Improve pipeline level snapshots #1379

maxulysse · 2024-09-13T07:58:39Z

make versions' snapshots pretty thanks to @edmundmiller
GREATLY improve and simplify pipeline level snapshoting thanks to @pinin4fjords
Led to the first releases of https://github.com/nf-core/nft-utils/ that removes all groovy functions and put it in a plugin

PR checklist

github-actions · 2024-09-13T08:01:03Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 1d35e2a

+| ✅ 174 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
nextflow_config - Config default ignored: params.ribo_database_manifest
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
multiqc_config - multiqc_config
modules_config - modules_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-rnaseq_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-rnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-rnaseq_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-rnaseq_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowRnaseq.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 3.16.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.hisat2_build_memory= 200.GB
nextflow_config - Config default value correct: params.gtf_extra_attributes= gene_name
nextflow_config - Config default value correct: params.gtf_group_features= gene_id
nextflow_config - Config default value correct: params.featurecounts_group_type= gene_biotype
nextflow_config - Config default value correct: params.featurecounts_feature_type= exon
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.trimmer= trimgalore
nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
nextflow_config - Config default value correct: params.umitools_extract_method= string
nextflow_config - Config default value correct: params.umitools_grouping_method= directional
nextflow_config - Config default value correct: params.aligner= star_salmon
nextflow_config - Config default value correct: params.pseudo_aligner_kmer_size= 31
nextflow_config - Config default value correct: params.min_mapped_reads= 5.0
nextflow_config - Config default value correct: params.kallisto_quant_fraglen= 200
nextflow_config - Config default value correct: params.kallisto_quant_fraglen_sd= 200
nextflow_config - Config default value correct: params.stranded_threshold= 0.8
nextflow_config - Config default value correct: params.unstranded_threshold= 0.1
nextflow_config - Config default value correct: params.deseq2_vst= true
nextflow_config - Config default value correct: params.rseqc_modules= bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
nextflow_config - Config default value correct: params.bracken_precision= S
nextflow_config - Config default value correct: params.skip_bbsplit= true
nextflow_config - Config default value correct: params.skip_preseq= true
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-rnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnaseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (590 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: cloud_tests_full.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-10-02 06:43:07

maxulysse · 2024-09-13T08:04:28Z

ok, so changing tests/default.nf.test.snap and tests/lib/UTILS.groovy did not trigger any pipeline level tests.

pinin4fjords · 2024-09-13T10:40:01Z

You've not actually added any of my bits ;-)

CHANGELOG.md

tests/lib/UTILS.groovy

tests/default.nf.test

tests/remove_ribo_rna.nf.test

maxulysse · 2024-09-19T12:47:14Z

As @pinin4fjords said relative path in snapshots would be a nice addition, especially for the file that only have stable names

tests/featurecounts_group_type.nf.test

pinin4fjords · 2024-10-01T08:55:00Z

I do love that this comes from the external plugin now. But why no relative paths, so we could distinguish files with the same name in different subdirs?

maxulysse · 2024-10-01T09:14:33Z

I do love that this comes from the external plugin now. But why no relative paths, so we could distinguish files with the same name in different subdirs?

I just quickly reworked the regexes into globs as it was faster, and a nice POC, I'll update with proper paths now

maxulysse · 2024-10-01T09:24:31Z

I do love that this comes from the external plugin now. But why no relative paths, so we could distinguish files with the same name in different subdirs?

I just quickly reworked the regexes into globs as it was faster, and a nice POC, I'll update with proper paths now

Or did you meant relative paths in the snapshots?

pinin4fjords

Really nice work @maxulysse !

make snapshot versions pretty

eada63d

update CHANGELOG

e567889

maxulysse added 7 commits September 13, 2024 12:53

update all snapshots

c652e79

Merge branch 'dev' into better_snapshots

f1d624e

update half of all snaps

d145a1b

Merge branch 'dev' into better_snapshots

6096641

more snapshots

29af996

update snapshots

caa80e6

update snapshots

03b6501

maxulysse commented Sep 14, 2024

View reviewed changes

CHANGELOG.md Show resolved Hide resolved

maxulysse and others added 5 commits September 14, 2024 09:37

Update CHANGELOG.md

4dc9fb8

update snapshots

2be93d8

do not sort output

6904250

Merge branch 'dev' into better_snapshots

0ae5f13

sort output by PATH

96c415d

pinin4fjords reviewed Sep 17, 2024

View reviewed changes

tests/lib/UTILS.groovy Outdated Show resolved Hide resolved

maxulysse added 4 commits September 17, 2024 14:23

update snapshots

ca3a646

Merge branch 'dev' into better_snapshots

fb6c429

snapshot more files

17054a4

snapshot more files

5b41e56

pinin4fjords reviewed Sep 18, 2024

View reviewed changes

tests/default.nf.test Outdated Show resolved Hide resolved

maxulysse added 4 commits September 18, 2024 11:21

feature counts snapshots

6aee372

typo

4d143b5

more snapshots

a3e0328

more snapshots

4811e91

pinin4fjords reviewed Sep 18, 2024

View reviewed changes

tests/remove_ribo_rna.nf.test Outdated Show resolved Hide resolved

update snapshots

30d629b

update regexes

ed2cf1f

maxulysse added 3 commits September 19, 2024 15:07

move pipeline regexes in UTILS_PIPELINE

9234922

simplify regexes

26737a7

fix regexes

3172eaa

maxulysse mentioned this pull request Sep 19, 2024

add pipeline level tests nf-core/sarek#1661

Merged

11 tasks

maxulysse added 8 commits September 19, 2024 21:21

snapshots all filenames

a6a3107

Merge branch 'dev' into better_snapshots

dc788b4

code polish

8550e6d

typo

5a62a0f

no snpashots of tasks size for workflow for remove_ribo_rna

712342a

Merge branch 'dev' into better_snapshots

134fe31

snapshot number of sucessful tasks

5bd3d87

typo

0df0995

maxulysse commented Sep 23, 2024

View reviewed changes

tests/featurecounts_group_type.nf.test Outdated Show resolved Hide resolved

maxulysse and others added 3 commits September 23, 2024 11:19

Update tests/featurecounts_group_type.nf.test

b21e93c

why was this not commited?

8dc2d34

use nft-utils

5d79bdc

maxulysse added 3 commits October 1, 2024 11:12

update nftignore

07ba1b9

Merge branch 'dev' into better_snapshots

00a87fc

update pipeline versions in snapshot

a83ce56

maxulysse added 3 commits October 1, 2024 12:13

update nftignore

7d14c74

update nftignore

2b856b7

use nft-utils 0.0.2 to get relative path in snapshots

1d35e2a

pinin4fjords approved these changes Oct 2, 2024

View reviewed changes

maxulysse merged commit 07197c5 into nf-core:dev Oct 2, 2024
24 checks passed

maxulysse deleted the better_snapshots branch October 2, 2024 08:15

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Improve pipeline level snapshots #1379

Improve pipeline level snapshots #1379

maxulysse commented Sep 13, 2024 •

edited

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github-actions bot commented Sep 13, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Sep 13, 2024

pinin4fjords commented Sep 13, 2024 •

edited

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maxulysse commented Sep 19, 2024 •

edited

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pinin4fjords commented Oct 1, 2024

maxulysse commented Oct 1, 2024

maxulysse commented Oct 1, 2024

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Improve pipeline level snapshots #1379

Improve pipeline level snapshots #1379

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maxulysse commented Sep 13, 2024 • edited Loading

PR checklist

github-actions bot commented Sep 13, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Sep 13, 2024

pinin4fjords commented Sep 13, 2024 • edited Loading

maxulysse commented Sep 19, 2024 • edited Loading

pinin4fjords commented Oct 1, 2024

maxulysse commented Oct 1, 2024

maxulysse commented Oct 1, 2024

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maxulysse commented Sep 13, 2024 •

edited

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github-actions bot commented Sep 13, 2024 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️

pinin4fjords commented Sep 13, 2024 •

edited

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maxulysse commented Sep 19, 2024 •

edited

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