Dev -> Master for v3.6 release #773

drpatelh · 2022-02-25T09:23:41Z

No description provided.

Bump pipeline version to 3.6dev

Co-authored-by: Harshil Patel <[email protected]>

Patch RSEM_PREPAREREFERENCE configuration

nf-core modules update

Sync pipeline with nf-core/tools dev to fix linting

Pipeline updates / addressing open issues

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

Bump pipeline version to 3.6

github-actions · 2022-02-25T09:25:00Z

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

Posted for pipeline commit f37d505

+| ✅ 130 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '3.6'
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 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 2022-03-04 13:18:31

JoseEspinosa

LGTM good job! Made a comment about the outdir directory, probably this has been discussed already and I missed it.

JoseEspinosa · 2022-03-04T10:12:24Z

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)
    - [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).


I guess this has been discussed already, but why not set the parameter in the test.config? I don't see the point of providing it several times in the ci.yml file, plus as user, the command is simpler to run tests

After, reviewing the whole code, I see that the reason is that outdir param is removed from the nextflow.config but still I think it should be set by default in the test.config.

If we set it to ./results in the test.config then we end up in the same position where we end up using relative paths when -profile test is used in the Cloud? The main problem is that there isn't a sensible default that works yet.

I see the cloud part is what I missed, fair enough

drpatelh and others added 30 commits December 17, 2021 17:13

Bump pipeline version to 3.6dev

607cf39

Merge pull request #747 from drpatelh/bump

288aa25

Bump pipeline version to 3.6dev

Patch RSEM_PREPAREREFERENCE configuration

3fdd664

Rename RSEM_PREPAREREFERENCE_TRANSCRIPTS to MAKE_TRANSCRIPTS_FASTA

7f14e06

Co-authored-by: Harshil Patel <[email protected]>

Merge pull request #763 from mahesh-panchal/patch_rsem_config

e75cb15

Patch RSEM_PREPAREREFERENCE configuration

Simplify process selectors in modules.config and quote everything

4142ec8

Adjust spacing

684b4f4

Run nf-core modules update

01de13e

Add when statement to local modules

3281aeb

Bump MultiQC version

f97169e

Revert MultiQC bump because something else broke

79b5c16

Revert contentious process selectors in modules.config

57792a6

Merge pull request #766 from drpatelh/update

03e774a

nf-core modules update

Template update for nf-core/tools version 2.3.dev0

96f6b72

Fix merge conflicts

28ef98c

Sync pipeline with nf-core/tools dev to fix linting

8fba444

Fix linting

accb04b

Fix linting again

41218aa

Update usage docs

b7a34cb

Update footnotes in usage docs

d04519c

Add NFCORE_RNASEQ prefix everywhere

b66f055

Merge pull request #767 from drpatelh/template

4f3ec49

Sync pipeline with nf-core/tools dev to fix linting

Add --publish_dir_mode back into pipeline #752

df102cd

Fix #759

71c0d38

Fix #744

d55892b

Update CHANGELOG

24c69fb

Fix ECLint

6775dc3

Fix process selector for CUSTOM_GETCHROMSIZES

091f952

Fix #753

a7915a6

Fix ECLint

f1146a2

drpatelh and others added 13 commits February 20, 2022 20:33

Easy fix for #754

47814c9

Merge pull request #770 from drpatelh/updates

ed4fd3e

Pipeline updates / addressing open issues

Fix #769

210069d

Fix #750

1f97e57

Refactor modules.config for optional rseqc modules

fb44c5e

Make --outdir mandatory

c3313c0

Fix linting

03d1789

Use modulo operation instead to get read number

e09cde4

Tweak Groovy syntax

738299e

Remove indentation for RSEQC logic in modules.config

3016c0b

Merge pull request #771 from drpatelh/updates

386bda0

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

Bump pipeline version to 3.6

9b1cc4b

Merge pull request #772 from drpatelh/updates

7c7f03e

Bump pipeline version to 3.6

mahesh-panchal approved these changes Feb 25, 2022

View reviewed changes

JoseEspinosa approved these changes Mar 4, 2022

View reviewed changes

Update CHANGELOG.md

f37d505

drpatelh merged commit 7106bd7 into master Mar 4, 2022

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Dev -> Master for v3.6 release #773

Dev -> Master for v3.6 release #773

drpatelh commented Feb 25, 2022

github-actions bot commented Feb 25, 2022 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

JoseEspinosa Mar 4, 2022

JoseEspinosa Mar 4, 2022

drpatelh Mar 4, 2022

JoseEspinosa Mar 4, 2022

Dev -> Master for v3.6 release #773

Dev -> Master for v3.6 release #773

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drpatelh commented Feb 25, 2022

github-actions bot commented Feb 25, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

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JoseEspinosa Mar 4, 2022

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github-actions bot commented Feb 25, 2022 •

edited

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