Dev -> Master for 3.12.0 release #1040
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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 <drpatelh@users.noreply.github.com>
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
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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] } | |||
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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.
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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 = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv" | ||
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| // Genome references | ||
| fasta = "${params.test_data_base}/reference/genome.fasta" |
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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?
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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.
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we need to do the same with methylseq and sarek
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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.
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Yep, that's because only the permissions were changed on the file and not any contents.
FIX: remove mem assignement for SAMTOOLS_SORT
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