Make --outdir mandatory, tin.py opt-in and fix #750 #771

drpatelh · 2022-02-21T23:24:50Z

nf-core/tools#1415 - Make --outdir a mandatory parameter
[#750] - Optionally ignore R1 / R2 after UMI extraction process
[#769] - Do not run RSeQC tin.py by default

github-actions · 2022-02-21T23:43:05Z

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

Posted for pipeline commit 3016c0b

+| ✅ 131 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

schema_description - No description provided in schema for parameter: umi_discard_read

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
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: lib/NfcoreSchema.groovy
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .markdownlint.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: 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/modules.config
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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yaml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowRnaseq.groovy
files_exist - File found: modules.json
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-rnaseq_logo.png
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.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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.version
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 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 .svg
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '3.6dev'
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
files_unchanged - .gitattributes matches the template
files_unchanged - .markdownlint.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/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.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
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore matches the template
files_unchanged - assets/multiqc_config.yaml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 21.10.3, Config: 21.10.3
readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (205 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json

Run details

nf-core/tools version 2.2
Run at 2022-02-22 09:28:30

mahesh-panchal

I would un-nest the if's but the decision is yours.

mahesh-panchal · 2022-02-22T08:34:14Z

conf/modules.config

-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/rscript" },
+        if ('bam_stat' in rseqc_modules) {


Suggested change

if ('bam_stat' in rseqc_modules) {

if (!params.skip_rseqc && 'bam_stat' in rseqc_modules) {

Perhaps combine this with above? I prefer anything we can do to get rid of these nested if's.
Also I'm realizing it's harder to review, because it's easy to mistake which level of nesting you're in.

Changed in 3016c0b

Can you double-check it looks good for me please?

We really need to find a way to avoid this logic duplication....I will try and speak to our very own Yoda.

The logic duplication can be avoided by a pipeline rewrite. The alternative is to use channel branching and ternary operators to select the correct input channels, along channel mixing and the when. It's not a simple change though.

But it would be nicer to still be able to put process invocations in if's. Maybe that's not what the data flow model was intended for though. 🤷🏽 Most people writing these workflows come from training using R or Python or what have you, and are not used to this data flow model.

subworkflows/nf-core/fastqc_umitools_trimgalore.nf

mahesh-panchal

LGTM.

drpatelh added 4 commits February 21, 2022 14:20

Fix nf-core#769

210069d

Fix nf-core#750

1f97e57

Refactor modules.config for optional rseqc modules

fb44c5e

Make --outdir mandatory

c3313c0

This was referenced Feb 21, 2022

Optionally ignore R1 / R2 after UMI extraction process #750

Closed

Do not run RSeQC tin.py by default #769

Closed

Fix linting

03d1789

drpatelh requested a review from mahesh-panchal February 21, 2022 23:36

mahesh-panchal approved these changes Feb 22, 2022

View reviewed changes

drpatelh added 3 commits February 22, 2022 09:14

Use modulo operation instead to get read number

e09cde4

Tweak Groovy syntax

738299e

Remove indentation for RSEQC logic in modules.config

3016c0b

mahesh-panchal approved these changes Feb 22, 2022

View reviewed changes

drpatelh merged commit 386bda0 into nf-core:dev Feb 22, 2022

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Make --outdir mandatory, tin.py opt-in and fix #750 #771

Make --outdir mandatory, tin.py opt-in and fix #750 #771

drpatelh commented Feb 21, 2022 •

edited

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github-actions bot commented Feb 21, 2022 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mahesh-panchal left a comment

mahesh-panchal Feb 22, 2022

drpatelh Feb 22, 2022

mahesh-panchal Feb 22, 2022

mahesh-panchal left a comment

	if ('bam_stat' in rseqc_modules) {
	if (!params.skip_rseqc && 'bam_stat' in rseqc_modules) {

Make --outdir mandatory, tin.py opt-in and fix #750 #771

Make --outdir mandatory, tin.py opt-in and fix #750 #771

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drpatelh commented Feb 21, 2022 • edited Loading

github-actions bot commented Feb 21, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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drpatelh commented Feb 21, 2022 •

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