Add agat sp complement annotations #129
Open
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
dorien-er
requested changes
Aug 27, 2024
| issue_tracker: https://github.com/NBISweden/AGAT/issues | ||
| repository: https://github.com/NBISweden/AGAT | ||
| references: | ||
| doi: 10.5281/zenodo.3552717 |
There was a problem hiding this comment.
Suggested change
| doi: 10.5281/zenodo.3552717 | |
| https://doi.org/10.5281/zenodo.3552717 |
| means all of them are kept. | ||
| type: integer | ||
| required: false | ||
| example: 100 |
There was a problem hiding this comment.
Suggested change
| example: 100 | |
| example: 100 | |
| min: 0 |
dorien-er
reviewed
Aug 29, 2024
| * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added only if the CDSs don't overlap. | ||
| * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added only if none of the l3 features overlap. | ||
|
|
||
| ! It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output. |
There was a problem hiding this comment.
Suggested change
| ! It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output. | |
| It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output. |
dorien-er
reviewed
Aug 29, 2024
Comment on lines
+40
to
+45
| Annotation(s) file you would like to use to complement the | ||
| reference annotation. You can specify as much file you want like. | ||
| The order you provide these files matter. Once the reference file has been | ||
| complemented by file1, this new annotation becomes the new | ||
| reference that will be complemented by file2 etc. | ||
| So, be aware of what you want if you use several addfiles. |
There was a problem hiding this comment.
Suggested change
| Annotation(s) file you would like to use to complement the | |
| reference annotation. You can specify as much file you want like. | |
| The order you provide these files matter. Once the reference file has been | |
| complemented by file1, this new annotation becomes the new | |
| reference that will be complemented by file2 etc. | |
| So, be aware of what you want if you use several addfiles. | |
| Annotation file(s) you would like to use to complement the reference annotation. You can specify as many files as you like. The order you provide these files matter. Once the reference file has been complemented by file1, this new annotation becomes the new reference that will be complemented by file2, etc. So, be aware of what you want if you use several addfiles. |
dorien-er
reviewed
Aug 29, 2024
Comment on lines
+65
to
+67
| Option to keep the non-overlapping gene only if the CDS size (in | ||
| nucleotide) is over the minimum size defined. Default = 0 that | ||
| means all of them are kept. |
There was a problem hiding this comment.
Suggested change
| Option to keep the non-overlapping gene only if the CDS size (in | |
| nucleotide) is over the minimum size defined. Default = 0 that | |
| means all of them are kept. | |
| Option to keep the non-overlapping gene only if the CDS size (in nucleotides) is over the minimum size defined. The default is 0, meaning all of them are kept. |
dorien-er
reviewed
Aug 29, 2024
| agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt | ||
| runners: | ||
| - type: executable | ||
| - type: nextflow |
There was a problem hiding this comment.
Suggested change
| - type: nextflow | |
| - type: nextflow | |
dorien-er
requested changes
Aug 29, 2024
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.
Description
Issue ticket number
Closes #xxxx
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributing guidelines
Proposed changes are described in the CHANGELOG.md
I have tested my code with
viash ns test --parallel -q <name or namespace>Check the correct box. Does this PR contain: