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addition of workflow and tests for mitogenome assembly
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@Delphine-L
Delphine-L committed Jan 3, 2024
1 parent ed5e267 commit 1d7ff93
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12 changes: 12 additions & 0 deletions workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/.dockstore.yml
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version: 1.2
workflows:
- name: main
subclass: Galaxy
publish: true
primaryDescriptorPath: /Mitogenome-Assembly-VGP0.ga
testParameterFiles:
- /Mitogenome-Assembly-VGP0-tests.yml
authors:
- name: VGP
url: https://vertebrategenomeproject.org
- name: Galaxy
29 changes: 29 additions & 0 deletions workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml
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- doc: Test outline for Mitogenome-Assembly-VGP0
job:
Collection of Pacbio Data:
class: Collection
collection_type: list
elements:
- class: File
identifier: pacbio_01.fasta.gz
location: https://www.dropbox.com/scl/fi/jm4g9koi4wek8vj76xzfx/pacbio_01.fasta.gz?rlkey=993pysom6vndt0jx7kfx7lqu0&dl=1
Species name (latin name): Theretra latreillii lucasii
Email adress: [email protected]
outputs:
contigs_stats:
path: test-data/contigs_stats.tsv
compare: diff
mitogenome_coverage:
asserts:
has_size:
value: 19000
delta: 2000
mitogenome_annotation:
asserts:
has_size:
value: 68000
delta: 5000
mitogenome_genbank:
assert:
has_n_line:
n: 480
348 changes: 348 additions & 0 deletions workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0.ga
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{
"a_galaxy_workflow": "true",
"annotation": "",
"comments": [],
"creator": [
{
"class": "Organization",
"name": "VGP",
"url": "https://vertebrategenomeproject.org"
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"format-version": "0.1",
"license": "CC-BY-4.0",
"version":"0.1",
"name": "Mitogenome-Assembly-VGP0",
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"name": "fasta_reference",
"type": "fasta"
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{
"description": "runtime parameter for tool MitoHiFi",
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{
"name": "mitogenome_fasta",
"type": "fasta"
},
{
"name": "mitogenome_genbank",
"type": "genbank"
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{
"name": "mitogenome_annotation",
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"tags": [
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"uuid": "57920bf9-1741-4170-badf-39fdfcdaa2e9",
"version": 4
}
3 changes: 3 additions & 0 deletions workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/test-data/contigs_stats.tsv
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# Related mitogenome is 15354 bp long and has 37 genes
contig_id frameshifts_found annotation_file length(bp) number_of_genes was_circular
final_mitogenome ND5;ATP6;ND3;ND4;COX2;ND1;ND4L;ND2;COX1;COX3;CYTB final_mitogenome.gb 15316 36 True

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