Merge pull request #514 from planemo-autoupdate/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8

Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 0.2.7 to 0.2.8

Author: mvdbeek

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

@@ -1,5 +1,19 @@
 # Changelog
 
+## [0.3] 2025-01-30
+
+### Changes
+
+- Hi-C data are now input as collections
+- Add optional trimming of Hi-C data
+- Set Metaeuk as Busco gene predictor
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1`
+- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0`
+
 
 ## [0.2.8] 2024-09-12
 

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

@@ -9,21 +9,23 @@ Example of trajectory :
 
 ## Inputs
 
-1. Scaffolded assembly [fasta]
-2. Database for busco lineage (recommended: latest)
-3. Busco lineage (recommended: vertebrata)
-4. Concatenated HiC forward reads [fastq]
-5. Concatenated HiC reverse reads [fastq]
-6. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0)
-7. Estimated genome size [txt]
-8. Haplotype name 
+1. Scaffolded assembly [gfa]
+2. Name of the haplotype
+3. HiC forward reads [fastq]
+4. HiC reverse reads [fastq]
+5. Trim Hi-C data? If `yes` Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks "noisy". 
+6. Database for busco lineage (recommended: latest)
+7. Busco lineage (recommended: vertebrata)
+8. Restriction enzyme sequence (recommended for VGP data: Arima Hi-C 2.0)
+9. Estimated genome size [txt]
 
 
 ### Outputs
 
 1. Scaffolds in [fasta] and [gfa] format
-2. QC: Assembly statistics
-3. QC: Nx plot
-4. QC: Size plot
-5. QC: BUSCO report
-6. QC: Pretext Maps before and after scaffolding
+2. If you selected `yes` for Hi-C trimming, the trimmed collections of Hi-C reads
+3. QC: Assembly statistics
+4. QC: Nx plot
+5. QC: Size plot
+6. QC: BUSCO report
+7. QC: Pretext Maps before and after scaffolding

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

@@ -4,14 +4,22 @@
       class: File
       location: https://zenodo.org/records/10037496/files/input%20GFA.gfa1?download=1
       filetype: gfa1
-    HiC Forward reads:
-      class: File
-      location: https://zenodo.org/records/10037496/files/HiC%20Forward%20reads.fastqsanger.gz?download=1
-      filetype: fastqsanger.gz
-    HiC reverse reads:
-      class: File
-      location: https://zenodo.org/records/10037496/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
-      filetype: fastqsanger.gz
+    Hi-C forward reads:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: HiC-Forward-reads
+        location: https://zenodo.org/records/10037496/files/HiC%20Forward%20reads.fastqsanger.gz?download=1
+        filetype: fastqsanger.gz
+    Hi-C reverse reads:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: HiC-Reverse-reads
+        location: https://zenodo.org/records/10037496/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
+        filetype: fastqsanger.gz
     Estimated genome size - Parameter File:
       class: File
       location: https://zenodo.org/records/10037496/files/Estimated%20genome%20size%20-%20Parameter%20File.txt?download=1
@@ -20,25 +28,26 @@
     Lineage: vertebrata_odb10
     Restriction enzymes: arima2
     Haplotype: hap1
+    Trim Hi-C Data?: false
   outputs:
     "Reconciliated Scaffolds: gfa":
       asserts:
         has_n_lines:
-          n: 169
+          n: 168
     'Reconciliated Scaffolds: fasta':
       asserts:
         has_n_lines:
-          n: 168
+          n: 166
         has_text:
           text: "scaffold_53.hap1"
     Busco Summary:
       asserts:
         has_text:
-          text: "C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354"
+          text: "C:1.1%[S:1.0%,D:0.0%],F:0.4%,M:98.5%,n:3354"
     Assembly Statistics for s2:
       asserts:
         has_line:
-          line: "# scaffolds	84"
+          line: "# scaffolds	83"
     Nx Plot:
       asserts:
         has_size: