Merge Dev to Master - nf-core/circdna Version 1.0 #28

DSchreyer · 2022-05-31T10:18:25Z

PR checklist

Merge Dev

…t module

… Added samtools faidx to not updata - removed meta data

Dev

…core module

…core modules

External DEV to nf-core/circdna dev PR

github-actions · 2022-05-31T10:19:43Z

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

Posted for pipeline commit a3386c5

+| ✅ 143 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
multiqc_config - 'assets/multiqc_config.yml' not found

✅ 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-circdna_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-circdna_logo_light.png
files_exist - File found: docs/images/nf-core-circdna_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: 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/WorkflowCircdna.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: .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-circdna_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 .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '1.0dev'
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/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-circdna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circdna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circdna_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 - lib/NfcoreTemplate.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_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (142 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: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.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

Run details

nf-core/tools version 2.4.1
Run at 2022-05-31 19:36:16

sguizard

Just remove the local copy of minimap2 module, otherwise LGTM!

apeltzer · 2022-05-31T18:54:23Z

minimap2 is already a nf-core one, samtools/Faidx should be an nf-core module too - this already exists

apeltzer · 2022-05-31T20:43:05Z

Guess you can merge and release @DSchreyer 🤘

DSchreyer and others added 30 commits March 9, 2022 16:06

Merge pull request #3 from DSchreyer/dev

f1c8686

Merge Dev

Added outdirs for ampliconclassifier

bcd79c3

Added cycleviz module; Changed cnvkit outfiles; Updated cnvkit segmen…

f4a5261

…t module

Merge branch 'nf-core:master' into master

d53d6e6

Updated README to pass markdownlint

d172377

Merge branch 'master' of github.com:DSchreyer/circdna

8ef2b9e

Small changes

b259a1c

Changes

e33e043

Fix changes

c37fb8d

No cnr output

52f0b00

Added stub test for ampliconarchitect run with test-data

b4805b2

Updated versions; Added stub to test run all software simultaneously;…

ba29c26

… Added samtools faidx to not updata - removed meta data

Updated docs usage and output; Updated metromap

5738273

Added samplesheet_bam to show formatting

afd1066

Added collect_seeds and amplified_intervals to replace PrepareAA.

0eac4b3

Added collect_seeds and amplified_intervals to replace PrepareAA

177f7ef

Updated readme

30bba58

Removed

0922b66

Small fixes

9999e0d

Small fixes

1bade3f

Removed

ed0e65e

Updates

9717bf5

Added pyc line

041468d

Added SAMTOOLS_SORT_BAM modules config; removed coverage.nf

2e432eb

Removed T1 from bam files

0010097

Modified samtools bam

e63e429

Small fixes

f170c4d

aa_cngain is now a string

ce5dbc5

Updated software version; added stub command

d0ad815

Merge pull request #6 from DSchreyer/dev

b87ff42

Dev

DSchreyer and others added 19 commits May 17, 2022 08:30

Nf-core tools 2.4

bb56280

Template Update

fcf8e7e

prettier

bedcd3e

Added email_template as it does not work with prettier

811ee73

Changed circlemap realign to use new faidx input; removed multiqc nf-…

332ae4a

…core module

Removed and added nf-core modules

f595ac8

Added nf-core modules and removed local ones; Changed code to fit nf-…

8ebdeff

…core modules

Removed BAM_STATS_SAMTOOLS_RAW warning

2bde7d8

Unicycler update

b72aa94

Fixed mapping issue; Runs on newest nf-core modules

89fb513

Updated metromap

2d134e4

updated modules; unicycler return

570410d

Removed cnvkit batch

035b07f

Removed unicycler input to nf-core module

65b9b5e

Modified test full config

b1253ce

Merge pull request #27 from DSchreyer/dev

2e0334d

External DEV to nf-core/circdna dev PR

Template Update v2.4

e83c05e

Removed images

9118d5b

nf-core lint; nf-core badge

244c0bf

DSchreyer assigned apeltzer May 31, 2022

DSchreyer requested review from apeltzer and sguizard May 31, 2022 10:56

sguizard approved these changes May 31, 2022

View reviewed changes

Removed local minimap2; Updated README.md

1a9deed

apeltzer approved these changes May 31, 2022

View reviewed changes

Removed samtools

a3386c5

DSchreyer merged commit b0152a3 into master May 31, 2022

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Merge Dev to Master - nf-core/circdna Version 1.0 #28

Merge Dev to Master - nf-core/circdna Version 1.0 #28

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DSchreyer commented May 31, 2022

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Merge Dev to Master - nf-core/circdna Version 1.0 #28

Merge Dev to Master - nf-core/circdna Version 1.0 #28

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DSchreyer commented May 31, 2022

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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apeltzer commented May 31, 2022

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