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nested nextflow schema params #49

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merged 27 commits into from
Mar 20, 2024
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0bdee2c
nested nextflow schema params
mattheww95 Mar 18, 2024
5cb4fc0
added utility config script
mattheww95 Mar 18, 2024
2cd9c6e
commited yml
mattheww95 Mar 18, 2024
7faa352
updated schema generic options
mattheww95 Mar 18, 2024
8bac17e
updated schema, and script for flattening
mattheww95 Mar 19, 2024
b1314a9
propogated hidden message to higher params
mattheww95 Mar 19, 2024
3bf5d87
added report_aggreagate to ignored params
mattheww95 Mar 19, 2024
43685c7
Merge branch 'dev' into updating-schema
apetkau Mar 20, 2024
66194e5
Re-enabled some linting
apetkau Mar 20, 2024
1e73639
Fixed up linting of nextflow config
apetkau Mar 20, 2024
76a0d17
Used schema builder to generate nextflow schema
apetkau Mar 20, 2024
d84fcb6
Changed default database locations to null
apetkau Mar 20, 2024
6ba53d3
Adjusted control flow options
apetkau Mar 20, 2024
4565b28
Additional description for parameters
apetkau Mar 20, 2024
4edc35c
Revert "Changed default database locations to null"
apetkau Mar 20, 2024
9e2e23d
Fixed up linting and running pipeline
apetkau Mar 20, 2024
e56de8f
Removed ignore validation
apetkau Mar 20, 2024
fd1d5c3
Updated schema with additional parameters
apetkau Mar 20, 2024
e6a4e2d
Added test to ensure validation of parameters
apetkau Mar 20, 2024
a82f40b
Additional changes and descriptions to schema
apetkau Mar 20, 2024
f480967
Adding more descriptions and ranges
apetkau Mar 20, 2024
ebc7596
Adding test case for min length and database path validation
apetkau Mar 20, 2024
a8c143e
Remove format
apetkau Mar 20, 2024
7cc886d
Added final descriptions in schema
apetkau Mar 20, 2024
0f95025
Added ignore parameters to avoid warnings in Nextflow
apetkau Mar 20, 2024
215d012
Added tests for species top hit
apetkau Mar 20, 2024
d944eb8
Fixed up tests
apetkau Mar 20, 2024
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2 changes: 1 addition & 1 deletion .nf-core.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ lint:
- assets/email_template.txt
- assets/sendmail_template.txt
- .gitignore
schema_params: False
schema_params: True
nextflow_config: False
multiqc_config: False
template:
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