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VGP 6 - Updates and fix awk expression that was breaking #1232

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VGP 6 - Updates and fix awk expression that was breaking #1232

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a73f43a
fix awk expression
Delphine-L May 7, 2026
f92bad4
fix changelog
Delphine-L May 7, 2026
9072f00
rename hap1 scaffolds as well
Delphine-L May 12, 2026
227660c
run the QC and gfa stats on the renamed fastas
Delphine-L May 12, 2026
25e932f
fix wrong input being used for hap1 renaming
Delphine-L May 12, 2026
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13 changes: 13 additions & 0 deletions workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,18 @@
# Changelog

## [0.10.6] - 2026-05-06

### Manual Changes
- Fix Typo in an awk command to rename scaffolds after purging.
- Rename the primary haplotype scaffolds after purging, matching the renaming already applied to haplotype 2.
- Add `Name mapping Hap1` workflow output (original → renamed scaffold table for the primary haplotype), analogous to the existing `Name mapping Alternate assembly` output.
- Tighten `Name of primary assembly` / `Name of alternate assembly` inputs: mark them required (`optional: false`), set defaults to `Hap1` / `Hap2`, and narrow the restriction lists so each input only offers labels appropriate to its haplotype.

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2`
- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.30+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0`

## [0.10.5] - 2026-01-26

### Manual changes
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9 changes: 8 additions & 1 deletion ...flows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6-tests.yml
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Expand Up @@ -51,16 +51,19 @@
Lineage: vertebrata_odb10
Name of primary assembly: Primary
Name of alternate assembly: Alternate
"What sequences are you purging?": contig"
"What sequences are you purging?": "contig"
outputs:
Cutoffs for primary assembly:
asserts:
has_text:
text: "1\t15\t15\t16\t16\t48"
Purged Primary Assembly:
decompress: true
asserts:
has_n_lines:
n: 156
has_text:
text: "contig_1.pri"
Purged Primary Assembly (gfa):
asserts:
has_n_lines:
Expand Down Expand Up @@ -107,3 +110,7 @@
asserts:
has_text:
text: "h2tg000050l_path_1\tcontig_1.alt"
Name mapping Hap1:
asserts:
has_text:
text: "h1tg000055l_path_1\tcontig_1.pri"
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