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add new workflow for WW sars-cov-2 amliconic analysis #154

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add new workflow for WW sars-cov-2 amliconic analysis #154

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bf0377d
add new workflow
PlushZ Nov 22, 2022
7e3ec18
add new workflow for ww artic sars-cov-2
PlushZ Dec 6, 2022
851d74f
Update workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-…
PlushZ Dec 6, 2022
9ed6cd7
retrigger checks
PlushZ Feb 13, 2023
657baf9
Reformat WF json
wm75 Mar 1, 2023
cdcb9b1
Improve labels & annotations, add WF tags
wm75 Mar 1, 2023
107ed3d
Update tools, remove filter failed from wf outputs
wm75 Mar 1, 2023
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15 changes: 15 additions & 0 deletions ...2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/.dockstore.yml
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version: 1.2
workflows:
- name: main
subclass: Galaxy
publish: true
primaryDescriptorPath: /WW-SARS-CoV-2-lineages-analysis-on-ARTIC-PE-data.ga
testParameterFiles:
- /WW-SARS-CoV-2-lineages-analysis-on-ARTIC-PE-data-tests.yml
authors:
- name: Polina Polunina
orcid: 0000-0002-0507-460
- name: "B\xE9r\xE9nice Batut"
orcid: 0000-0001-9852-198
- name: Wolfgang Maier
orcid: 0000-0002-9464-664
5 changes: 5 additions & 0 deletions ...t-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/CHANGELOG.md
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# Changelog

## [0.1]

- Initial version of COVID-19: variation analysis on ARTIC PE data workflow
4 changes: 4 additions & 0 deletions ...iant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/README.md
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SARS-CoV-2 wastewater surveillance: lineages analysis on ARTIC PE data
---------------------------------------------

The workflow for SARS-CoV-2 wastewater Illumina-sequenced ARTIC data analysis
63 changes: 63 additions & 0 deletions ...llumina-artic-variant-analysis/WW-SARS-CoV-2-lineages-analysis-on-ARTIC-PE-data-tests.yml
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- doc: Test outline for WW-SARS-CoV-2:-lineages-analysis-on-ARTIC-PE-data
job:
NC_045512.2 FASTA sequence of SARS-CoV-2:
class: File
path: test-data/NC_045512.2 FASTA sequence of SARS-CoV-2.fasta
filetype: fasta
ARTIC primer BED:
class: File
path: test-data/ARTIC primer BED.bed
filetype: bed
ARTIC primers to amplicon assignments:
class: File
path: test-data/ARTIC primers to amplicon assignments.bed
filetype: bed
BED defining amplicons for COJAC:
class: File
path: test-data/BED defining amplicons for COJAC.bed
filetype: bed
Paired Collection:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: sample1.fastq
elements:
- class: File
identifier: forward
path: test-data/Paired Collection_forward.fastqsanger.gz
- class: File
identifier: reverse
path: test-data/Paired Collection_reverse.fastqsanger.gz
- class: Collection
type: paired
identifier: sample13.fastq
elements:
- class: File
identifier: forward
path: test-data/Paired Collection_forward.fastqsanger.gz
- class: File
identifier: reverse
path: test-data/Paired Collection_reverse.fastqsanger.gz
outputs:
'Cojac: mutbamscan on input dataset(s): Mutation cooccurrence (yaml)':
element_tests:
sample1.fastq:
asserts:
has_text:
text: "73_AY42"
sample13.fastq:
asserts:
has_text:
text: "76_BA1"
'Freyja: Demix on input dataset(s): Lineages abundances summary':
element_tests:
sample1.fastq:
asserts:
has_text:
text: "Omicron"
sample13.fastq:
asserts:
has_text:
text: "summarized"
1 change: 1 addition & 0 deletions ...er-pe-illumina-artic-variant-analysis/WW-SARS-CoV-2-lineages-analysis-on-ARTIC-PE-data.ga
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209 changes: 209 additions & 0 deletions ...g/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/ARTIC primer BED.bed
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