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/PretextMap_Generation-tests.yml

@@ -8,14 +8,14 @@
       class: File
       location: https://zenodo.org/records/14218240/files/Haplotype%202.fasta
       filetype: fasta
-    HiC reads - forward:
+    Collection of HiC reads - forward:
       class: Collection
       collection_type: list
       elements:
       - class: File
         identifier: HiC forward reads
         location: https://zenodo.org/records/14218240/files/Hi-C%20forward%20reads.fastqsanger.gz
-    HiC reads - reverse:
+    Collection of HiC reads - reverse:
       class: Collection
       collection_type: list
       elements:

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

@@ -322,10 +322,10 @@
             "inputs": [
                 {
                     "description": "",
-                    "name": "HiC reads - forward"
+                    "name": "Collection of HiC reads - forward"
                 }
             ],
-            "label": "HiC reads - forward",
+            "label": "Collection of HiC reads - forward",
             "name": "Input dataset collection",
             "outputs": [],
             "position": {
@@ -349,10 +349,10 @@
             "inputs": [
                 {
                     "description": "",
-                    "name": "HiC reads - reverse"
+                    "name": "Collection of HiC reads - reverse"
                 }
             ],
-            "label": "HiC reads - reverse",
+            "label": "Collection of HiC reads - reverse",
             "name": "Input dataset collection",
             "outputs": [],
             "position": {

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

@@ -10,8 +10,8 @@ This workflow generates Hi-C contact maps for diploid genome assemblies in the P
 3. **Do you want to add suffixes to the scaffold names?** Select yes if the scaffold names in your assembly do not contain haplotype information.
 4. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names.
 5. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names.
-6. **HiC reads - forward**  [fastq] Collection containing the Hi-C forward reads
-7. **HiC reads - reverse**  [fastq] Collection containing the Hi-C reverse reads
+6. **Collection of HiC reads - forward**  [fastq] Collection containing the Hi-C forward reads
+7. **Collection of HiC reads - reverse**  [fastq] Collection containing the Hi-C reverse reads
 8. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with some Arima Hi-C if the Hi-C map looks "noisy".
 9.  **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates.
 10. **PacBio reads collection** [fastq] Collection of PacBio reads.