeScope transformed log plot:
-      file: test-data/GenomeScope_Transformed_log_plot.png
-      compare: sim_size
-      delta: 10000
+      asserts:
+        has_size:
+            value: 195200
+            delta: 10000
     GenomeScope summary:
       asserts:
         - has_text_matching:
-            expression: '27,84. bp'
-        - has_text_matching:
-            expression: '35,91. bp'
+            expression: '7,859,... bp'
     GenomeScope Model Parameters:
       asserts:
         - has_text_matching:
-            expression: '0.09184.*'
+            expression: '0.012.*'
         - has_text_matching:
-            expression: '27.44.*'
+            expression: '12.45.*'
     Merged Meryl Database:
       asserts:
         has_size:
-            value: 105703
-            delta: 10000
+            value: 27710666
+            delta: 1000000
+    Reads Statistics:
+      asserts:
+        has_text: 
+          text: "# reads	21224"