VGP precuration - version 3.0

workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md

@@ -1,5 +1,27 @@
 # Changelog
 
+## [2.5] - 2026-05-14
+
+### Added
+- BWA-MEM is now used for large genomes (>10 Gb) instead of BWA-MEM2 used for smaller genomes.
+- New input `Estimated Genome Size` (single-value file with the estimated genome size in bp) drives the BWA-MEM vs BWA-MEM2 aligner selection.
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.4+galaxy1` (high-resolution PretextMap steps; the low-resolution variants remain on `0.2.4+galaxy0`)
+
+### Changed
+- Input `Generate high resolution Hi-C maps` renamed to `Generate ultra resolution Hi-C maps`.
+
+### Removed
+- Input `Will you use a second haplotype?` — the workflow now infers single- vs two-haplotype mode from whether `Haplotype 2` is provided.
+- Output `Both Haplotypes merged` (no longer surfaced; merge happens internally).
+- Outputs `Hi-C duplication stats on Scaffolds: MultiQc` and `Hi-C duplication stats on Scaffolds: Raw` (MultiQC step removed; the plain `Hi-C duplication stats on Scaffolds` output is retained).
+- Outputs `Pairtools Multiqc Stats on Scaffolds` and `Pairtools MultiQc on Scaffolds: Plots`.
+
+### Note
+- RefSeq-based related-species detection and JBrowse2 visualization have been moved to a separate workflow.
+
+
 ## [2.4] - 2026-04-29
 
 ### Automatic update

workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/README.md

@@ -13,10 +13,10 @@ The Pretext files can be opened in PretextView for manual curation of genome ass
 ### Required Inputs
 
 1. **Haplotype 1** [fasta] - Primary haplotype assembly
-2. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies
-3. **Haplotype 2** [fasta] - Secondary haplotype assembly (required if using two haplotypes)
-4. **Hi-C reads** [fastq] - Paired collection containing Hi-C data
-5. **PacBio reads** [fastq] - Collection of PacBio HiFi reads
+2. **Haplotype 2** [fasta] - Secondary haplotype assembly (leave unset for single-haplotype mode)
+3. **Hi-C reads** [list:paired collection, fastq] - Paired collection containing Hi-C data
+4. **PacBio reads** [list collection, fastq.gz] - Collection of PacBio HiFi reads
+5. **Estimated Genome Size** [file] - Single-value file with the estimated genome size in bp; used to switch from BWA-MEM2 to BWA-MEM for genomes larger than 10 Gb
 
 ### Assembly Annotation Parameters
 
@@ -49,7 +49,7 @@ The Pretext files can be opened in PretextView for manual curation of genome ass
 
 ### Hi-C Map Resolution
 
-20. **Generate high resolution Hi-C maps** [boolean] - Generate high resolution Pretext maps (slower, requires more resources)
+20. **Generate ultra resolution Hi-C maps** [boolean] - Generate ultra resolution Pretext maps (slower, requires more resources)
 
 ### Visualization Options
 
@@ -61,61 +61,53 @@ The Pretext files can be opened in PretextView for manual curation of genome ass
 
 1. **Assembly for curation** [fasta] - Merged assembly (if two haplotypes used) or single haplotype with optional suffix
 2. **Assembly Info** [tabular] - Summary statistics from gfastats
-3. **Both Haplotypes merged** [fasta] - Concatenated assembly file
+3. **Decontaminated Hap1 with Suffix** [fasta] - Haplotype 1 with suffix applied
+4. **Decontaminated Hap2 with Suffix** [fasta] - Haplotype 2 with suffix applied
 
 ### Gene Annotation Outputs
 
-4. **Compleasm Genes track** [GFF] - Combined gene annotations for Pretext track (if gene annotations enabled)
+5. **Compleasm Genes track** [GFF] - Combined gene annotations for Pretext track (if gene annotations enabled)
 
 ### Hi-C Alignment Outputs
 
-5. **Merged Hi-C Alignments on Scaffolds** [BAM] - Combined Hi-C read alignments
-6. **Precuration Hi-C alignments** [BAM] - Hi-C alignments before filtering
-7. **Trimmed Hi-C data** [fastq] - Hi-C reads after adapter trimming (if trimming enabled)
-8. **Hi-C duplication stats on Scaffolds** [tabular] - Samtools markdup statistics (if duplicate removal enabled)
-9. **Hi-C duplication stats on Scaffolds: MultiQc** [HTML] - MultiQC report of duplicate statistics (if duplicate removal enabled)
-10. **Hi-C duplication stats on Scaffolds: Raw** [tabular] - Raw Samtools markdup metrics (if duplicate removal enabled)
-11. **Pairtools Multiqc Stats on Scaffolds** [tabular] - Pairtools statistics
-12. **Pairtools MultiQc on Scaffolds: Plots** [HTML] - Pairtools MultiQC plots
+6. **Merged Hi-C Alignments on Scaffolds** [BAM] - Combined Hi-C read alignments
+7. **Precuration Hi-C alignments** [BAM] - Hi-C alignments before filtering
+8. **Trimmed Hi-C data** [fastq] - Hi-C reads after adapter trimming (if trimming enabled)
+9. **Hi-C duplication stats on Scaffolds** [tabular] - Samtools markdup statistics (if duplicate removal enabled)
 
 ### PacBio Processing Outputs
 
-13. **HiFi reads without adapters** [fastq] - Adapter-trimmed PacBio reads (if adapter removal enabled)
-14. **HiFi reads adapters trimming report** [tabular] - Cutadapt trimming statistics (if adapter removal enabled)
+10. **HiFi reads without adapters** [fastq] - Adapter-trimmed PacBio reads (if adapter removal enabled)
+11. **HiFi reads adapters trimming report** [tabular] - Cutadapt trimming statistics (if adapter removal enabled)
 
 ### PacBio Coverage Outputs
 
-15. **BigWig Coverage** [bigwig] - PacBio read coverage track
-16. **Coverage Gaps Track** [bedgraph] - Regions with low or no PacBio coverage
-17. **Merged HiFi Alignments** [BAM] - Combined PacBio alignments
+12. **BigWig Coverage** [bigwig] - PacBio read coverage track
+13. **Coverage Gaps Track** [bedgraph] - Regions with low or no PacBio coverage
+14. **Merged HiFi Alignments** [BAM] - Combined PacBio alignments
 
 ### Telomere Outputs
 
-18. **Telomere Report** [tabular] - Comprehensive telomere analysis from Teloscope
-19. **terminal telomeres** [bedgraph] - All detected telomeric regions
-20. **P telomeres bed** [BED] - P-arm (5') telomeres only
-21. **Q telomeres Bed** [BED] - Q-arm (3') telomeres only
+15. **Telomere Report** [tabular] - Comprehensive telomere analysis from Teloscope
+16. **terminal telomeres** [bedgraph] - All detected telomeric regions
+17. **P telomeres bed** [BED] - P-arm (5') telomeres only
+18. **Q telomeres Bed** [BED] - Q-arm (3') telomeres only
 
 ### Gap Outputs
 
-22. **Gaps Bed** [BED] - Assembly gap coordinates
-23. **Gaps Bedgraph** [bedgraph] - Assembly gap track for Pretext
-
-### Assembly Haplotype Outputs
-
-24. **Decontaminated Hap1 with Suffix** [fasta] - Haplotype 1 with suffix applied
-25. **Decontaminated Hap2 with Suffix** [fasta] - Haplotype 2 with suffix applied
+19. **Gaps Bed** [BED] - Assembly gap coordinates
+20. **Gaps Bedgraph** [bedgraph] - Assembly gap track for Pretext
 
 ### Pretext Map Outputs
 
 All Pretext outputs are generated in two versions:
 - **With MAPQ filtering** (default MAPQ ≥ 10): Cleaner maps with high-confidence contacts
 - **Without filtering (Multimapping)**: Shows all mapped contacts including low-quality alignments
 
-26. **Pretext All tracks** [pretext] - Contact map with all annotation tracks (MAPQ filtered)
-27. **Pretext All tracks - Multimapping** [pretext] - Contact map with all tracks (unfiltered)
-28. **Pretext Snapshot With tracks** [PNG] - Image of contact map with tracks (MAPQ filtered)
-29. **Pretext Snapshot With tracks - Multimapping** [PNG] - Image of contact map with tracks (unfiltered)
+21. **Pretext All tracks** [pretext] - Contact map with all annotation tracks (MAPQ filtered)
+22. **Pretext All tracks - Multimapping** [pretext] - Contact map with all tracks (unfiltered)
+23. **Pretext Snapshot With tracks** [PNG] - Image of contact map with tracks (MAPQ filtered)
+24. **Pretext Snapshot With tracks - Multimapping** [PNG] - Image of contact map with tracks (unfiltered)
 
 ## Usage Notes
 

workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml

@@ -1,8 +1,8 @@
 # Planemo test configuration for Hi-C contact map workflow
-# Test 1: Single read set per technology (no collections)
-# Test 2: Multiple read sets with collections
+# Test 1: Diploid (two haplotypes), single read set per technology
+# Test 2: Single haplotype, multiple read sets with collections
 
-- doc: Test 1 - Single read set per technology
+- doc: Test 1 - Diploid, single read set per technology
   job:
     Haplotype 1:
       class: File
@@ -49,7 +49,6 @@
         - hash_function: SHA-1
           hash_value: 84fe8fad10155f9edd1365ba13bb5f30f0d1d881
     Do you want to add suffixes to the scaffold names?: true
-    Will you use a second haplotype?: true
     First Haplotype suffix: H1
     Second Haplotype suffix: H2
     Do you want to trim the Hi-C data?: false
@@ -62,9 +61,13 @@
     Species Name: Test_species
     Assembly Name: toLid
     Lineage for Compleasm: vertebrata_odb10
-    Database for Compleasm: v5 
-    Generate gene annotations: false
-    Generate high resolution Hi-C maps: false
+    Database for Compleasm: v5
+    Generate gene annotations: true
+    Generate ultra resolution Hi-C maps: false
+    Estimated Genome Size:
+      class: File
+      location: https://zenodo.org/records/19925237/files/real_size.txt
+      filetype: txt
   outputs:
     Assembly for curation:
       asserts:
@@ -103,22 +106,20 @@
         has_size:
           value: 800000
           delta: 400000
-    "Hi-C duplication stats on Scaffolds: Raw":
-      asserts:
-        has_text:
-          text: "total_dups\t3941"
     Precuration Hi-C alignments:
       asserts:
         has_size:
           value: 7427810
           delta: 50000
     Hi-C duplication stats on Scaffolds:
       asserts:
-        - has_text:
-            text: "EXCLUDED: 1042"
-        - has_text_matching:
-            expression: "READ: (\\d+)\\nWRITTEN: (?!\\1\\b)\\d+"
-- doc: Test 2 - Multiple read sets with collections
+        has_text:
+          text: "EXCLUDED: 1042"
+    Compleasm Genes track:
+      asserts:
+        has_text:
+          text: "scaffold_1.H2\t106669\t106765"
+- doc: Test 2 - Single haplotype, multiple read sets with collections
   job:
     Haplotype 1:
       class: File
@@ -127,13 +128,6 @@
       hashes:
       - hash_function: SHA-1
         hash_value: a0ee25fd9f7cf223ca40ff530e1201589fade212
-    Haplotype 2:
-      class: File
-      location: https://zenodo.org/records/18664706/files/Haplotype_2.fasta
-      filetype: fasta
-      hashes:
-      - hash_function: SHA-1
-        hash_value: 166cb118625113e39593bedb10aaea028c20f77d
     Hi-C reads:
       class: Collection
       collection_type: list:paired
@@ -187,7 +181,6 @@
         - hash_function: SHA-1
           hash_value: f0408118bf8d116d0d560d2899fc4861c930c067
     Do you want to add suffixes to the scaffold names?: true
-    Will you use a second haplotype?: true
     First Haplotype suffix: H1
     Second Haplotype suffix: H2
     Do you want to trim the Hi-C data?: false
@@ -201,8 +194,12 @@
     Assembly Name: toLid
     Lineage for Compleasm: vertebrata_odb10
     Database for Compleasm: v5
-    Generate gene annotations: true
-    Generate high resolution Hi-C maps: false
+    Generate gene annotations: false
+    Generate ultra resolution Hi-C maps: false
+    Estimated Genome Size:
+      class: File
+      location: https://zenodo.org/records/19925237/files/large_size.txt
+      filetype: txt
   outputs:
     Assembly for curation:
       asserts:
@@ -223,40 +220,24 @@
     BigWig Coverage:
       asserts:
         has_size:
-          value: 20000
-          delta: 10000
-    P telomeres bed:
-      asserts:
-        - has_text:
-            text: "scaffold_10.H2"
-        - has_text:
-            text: "scaffold_1.H1\t488600\t500600\t12000"
-    Merged Hi-C Alignments on Scaffolds:
+          value: 7000
+          delta: 2000
+    Precuration Hi-C alignments:
       asserts:
         has_size:
-          value: 15000000
-          delta: 6000000
+          value: 12805288
+          delta: 2000000
     Pretext All tracks:
       asserts:
         has_size:
-          value: 2000000
-          delta: 1000000
+          value: 940000
+          delta: 200000
     Pretext All tracks - Multimapping:
       asserts:
         has_size:
-          value: 2000000
-          delta: 1000000
-    Compleasm Genes track:
-      asserts:
-        has_text:
-          text: "scaffold_1.H2\t106669\t106765"
-    "Hi-C duplication stats on Scaffolds: Raw":
+          value: 940000
+          delta: 200000
+    P telomeres bed:
       asserts:
         has_text:
-          text: "total_dups\t3941\t2623"
-    Hi-C duplication stats on Scaffolds:
-      asserts:
-        - has_text:
-            text: "EXCLUDED: 1725"
-        - has_text_matching:
-            expression: "READ: (\\d+)\\nWRITTEN: \\1\\b"
+          text: "scaffold_1.H1\t488600\t500600\t12000"