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Dev -> Master for v1.12.0 release #286

Merged
merged 298 commits into from
Feb 29, 2024
Merged

Dev -> Master for v1.12.0 release #286

merged 298 commits into from
Feb 29, 2024

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drpatelh
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drpatelh and others added 30 commits January 6, 2024 20:35
@drpatelh
Use relative path for --outdir because outputDir will be unique path
584fb2d
@drpatelh
Update snapshots
18a7c27
@drpatelh
Update snapshots and replace with explicit tests
95b30a6
@drpatelh
Fix snapshot for sra_skip_fastq_download
7cc221d
@drpatelh
Replace results with outputDir
f08543d
@drpatelh
Reorder samples in first column of samplesheet and mappings
b0d4905
@drpatelh
Regenerate snapshots and remove metadata test
b7cfca7
@drpatelh
Remove all workflow snapshots
f705af8
@drpatelh
Tidy up tests and configuration
6a0120d
@drpatelh
Use smaller test data to speed up test runtimes
f6510d5
@drpatelh
Update pipeline test to load test.config directly
8fc22ec
@drpatelh
Merge pull request #243 from drpatelh/fixes
addb060 
Fixes for PR #238
@drpatelh
Fix merge conflicts
449d187
@drpatelh
Standardise nf-test env vars and add tap output option
61b36d8
@drpatelh
Use env var to evaluate nf-test workDir
25eac03
@drpatelh
Bump tower-launch plugin version and switch off default tests for GCP
3255d8f
@drpatelh
Fix prettier
86618c1
@drpatelh
Use SHA in paths to test data used in pipeline
a5f4ec4
@drpatelh
Be more explicit with pipeline tests
d2ea5cf
@drpatelh
Add --nf_core_pipeline specific tests at the workflow level
375a4e5
@drpatelh
Use pdiff instead of icdiff for nf-test snapshot diffs
5b9348c
@drpatelh
Update workflow tests to use assertAll
e392e37
@drpatelh
Add more explicit pipeline tests for file paths and samplesheet contents
30333c4
@drpatelh
Remove comments
a367b4b
@drpatelh
Use closures for with statements in assertAll blocks
b31ab04
@drpatelh
Fix ECLint
c135899
@drpatelh
Update all nf-core modules and subworkflows
20769af
@drpatelh
Install new utils subworkflows
bce4b7a
@drpatelh
Re-add nextflow config files for publishing
596ca7c
@drpatelh
Rename local subworkflow to utils_nfcore_fetchngs_pipeline
d0efbac
maxulysse and others added 12 commits February 28, 2024 12:15
@drpatelh drpatelh mentioned this pull request Feb 28, 2024
Merged
3 tasks
drpatelh and others added 13 commits February 28, 2024 12:08
@drpatelh
Update CHANGELOG
669b868
@drpatelh
Remove --outdir definition in nf-tests for workflows
cbe835e
@drpatelh
Fix missed tests for nf-core modules
502bc70
@drpatelh
Change outdir path in local subworkflow
5b20998
@drpatelh
Merge pull request #295 from maxulysse/less_stringent_test_expectation
89e3716 
be less stringent with tests expectation
@drpatelh
Merge branch 'dev' into fixes
969fc43
@drpatelh
Re-install modules and subworkflows from nf-core
92cbb7d
@drpatelh
Add Sateesh to contributors for reviews
7a9d811
@drpatelh
Fix nf-tests
f6cf223
@drpatelh
Merge pull request #296 from drpatelh/fixes
03ac573 
Remove params.outdir from tests where required and update snapshots
@drpatelh
export CONDA_PREFIX into container when using Singularity and Apptainer
0649425
@drpatelh
Update CHANGELOG
cdc31b9
@drpatelh
Merge pull request #298 from drpatelh/fixes
755ca35 
export CONDA_PREFIX into container when using Singularity and Apptainer
@drpatelh drpatelh merged commit 8ec2d93 into master Feb 29, 2024
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Reviewers

@sateeshperi sateeshperi sateeshperi left review comments

@adamrtalbot adamrtalbot adamrtalbot approved these changes

@pinin4fjords pinin4fjords pinin4fjords approved these changes

@maxulysse maxulysse maxulysse approved these changes

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7 participants
@drpatelh @maxulysse @pinin4fjords @adamrtalbot @sateeshperi @nf-core-bot @edmundmiller