Dev -> Master for v3.7 release #816

drpatelh · 2022-04-29T15:29:28Z

No description provided.

Bump pipeline version to 3.7dev

Important! Template update for nf-core/tools v2.3

…genomes

Add outputs for umitools dedup summary stats

…tract Issue797 skip umitools extract

Add Pipeline diagram

Fix #762 and #775

github-actions · 2022-04-29T15:52:16Z

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

Posted for pipeline commit 43e2ef3

+| ✅ 143 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '3.7'

❔ 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: .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 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: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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 - .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
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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (208 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.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'.

Run details

nf-core/tools version 2.3.2
Run at 2022-05-03 10:21:23

JoseEspinosa

Awesome @drpatelh 🥇

.prettierignore

workflows/rnaseq.nf

mahesh-panchal

LGTM

Co-authored-by: Daniel Straub <[email protected]>

Added paragraph about the usage of rnaseq with prokaryotic data based on Issue #765

fixed HISAT2 route

Tweak docs for prokaryotes

drpatelh and others added 30 commits March 4, 2022 15:44

Bump pipeline version to 3.7dev

8aa566e

Bump pipeline version to 3.7dev

24457c3

Merge pull request #777 from drpatelh/bump

474fe35

Bump pipeline version to 3.7dev

Template update for nf-core/tools version 2.3

a560af6

Merge branch 'dev' into nf-core-template-merge-2.3

584a584

Update .yamllint.yml

bcdfaff

Update check_samplesheet.py

17b6ae4

Update .nf-core.yml

8d1de9d

Update input_check.nf

fa2ac1c

Merge pull request #784 from nf-core/nf-core-template-merge-2.3

587c61b

Important! Template update for nf-core/tools v2.3

added adaptations for prokaryotic data below the paragraph reference …

4cff9e9

…genomes

added adaptations for prokaryotic data below the paragraph reference …

86db450

…genomes

fixing linting

67fc1df

fixing linting

49b18ed

fix linting

96bcd15

Merge branch 'master' of https://github.com/jenmuell/rnaseq

1002765

fix linting

06adf08

fix linting

35eb238

fix linting

e556922

fix linting

46cd8f2

fix linting

af4a329

fixed linting final

36f80ba

Add outputs for umitools dedup summary stats

d021828

Merge pull request #792 from drpatelh/sync

5aadd93

Add outputs for umitools dedup summary stats

Template update for nf-core/tools version 2.3.1

d9cf53a

Template update for nf-core/tools version 2.3.2

4caab23

Fix merge conflicts

8190129

Update CHANGELOG after merging template updates

356fbd9

Fix prettier

5f748a3

Fix nf-core lint

a5d24da

drpatelh and others added 12 commits April 29, 2022 14:46

Apply suggestions from code review

b5981a3

Merge pull request #807 from MatthiasZepper/issue797-skip_umitools_ex…

ee5b7f6

…tract Issue797 skip umitools extract

Merge pull request #812 from jfy133/pipeline-diagram

13503cc

Add Pipeline diagram

Rename metro maps

7c84b7c

Add note about recent updates to AWS iGenomes

0e8e5fa

Change release date

bc68233

Fix #775

a8ede59

Update CHANGELOG

98fc9ba

Fix #762

4996b00

Fix Prettier

e722739

Merge pull request #815 from drpatelh/updates

c5bff79

Fix #762 and #775

Update nextflow.config

d7946a8

drpatelh requested review from JoseEspinosa and mahesh-panchal April 29, 2022 15:30

JoseEspinosa approved these changes Apr 29, 2022

View reviewed changes

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mahesh-panchal approved these changes Apr 29, 2022

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mahesh-panchal approved these changes May 2, 2022

View reviewed changes

G-Sarah and others added 11 commits May 2, 2022 13:55

fixed HISAT2 route

35b98ed

arrange stage 2 layout

ba57121

arrange stage 2 layout

4b4b861

Update docs/usage.md

cddc77b

Co-authored-by: Daniel Straub <[email protected]>

Update docs/usage.md

7b047ce

Co-authored-by: Daniel Straub <[email protected]>

Merge pull request #790 from jenmuell/master

f5d5707

Added paragraph about the usage of rnaseq with prokaryotic data based on Issue #765

resolved file name issue

62744bb

Merge pull request #818 from nf-core/diagram-fix

f091ffe

fixed HISAT2 route

Tweak docs for prokaryotes

9f9e74f

Update CHANGELOG

1eb39b3

Merge pull request #820 from drpatelh/updates

43e2ef3

Tweak docs for prokaryotes

drpatelh merged commit e0dfce9 into master May 3, 2022

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Dev -> Master for v3.7 release #816

Dev -> Master for v3.7 release #816

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drpatelh commented Apr 29, 2022

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Dev -> Master for v3.7 release #816

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drpatelh commented Apr 29, 2022

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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github-actions bot commented Apr 29, 2022 •

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