Dev -> Master for 3.12.0 release #1040
Merged
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
Bump pipeline version to 3.12.0dev
Important! Template update for nf-core/tools v2.8
The `docker.registry` configuration should always be set, as running on cloud executors will need to pull docker images but will not necessarily use the `docker` profile.
restore process.shell declaration
Corrected spelling of name "Edmund Miller".
Set a default docker registry outside of profile scope.
Update README.md
Add public_aws_ecr.config and use in CI tests
Co-authored-by: Harshil Patel <[email protected]>
Fix for public_aws_ecr profile that didn't match modules sometimes
PROFILES: test -> test_cache + restore test
…onal_fasta Update warning about additional_fasta and gene BED
Bump pipeline version to 3.12.0
|
maxulysse
approved these changes
Jun 1, 2023
adamrtalbot
approved these changes
Jun 1, 2023
| @@ -235,7 +235,7 @@ workflow PREPARE_GENOME { | |||
| ch_hisat2_index = Channel.value(file(hisat2_index)) | |||
| } | |||
| } else { | |||
| ch_hisat2_index = HISAT2_BUILD ( ch_fasta, ch_gtf, ch_splicesites ).index | |||
| ch_hisat2_index = HISAT2_BUILD ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] }, ch_splicesites.map { [ [:], it ] } ).index.map { it[1] } | |||
There was a problem hiding this comment.
This is kinda ugly. We could add a method add_empty_map, or even an operator to do this? Probably not worth it for this release but it would make it cleaner.
There was a problem hiding this comment.
Agree. Had to introduce it because the upstream modules been update to use meta for the references.
MatthiasZepper
approved these changes
Jun 2, 2023
| input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv" | ||
|
|
||
| // Genome references | ||
| fasta = "${params.test_data_base}/reference/genome.fasta" |
There was a problem hiding this comment.
Is it on purpose that you replaced the ${params.test_data_base} with the absolute Github URL in the test.config, but kept it around here?
There was a problem hiding this comment.
Yep, the test_cache.config will be used in Github Actions so we can clone the branch with the test data (and be able to do the same in offline environments) to run the minimal tests - this is mostly because we had CI tests failing quite frequently when using absolute paths. The test.config was reverted to be the same as other pipelines with absolute paths.
There was a problem hiding this comment.
we need to do the same with methylseq and sarek
There was a problem hiding this comment.
In the Github's browser-based review mode, this file to me is shown empty. But when I check out the current Dev branch in VS Code, it is there, so I suppose everything is alright.
There was a problem hiding this comment.
Yep, that's because only the permissions were changed on the file and not any contents.
FIX: remove mem assignement for SAMTOOLS_SORT
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.
No description provided.