added default -doMajorMinor 1 to output angsd beagle format #690
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ed typo in error message about angsd output format
|
You will need to add this change to the |
|
Ok I THINK I got it right now... |
jfy133
requested changes
Mar 9, 2021
CHANGELOG.md
Outdated
Comment on lines
12
to
23
| - [#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 |
There was a problem hiding this comment.
Was this all meant to be deleted? Your change should just be appened to the endof the list.
There was a problem hiding this comment.
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
approved these changes
Mar 10, 2021
|
Looks good to me! Merging! |
|
Thanks very much @alexandregilardet ! Feel free to make an extra PR adding yourself to the |
2 tasks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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).