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VGP 4 - update tools and add Hi-C read trimming option (replace broken PR 507) #633

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VGP 4 - update tools and add Hi-C read trimming option (replace broken PR 507) #633

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4be69db
update tools
Delphine-L Dec 13, 2024
e819910
update tools
Delphine-L Dec 13, 2024
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45 changes: 27 additions & 18 deletions ...s/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml
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Original file line number Diff line number Diff line change
@@ -1,13 +1,21 @@
- doc: Test outline for Assembly-Hifi-HiC-phasing-VGP4
job:
HiC forward reads:
class: File
location: https://zenodo.org/records/10068595/files/HiC%20forward%20reads.fastqsanger.gz?download=1
filetype: fastqsanger.gz
HiC reverse reads:
class: File
location: https://zenodo.org/records/10068595/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/10068595/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/10068595/files/HiC%20reverse%20reads.fastqsanger.gz?download=1
filetype: fastqsanger.gz
Genomescope Model Parameters:
class: File
path: test-data/Genomescope Model Parameters.tabular
Expand All @@ -20,7 +28,7 @@
class: File
location: https://zenodo.org/records/10068595/files/Meryl%20Database.meryldb?download=1
filetype: meryldb
Pacbio Reads Collection:
Pacbio Reads:
class: Collection
collection_type: list
elements:
Expand All @@ -33,26 +41,27 @@
Name for Haplotype 2: Hap2
Homozygous Read Coverage: null
Database for Busco Lineage: v5
Trim Hi-C reads?: false
outputs:
Hifiasm HiC hap1:
assert:
has_n_line:
n: 168
Hifiasm Hi-C hap1:
asserts:
has_n_lines:
n: 114
Estimated Genome size: 2288021
Busco Summary Hap1:
asserts:
has_text:
text: "C:1.0%[S:1.0%,D:0.0%],F:0.4%,M:98.6%,n:3354"
text: "C:0.8%[S:0.8%,D:0.0%],F:0.3%,M:98.9%,n:3354"
Nx Plot:
asserts:
has_size:
value: 65000
delta: 10000
usable hap1 gfa:
assert:
has_n_line:
n: 173
asserts:
has_n_lines:
n: 119
Assembly statistics for Hap1 and Hap2:
asserts:
has_text:
text: "# scaffolds 72 35"
text: "# scaffolds 57 51"
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