added default -doMajorMinor 1 to output angsd beagle format #690
Merged
jfy133 merged 5 commits intonf-core:devfrom Mar 10, 2021
Merged
added default -doMajorMinor 1 to output angsd beagle format #690jfy133 merged 5 commits intonf-core:devfrom
jfy133 merged 5 commits intonf-core:devfrom
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…ed typo in error message about angsd output format
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You will need to add this change to the |
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Ok I THINK I got it right now... |
jfy133
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Mar 9, 2021
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Good catch on the typos in the validation section.
There was a mistake in the changelog I think, but otherwise I think we are good to go.
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| - [#666](https://github.com/nf-core/eager/issues/666) - Fixed input file staging for `print_nuclear_contamination` | ||
| - [#631](https://github.com/nf-core/eager/issues/631) - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled | ||
| - 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. | ||
| - [#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. | ||
| - [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 |
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Was this all meant to be deleted? Your change should just be appened to the endof the list.
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Sorry I got a bit confused because I was on my master branch so I didn't have the dev section in the CHANGELOG.md
jfy133
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Mar 10, 2021
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Looks good to me! Merging! |
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Thanks very much @alexandregilardet ! Feel free to make an extra PR adding yourself to the |
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To output ANGSD beagle format, the argument -doMajorMinor to infer major and minor alleles is required. For now, eager would output a corrupted .glf.gz file if 'beagle' is selected as output with the following .command.err:
-> For dumping beaglestyle output you need to estimate major/minor: -doMajorMinor
I added as default the -doMajorMinor 1 argument which I'm more familiar with (http://www.popgen.dk/angsd/index.php/Major_Minor).
PR checklist
nf-core lint .).nextflow run . -profile test_tsv,crick).