Deduplicate UMI before read counting #593

drpatelh · 2021-04-14T11:51:41Z

Closes #576

github-actions · 2021-04-14T11:52:49Z

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

Posted for pipeline commit e39c6f3

+| ✅ 105 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

files_exist - File not found: environment.yml
files_exist - File not found: Dockerfile
nextflow_config - Config variable not found: process.container
readme - README did not have a Nextflow minimum version badge.
schema_params - Schema param config_profile_name not found from nextflow config

❔ Tests ignored:

files_exist - File is ignored: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
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 does not exist: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml
actions_awsfulltest - actions_awsfulltest
conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: CHANGELOG.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.md
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File found: .github/markdownlint.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.png
files_exist - File found: docs/images/nf-core-rnaseq_logo.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: main.nf
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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: .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: 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: '3.1dev'
files_unchanged - .gitattributes 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.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
files_unchanged - .github/markdownlint.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-rnaseq_logo.png matches the template
files_unchanged - docs/images/nf-core-rnaseq_logo.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
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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (228 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.13.3
Run at 2021-04-15 07:28:09

drpatelh added 5 commits April 14, 2021 12:48

Update CHANGELOG

c585c53

Add umitools implementation

f1838df

Reword subworfklow summary

67d0c57

Add module options to modules.config

9c1837b

Bump preseq version

8a13268

drpatelh added 2 commits April 14, 2021 12:53

Add Preseq version change to CHANGELOG

1126554

Add subworkflow to dedup and index umitools output

305187f

apeltzer approved these changes Apr 14, 2021

View reviewed changes

drpatelh and others added 5 commits April 14, 2021 18:41

Merge branch 'dev' into umi

229886e

Clean up MultiQC file extensions

9ac158b

Fix nf-core#574

9419b81

Remove comments

0f09140

Fix nf-core#568

d3ea272

drpatelh mentioned this pull request Apr 14, 2021

umi_tools dedup : Run before salmon to dedup counts #576

Closed

Update rnaseq.nf

e39c6f3

drpatelh merged commit d7f5981 into nf-core:dev Apr 15, 2021

drpatelh deleted the umi branch April 15, 2021 11:06

hendrikweisser mentioned this pull request Dec 13, 2022

Add UMI deduplication before quantification in tube map #906

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Deduplicate UMI before read counting #593

Deduplicate UMI before read counting #593

drpatelh commented Apr 14, 2021

github-actions bot commented Apr 14, 2021 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Deduplicate UMI before read counting #593

Deduplicate UMI before read counting #593

Conversation

drpatelh commented Apr 14, 2021

github-actions bot commented Apr 14, 2021 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Apr 14, 2021 •

edited

Loading

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