test: Add test assets - #12

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beatrizsavinhas wants to merge 132 commits into

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add-test-assets

Commits on Jun 24, 2026

Add NEXTFLOW_RUN module
beatrizsavinhas
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60d6239

Commits on Jun 25, 2026

Merge branch 'dev' into add-cascade
beatrizsavinhas
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0d39b0e
Merge branch 'dev' into add-cascade
beatrizsavinhas
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940a0f6
Merge branch 'dev' into add-cascade
beatrizsavinhas
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4c65c5d
Merge branch 'dev' into add-cascade
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9f11e74
Merge branch 'dev' into add-cascade
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aa9ef26
Merge branch 'dev' into add-cascade
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41e99ce
Merge branch 'dev' into add-cascade
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12e30c5

Commits on Jun 26, 2026

Commits on Jun 29, 2026

Update snapshot to collet output only.
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2814025
Update snapshot to collet stable_path and stable_content.
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c1b81b2
Update changelog.
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93b17a6
Update changelog.
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447aee6
Update implementation to have flexible outdir.
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b137933
Update test to not snapshot unstable file.
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5e9c171
Fix revision in test.
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cef23c7
Revert flexible outdir feature.
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779d06e
Update test to capture software versions.
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f87c4cb
Update snapshots with arm64.
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2e4665d
Add main workflow with NFCORE_ONCOANALYSER.
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025046a
Add input parameters.
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cdccf51
Update main.nf
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69a9e55
Update test config
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e4fa06b
Update default parameters to match val variable type.
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6a98cdb
feat: Add `NEXTFLOW_RUN` local module (#2)
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56e73ff
Merge branch 'dev' into add-oncoanalyser
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Merge branch 'dev' into add-cascade
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Merge branch 'add-cascade' into add-oncoanalyser
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Merge branch 'dev' into add-cascade
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Merge branch 'add-cascade' into add-oncoanalyser
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6507e8f
Merge branch 'dev' into add-cascade
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cfea055
Merge branch 'add-cascade' into add-oncoanalyser
beatrizsavinhas
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f8b85aa
Update setting for cache_dir.
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cdab1c1
Fix linting issue with block order in NEXTFLOW_RUN.
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6b549fa
Merge branch 'add-cascade' into add-oncoanalyser
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2b6ef10
Remove cache_dir parameter from test.config.
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c18879a
Update pipeline test to match output directory strategy.
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32350c5

Commits on Jun 30, 2026

Commits on Jul 1, 2026

Revert changes to default test to use params.outdir.
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1d43712

Commits on Jul 2, 2026

Update test config to run in stub and remove unused arguments.
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43d01f5
Fix indentation in test config
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d36495e
Ad publish block to main.nf
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ccd417c
Update test name.
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a90a887
Merge branch 'dev' into add-cascade
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de4f08f
Merge branch 'dev' into add-cascade
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c031ff9
Merge dev and move code to worfklows/oncoflow.nf
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c9ca68b
Move code to worfklows/oncoflow.nf
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f9fa106
Add publish block.
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369f5c3
Fix bug in publish block.
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c7b4507
Merge branch 'dev' into add-cascade
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32162f2
Merge add-cascade.
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be3090b
Change NEXTFLOW_RUN module test to run nf-core/demo in stub.
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cff68d5
Merge branch 'add-cascade' into add-oncoanalyser
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afd215a
Update test config name and description.
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c21e966
Update default test name.
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05e9040
Update default test snapshot.
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738c7c3

Commits on Jul 3, 2026

Restore test.
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7dbd938
Update snapshot.
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style: NEXTFLOW_RUN.
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aa51fbc
Merge branch 'dev' into add-cascade
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c58cab1
Merge branch 'add-cascade' into add-oncoanalyser
beatrizsavinhas
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fc4f3b1
Update changelog.
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42d01eb
style: modules/local/nextflow/run/main.nf
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c7342c5
Update nftignore to also ignore `pipeline_info` files for all called pipelines.
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eaca0be
Update default test to use ignore file.
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2d8c3db
Update snapshot.
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8679d89
Update changelog.
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66eb6ff
Update .nftignore to ignore pipeline_info, multiqc and vep files for all run pipelines.
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d9b6e93
Update default test to not capture `pipeline_info` files for run pipelines.
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45ef5a4
Update changelog.
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cc769a4
Update changelog.
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a3d94be
Add `Changed` header to changelog. Move relevant entries there.
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7152e7a
Update snapshot.
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eb77d34
Merge branch 'add-cascade' into add-oncoanalyser
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8352e52
Remove vep files from nftignore
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db3cc04

Commits on Jul 6, 2026

Update nftignore to ignore gzipped files from oncoanalyser.
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7244158
Update snapshot.
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4b0c987
Update changelog.
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df10611
Update changelog.
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09ccfb2
Ignore .command.log in tests
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d4c0876
Ignore all .command.* files in tests
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898808d
Create oncoanalyser named parameters.
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edb0d1f
Refiner nextflow_schema, organise input parameters and add info strings in take blocks.
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8269760
Update changelog.
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6f21598
Remove commented out code.
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2479a3f
Style: refactor info strings.
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5c5c704
Add CREATE_ONCOREFINER_PARAMS_FILE local module.
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3941489
Change notation for take blocks to use .
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Merge branch 'add-oncoanalyser' into add-create-oncorefiner-params-file
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71b0ecf
Add metadata parameters.
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4392a60
Publish oncorefiner params file.
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a553d44
Fix bug with relative paths in params file.
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f712510
Update subject_id to match test data from oncoanalyser.
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f2742ca
Update module test and snapshot.
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6344ed8
Update default test snapshot.
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589b6cc
Rename oncoanalyser_config.
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134607a
Update oncoanalyser_config description.
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b6d09f8
Apply suggestion from @fellen31

beatrizsavinhas
and
fellen31
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e329f1a
Harshil alignment in oncoflow.nf
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5ca66c9
Apply suggestion from @fellen31

beatrizsavinhas
and
fellen31
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f491a3f
Harshil alignment in nextflow.config
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dd8490a
Add pattern for oncoanalyser_params_file.
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d5ff51d
Simplify ignore statements in default test and nftignore. Update snapshot.
beatrizsavinhas
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f73a519

Commits on Jul 7, 2026

Update module test and snapshot.
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8740f94
Update changelog.
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47ca313
Merge branch 'add-oncoanalyser' into add-create-oncorefiner-params-file
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266774f
Fix " in params file generation.
beatrizsavinhas
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a46f87d
Apply suggestions from code review

beatrizsavinhas
and
fellen31
authored
955fb5f
Update test to replace "<output_directory>"
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ab378c5
Adjust default test to snapshot params file contente
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59e6c78
Remove ext.args from module.
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b465cb6
update variable names oncorefiner_params_file
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f9a9bb0
Correct meta.yml
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0ac04d6
feat: Add `NFCORE_ONCOANALYSER` to main workflow (#3)
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6ca45a9
Merge branch 'add-cascade' into add-create-oncorefiner-params-file
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d1ce895
fix: Address review comments for `add-create-oncorefiner-params-file` (#6)
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43ca4cc
Fix bug with incorrect `snv_vcf_path` and `sv_vcf_path`.
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b5dc565
Remove Additonal from info string.
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8cab2ce
Correct order in changelog.
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209a6c1
Corrext changelog.
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4a1f2dc

Commits on Jul 8, 2026

fix: `CREATE_ONCOREFINER_PARAMS_FILE` to add support for tumor only analysis (#7)
beatrizsavinhas
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a09f2d7

Commits on Jul 9, 2026