Template update for nf-core/tools v2.14.1 #41
Closed
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
Important! Template update for nf-core/tools v2.9
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Updated README info.
Current additions to set up base pipeline will be merged so more development can happen on different component to push towards first release. Still lots of things missing, but many standard modules are installed in the pipeline already.
Important! Template update for nf-core/tools v2.10
Hardcoded test for ashlar, mesmer, mcquant.
new format is sample,cycle_number,channel_count,image_tiles
* Ran nf-core modules update deepcell/mesmer * Deleted local mesmer patch as it's no longer necessary * Adjusted modules config to eliminate containerOptions (not needed any longer) and manually set the prefix to match our previous locally patched behavior * Added test config to mount the local /tmp/.keras in the container at the same path to provide caching of the ~100 MB model file the container downloads at runtime * Updated test snapshot for new version number
nf-validate guarantees Channel.fromSamplesheet lists are ordered according to the field order in the schema, so we can hard-code the column indexes rather than using the old sample_sheet_index_map mechanism.
This fixes the race condition where Ashlar and Mesmer outputs were getting mixed up across samples due to nextflow's asynchronous execution.
Generates actual CSV file content in memory and hashes that, rather than returning a list-of-lists of values to be literally included in the test snapshot. The literal values don't belong in pipeline tests but rather module tests for mcquant.
This helps reduce the inter-computer variation in the output.
The inter-system floating point variation in basicpy output has proven to be too substantial to paper over by just rounding the values. We'll just verify the output csv files have the right headers and the right number of rows since that is still stable. Also fixes a small bug in the summarizeCsv helper where it previously returned a String instead of the intended Map.
* Remove unneeded symlink to schema in assets/ * Remove explicit parameters_schema arg in fromSamplesheet calls
Sample sheet update Thank you to everyone who worked on and discussed this PR!
… into nf-core-template-merge-2.14.1
|
|
oops wrong target branch |
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.
Manual conflict resolution for tools v2.14.1.
PR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).