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Fix Colour chem validation #694

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merged 2 commits into from
Mar 12, 2021
Merged

Fix Colour chem validation #694

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71ebc62
Add fix for broken colour chem. validation
jfy133 Mar 10, 2021
a17acad
Merge pull request #697 from nf-core/dev
jfy133 Mar 12, 2021
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9 changes: 5 additions & 4 deletions CHANGELOG.md
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Expand Up @@ -14,14 +14,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
- [#652](https://github.com/nf-core/eager/issues/652) Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
- [#626](https://github.com/nf-core/eager/issues/626) - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty
- Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data. `
- [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file.
- Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
- [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file
- [#688](https://github.com/nf-core/eager/issues/668) - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library
- [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex.
- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails.
- [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex
- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails
- [672](https://github.com/nf-core/eager/issues/672) - Removed java parameter from picard tools which could cause memory issues
- [679](https://github.com/nf-core/eager/issues/679) - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments
- [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case
- [#693](https://github.com/nf-core/eager/issues/693) - Fixed broken TSV input validation for the Colour Chemistry column

### `Dependencies`

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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -3598,7 +3598,7 @@ def extract_data(tsvFile) {
if (!udg.matches('none') && !udg.matches('half') && !udg.matches('full')) exit 1, "[nf-core/eager] error: UDG treatment can only be 'none', 'half' or 'full'. See '--help' flag and documentation under 'running the pipeline' for more information. You have '${udg}'"

// Check valid colour chemistry
if (!colour == 2 && !colour == 4) exit 1, "[nf-core/eager] error: Colour chemistry in TSV can either be 2 (e.g. NextSeq/NovaSeq) or 4 (e.g. HiSeq/MiSeq)"
if (!colour.matches('2') && !colour.matches('4')) exit 1, "[nf-core/eager] error: Colour chemistry in TSV can either be 2 (e.g. NextSeq/NovaSeq) or 4 (e.g. HiSeq/MiSeq)"

// Ensure that we do not accept incompatible chemistry setup
if (!seqtype.matches('PE') && !seqtype.matches('SE')) exit 1, "[nf-core/eager] error: SeqType for one or more rows in TSV is neither SE nor PE! see '--help' flag and documentation under 'running the pipeline' for more information. You have: '${seqtype}'"
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