Dev -> Master for v3.10 release #914

drpatelh · 2022-12-20T16:16:51Z

No description provided.

Update modules to latest restructuring on nf-core/modules

Important! Template update for nf-core/tools v2.6

Because I just found out about these and want to try them out somewhere.

Fancy GitHub blockquote admonitions

Fix SAMTOOLS_INDEX output

clarification of star and salmon outputs from issue #722

nf-core subworkflows install

Add 'auto' option to auto-detect strandedness

FInal pre-release fixes

update subway map

github-actions · 2022-12-20T17:13:18Z

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

Posted for pipeline commit 4f29256

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '3.10'
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

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/NfcoreTemplate.groovy

✅ 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: 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.yml
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 found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: .nf-core.yaml
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: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
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.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 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 - .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
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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: 22.10.1, Config: 22.10.1
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (235 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
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.7.2
Run at 2022-12-20 22:00:10

Remove last meta map clone

Bump pipeline version to v3.10 and other small tweaks

robsyme

Monster merge, but I'm happy with all of the commits that comprised this PR. We're also running a full-sized test now, and will update here with the results.

CHANGELOG.md

FriederikeHanssen · 2022-12-20T20:58:13Z

workflows/rnaseq.nf

    }
-    .groupTuple(by: [0])
+    .groupTuple()


what about using sizehere so the tuple advances as soon as possible?

Good question! I'll leave @robsyme to comment here. Asked him exactly the same question.

Good question.
To emit asap, we'd need to calculate the number of technical replicates at an earlier stage - probably during samplesheet validation. This is certainly possible, but because there are no long-running processes between samplesheet generation and this grouping operation, there is no real speedup to be gained.
I'm a huge fan of using groupKey as often as possible, but in this case there is no advantage.

Ok makes sense.

FriederikeHanssen

looks good :) Maybe someone with a little more in depth knowledge of what the pipeline does should approve though :)

FriederikeHanssen

Looks good to me now! Not deep into rnaseq analysis, but I suppose the features were discussed beforehand on slack.

robsyme · 2022-12-21T15:26:10Z

🥳

nf-core-bot and others added 30 commits October 4, 2022 22:04

Template update for nf-core/tools version 2.6

72edef2

Run nf-core modules update

2f4dd63

Re-install custom/getchromsizes module

6f06f48

Patch custom/getchromsizes module

828fe45

Fix relative paths after module restructuring

cc379c7

Bump pipeline version to 3.10dev

17f60e8

Fix nf-core lint

02a7136

Fix merge conflicts

bd18b6c

Get -profile test running

a208353

Revert modules.json

b11f984

Merge pull request #881 from drpatelh/restructure

4721317

Update modules to latest restructuring on nf-core/modules

Merge branch 'dev' into nf-core-template-merge-2.6

04cebb5

Merge pull request #880 from nf-core/nf-core-template-merge-2.6

2a32479

Important! Template update for nf-core/tools v2.6

clarification of star and salmon outputs from issue #722

d57912d

refactor(hisat2): nf-core subworkflows install fastq_align_hisat2

207640c

refactor(samtools): nf-core subworkflows install bam_sort_stats_samtools

295f967

refactor: nf-core subworkflows install bam_markduplicates_picard

0688de7

refactor: nf-core subworkflows install bam_rseqc

f5c6ad7

refactor: nf-core subworkflows install bam_dedup_stats_samtools_umitools

cfc96f5

refactor: nf-core subworkflows install bedgraph_bedclip_bedgraphtobigwig

d7aa733

refactor: nf-core subworkflows install fastq_fastqc_umitools_trimgalore

2cf2c96

Fancy GitHub blockquote admonitions

62585e3

Because I just found out about these and want to try them out somewhere.

Merge pull request #890 from nf-core/readme-admonitions

7bc7708

Fancy GitHub blockquote admonitions

Fix SAMTOOLS_INDEX output pattern

e0592bb

Template update for nf-core/tools version 2.7.1

e8d1627

Merge pull request #903 from claire-prince/Fix-SAMTOOLS_INDEX-output

4ff430a

Fix SAMTOOLS_INDEX output

Merge pull request #885 from nf-core/ctuni-patch-1

fd34718

clarification of star and salmon outputs from issue #722

Merge pull request #886 from nf-core/subworkflows-install

24eb379

nf-core subworkflows install

Fix merge conflicts

ed9d58e

Update all modules and subworkflows

d0d65f1

drpatelh and others added 19 commits December 20, 2022 12:15

Spacing...

09893dc

first attempt

2f0a5ce

second attempt

5c30ef7

45 degree angles

7335508

Merge pull request #910 from drpatelh/strand

99a662b

Add 'auto' option to auto-detect strandedness

Fix #898

a810fcf

Update usage docs for #889

f8978f7

Update CHANGELOG

e5f8f4e

Merge pull request #913 from drpatelh/fixes

7a8cfe6

FInal pre-release fixes

Bump pipeline version to 3.10

b10425d

Update README

489dec8

extend figure

a5e14fb

Update CHANGELOG

968c400

Merge pull request #912 from maxulysse/update_subway_map

0d4aa41

update subway map

Add Edmund to credits

cd7213e

Add software version changes to CHANGELOG

c847380

Rename process to UMITOOLS_PREPAREFORSALMON for clarity

92154a3

Remove last meta map clone

ccee5f4

Shorter id

4ab556c

drpatelh added 2 commits December 20, 2022 17:21

Merge pull request #915 from nf-core/metamap-tidy

c16fe7c

Remove last meta map clone

Merge pull request #916 from drpatelh/fixes

763537a

Bump pipeline version to v3.10 and other small tweaks

robsyme approved these changes Dec 20, 2022

View reviewed changes

FriederikeHanssen reviewed Dec 20, 2022

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

FriederikeHanssen reviewed Dec 20, 2022

View reviewed changes

Update CHANGELOG.md

4f29256

FriederikeHanssen approved these changes Dec 21, 2022

View reviewed changes

drpatelh merged commit adce7ce into master Dec 21, 2022

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Dev -> Master for v3.10 release #914

Dev -> Master for v3.10 release #914

drpatelh commented Dec 20, 2022

github-actions bot commented Dec 20, 2022 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

robsyme left a comment

FriederikeHanssen Dec 20, 2022

drpatelh Dec 20, 2022

robsyme Dec 20, 2022 •

edited

Loading

FriederikeHanssen Dec 21, 2022

FriederikeHanssen left a comment

FriederikeHanssen left a comment

robsyme commented Dec 21, 2022

Dev -> Master for v3.10 release #914

Dev -> Master for v3.10 release #914

Conversation

drpatelh commented Dec 20, 2022

github-actions bot commented Dec 20, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

robsyme left a comment

Choose a reason for hiding this comment

FriederikeHanssen Dec 20, 2022

Choose a reason for hiding this comment

drpatelh Dec 20, 2022

Choose a reason for hiding this comment

robsyme Dec 20, 2022 • edited Loading

Choose a reason for hiding this comment

FriederikeHanssen Dec 21, 2022

Choose a reason for hiding this comment

FriederikeHanssen left a comment

Choose a reason for hiding this comment

FriederikeHanssen left a comment

Choose a reason for hiding this comment

robsyme commented Dec 21, 2022

github-actions bot commented Dec 20, 2022 •

edited

Loading

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

robsyme Dec 20, 2022 •

edited

Loading