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Update rundir to accept either tar file or directory #110

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Merged
merged 2 commits into from
Mar 26, 2025
Merged

Update rundir to accept either tar file or directory #110

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0db3b72
Update schema to accept tar file or directory
mahesh-panchal Mar 26, 2025
04d8375
Update CHANGELOG.md
mahesh-panchal Mar 26, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
- [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
- [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
- [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.

### `Fixed`

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26 changes: 18 additions & 8 deletions assets/schema_input.json
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Expand Up @@ -17,21 +17,31 @@
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
"pattern": "\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ files for read 1 must be provided and must have extension '.fq.gz' or '.fastq.gz'"
},
"fastq_2": {
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
"pattern": "\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ files for read 2 are optional and must have extension '.fq.gz' or '.fastq.gz' if provided"
},
"rundir": {
"type": "string",
"format": "path",
"exists": true,
"errorMessage": "Run directory must be a path",
"oneOf": [
{
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "\\.tar\\.gz$"
},
{
"type": "string",
"format": "directory-path",
"exists": true
}
],
"errorMessage": "Run directory must be a path or tar directory",
"meta": ["rundir"]
},
"tags": {
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