-
Notifications
You must be signed in to change notification settings - Fork 89
feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input. #584
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Merged
Merged
feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input. #584
Changes from 1 commit
Commits
Show all changes
40 commits
Select commit
Hold shift + click to select a range
35d936d
feat: updated version of pretext workflow developed by Delphine that …
Smeds 5ce525d
Fix connections between optional parameters and mandatory inputs,...
Delphine-L 4e20b69
add license, authors, and diverse labels and tags
Delphine-L b666689
change telomere track height to correspond to the size of the telomeres
Delphine-L 42a7240
Add README and CHANGELOG
Delphine-L e6c4591
update pretextgraph to fix track display issue, and add parameters to…
Delphine-L 6cc5b23
add new parameter to the README
Delphine-L 851f762
Remove explicit data conversion, it got fixed in galaxy
Delphine-L 0cf305a
Rename folder
Delphine-L 2a0c7bb
add release number and remove parameter from the READMA
Delphine-L 4de0fbc
expose output to be used for Jbrowse2 workflow
Delphine-L 3cf74ab
add tests
Delphine-L 95bd01c
replace dockstore file after cleaning my local repository
Delphine-L 2779664
add Marius comments
Delphine-L d4ba83e
rename folder
Delphine-L ce121eb
Make more clear that HiC reads need to be in collections
Delphine-L a8fc19f
use smaller test data
Delphine-L c4611ad
Remove unnecessary specification that the input is a collection
Delphine-L 1ff2cd8
add marius comments and more details about the inputs
Delphine-L 306265e
correct typo
Delphine-L 4707632
use even smaller data
Delphine-L 14c03d2
rename output of Gfastats
Delphine-L 425d64c
update tools
Delphine-L db8b8ad
renaming folder with more descriptive name
Delphine-L 67f1492
change folder name to lower case
Delphine-L 0911819
Improve name of the Workflow
Delphine-L 3264afa
update dockstore file
Delphine-L e01dabe
make hap2 optionnal, correct input names in test
Delphine-L 04217d4
replace filter and merge by bwamem2 sp option and use smaller data fo…
Delphine-L c7b78b5
skip telomere track if no telomeres are found and smaller test data
Delphine-L 62aaceb
correct missing input in tests
Delphine-L 9587f82
add second test
Delphine-L fff0f60
remove unnecessary name sorting
Delphine-L c86520d
Update README.md
Delphine-L 2d6620b
add Beta to the workflow name
Delphine-L 7d241b4
Update workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual…
Delphine-L 9ecfd15
Update workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual…
Delphine-L 65de146
Update CHANGELOG.md with beta version number
Delphine-L b7c176f
replace the tool for merging alignments with samtool merge
Delphine-L 7c5c96b
update bwa-mem2
Delphine-L File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or 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
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.
Uh oh!
There was an error while loading. Please reload this page.