Merge pull request #1135 from Delphine-L/vgp8

Update vgp 8 and remove Markduplicates to replace it with samtools markdup

Author: mvdbeek

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

@@ -1,8 +1,29 @@
 # Changelog
 
+## [3.4] - 2026-03-09
+
+### Changes
+- Remove "Alignment General Stats 2" output that was incompatible with MultiQC v1.33 (element `general_stats_table` no longer exists in the `png_plot` output collection)
+- Set new PretextMap `high_res` parameter to `false`
+- Replace Picards MarkDuplicates tool by Samtools markdup
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2`
+- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.2.3+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy3`
+- `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.3+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0`
+
+
 ## [3.3] - 2025-12-10
 
-## Changes
+### Changes
 - Show PretextMap files in history for easier export. 
 
 ### Automatic update

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

@@ -10,25 +10,28 @@ Example of VGP trajectory :
 
 ## Inputs
 
-1. Genome assembly [gfa]
-2. Haplotype being scaffolded (Will be added to scaffold names: e.g. `>scaffold_01_H1`)
-3. HiC reads paired collection [fastq]
-5. Trim Hi-C data? If `yes`, trim five bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks "noisy" and the reads haven't been trimmed before. 
-6. Minimum Mapping Quality [int] (Default:20). Minimum mapping quality for Hi-C alignments. Set to 0 if you want no filtering.  
-6. Database for busco lineage (recommended: latest)
-7. Busco lineage (recommended for VGP data: vertebrata)
-8. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0)
-9. Estimated genome size [txt] (Output from the contigging workflows 3,4, or 5). A simple text file containing the estimated genome size as an integer. E.g. `2288021`
+1. Species Name [text] Name of the species being assembled.
+2. Assembly Name [text] Name of the assembly.
+3. Genome assembly [gfa]
+4. Haplotype being scaffolded (Will be added to scaffold names: e.g. `>scaffold_01_H1`)
+5. HiC reads paired collection [fastq]
+6. Trim Hi-C data? If `yes`, trim five bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks "noisy" and the reads haven't been trimmed before.
+7. Minimum Mapping Quality [int] (Default:20). Minimum mapping quality for Hi-C alignments. Set to 0 if you want no filtering.
+8. Database for Compleasm lineage (recommended: latest)
+9. Compleasm lineage (recommended for VGP data: vertebrata)
+10. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0)
+11. Estimated genome size [txt] (Output from the contigging workflows 3,4, or 5). A simple text file containing the estimated genome size as an integer. E.g. `2288021`
 
 
 ### Outputs
 
 1. Scaffolds in [fasta] and [gfa] format with the haplotype in the scaffold names.
 2. If you selected `yes` for Hi-C trimming, the trimmed collections of Hi-C reads.
 3. QC: Assembly statistics.
-4. QC: Hi-C duplications statistics.
-5. QC: Nx plot.
-6. QC: Size plot.
-7. QC: Compleasm report.
-8. QC: Pretext Maps before and after scaffolding.
-9. QC: Statistics on Hi-C alignements before and after scaffolding
+4. QC: Hi-C duplications statistics on contigs and scaffolds.
+5. QC: Pairtools MultiQC stats on contigs and scaffolds.
+6. QC: Nx plot.
+7. QC: Size plot.
+8. QC: Compleasm summary and full table.
+9. QC: Pretext Maps before and after scaffolding.
+10. QC: Statistics on Hi-C alignements before and after scaffolding

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

@@ -171,10 +171,6 @@
     Lineage: vertebrata_odb10
     Restriction enzymes: arima2
   outputs:
-    Markdup Stats:
-      asserts:
-      - has_text:
-          text: "Unknown Library\t4\t16976\t3251\t4\t0\t2255\t1970\t0.132819\t390034"
     Suffixed AGP:
       asserts:
       - has_text:
@@ -190,13 +186,13 @@
     Scaffolding Plots:
       asserts:
       - has_size:
-          value: 93200
-          delta: 5000
+          value: 118911
+          delta: 30000
     Hi-C Alignment Stats scaffolds:
       asserts:
       - has_text:
           text: "SN\treads mapped and paired:\t33952"
-    Hi-C alignments stats multiqc:
+    Hi-C alignments on Scaffolds stats multiqc:
       asserts:
       - has_text:
           text: "Hi-C Alignment Stats pre-scaffolding for Haplotype 1\t1.26354"
@@ -211,10 +207,6 @@
       asserts:
       - has_text:
           text: "SN\treads mapped and paired:\t33952"
-    Markduplicates Summary:
-      asserts:
-      - has_text:
-          text: "Unknown Library\t4\t16976\t3251\t4\t0\t2255\t1970\t0.132819\t390034"
     Compleasm Full Table Busco:
       asserts:
       - has_n_lines:
@@ -231,6 +223,17 @@
       asserts:
       - has_text:
           text: "bases mapped:\t5093400"
+    'Hi-C duplication stats on scaffolds: Raw':
+      asserts:
+      - has_text:
+          text: "total_dups\t1327"
+      - has_text:
+          text: "total_nodups\t5990"
+    'Hi-C duplication stats on scaffolds: MultiQc':
+      asserts:
+      - has_size:
+          value: 2185479
+          delta: 500000
     Scaffolds Compleasm Summary:
       asserts:
       - has_text: