Merge branch 'galaxyproject:main' into exports

workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml

@@ -31,6 +31,7 @@
     Bits for bloom filter: 32
     Name for Haplotype 1: Hap1
     Name for Haplotype 2: Hap2
+    Homozygous Read Coverage: null
   outputs:
     Hifiasm HiC hap1:
       assert: 

workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md

@@ -1,6 +1,30 @@
 # Changelog
 
 
+
+## [0.1.10] 2024-04-23
+
+### Changed
+
+- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0`
+
+
+## [0.1.9] 2024-04-19
+
+### Manual Updates
+
+- Add the option to provide Homozygous Read coverage parameter
+
+### Automatic update
+
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4`
+
+
 ## [0.1.8] 2024-03-25
 
 ### Manual update

workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5-tests.yml

@@ -16,6 +16,10 @@
       class: File
       location: https://zenodo.org/records/10056319/files/Genomescope%20Summary.txt?download=1
       filetype: txt
+    Genomescope Model Parameters:
+      class: File
+      path: test-data/GenomeScope_Model_parameters.tabular
+      filetype: tabular
     'Pacbio Reads Collection : child':
       class: Collection
       collection_type: list
@@ -44,15 +48,17 @@
         identifier: hap2_1.fq
         location: https://zenodo.org/records/10056319/files/Sub_hap2_1.fastqsanger?download=1
     SAK input file (Optional): null
+    Homozygous Read Coverage: null
     Bits for bloom filter: 32
     Name for Haplotype 1: Hap1
     Name for Haplotype 2: Hap2
+    Lineage: vertebrata_odb10 
   outputs:
     Estimated Genome size: 2288021 
     Assembly statistics for Hap1 and Hap2:
       asserts:
         has_line:
-          line: "# contigs	85	49"
+          line: "# contigs	85	23"
     usable hap1 gfa:
       asserts:
         has_n_lines: