v1.0.0 #41

antunderwood · 2021-06-16T19:37:20Z

PR checklist

This is it guys - PR for 1st release 🏁

Updates with latest boilerplate code from nf-core create

…me size

Dsl2 mash sketch

Pre-release fixes and syncing with latest DSL2 pipeline template

Fixes

Preparing for release

github-actions · 2021-06-16T19:38:15Z

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

Posted for pipeline commit 06483f5

+| ✅ 106 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  43 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: environment.yml
files_exist - File not found: Dockerfile
nextflow_config - Config variable not found: process.container
nextflow_config - Config manifest.version should end in dev: '1.0.0'
params_used - Config variable not found in main.nf: params.input
params_used - Config variable not found in main.nf: params.reference
params_used - Config variable not found in main.nf: params.trim
params_used - Config variable not found in main.nf: params.save_trimmed_fail
params_used - Config variable not found in main.nf: params.adapter_file
params_used - Config variable not found in main.nf: params.subsampling_off
params_used - Config variable not found in main.nf: params.subsampling_depth_cutoff
params_used - Config variable not found in main.nf: params.genome_size
params_used - Config variable not found in main.nf: params.remove_recombination
params_used - Config variable not found in main.nf: params.non_GATC_threshold
params_used - Config variable not found in main.nf: params.rapidnj
params_used - Config variable not found in main.nf: params.fasttree
params_used - Config variable not found in main.nf: params.iqtree
params_used - Config variable not found in main.nf: params.raxmlng
params_used - Config variable not found in main.nf: params.multiqc_config
params_used - Config variable not found in main.nf: params.multiqc_title
params_used - Config variable not found in main.nf: params.outdir
params_used - Config variable not found in main.nf: params.tracedir
params_used - Config variable not found in main.nf: params.publish_dir_mode
params_used - Config variable not found in main.nf: params.email
params_used - Config variable not found in main.nf: params.email_on_fail
params_used - Config variable not found in main.nf: params.plaintext_email
params_used - Config variable not found in main.nf: params.max_multiqc_email_size
params_used - Config variable not found in main.nf: params.skip_multiqc
params_used - Config variable not found in main.nf: params.enable_conda
params_used - Config variable not found in main.nf: params.validate_params
params_used - Config variable not found in main.nf: params.monochrome_logs
params_used - Config variable not found in main.nf: params.help
params_used - Config variable not found in main.nf: params.singularity_pull_docker_container
params_used - Config variable not found in main.nf: params.hostnames
params_used - Config variable not found in main.nf: params.config_profile_description
params_used - Config variable not found in main.nf: params.config_profile_contact
params_used - Config variable not found in main.nf: params.config_profile_url
params_used - Config variable not found in main.nf: params.max_memory
params_used - Config variable not found in main.nf: params.max_cpus
params_used - Config variable not found in main.nf: params.max_time
readme - README did not have a Nextflow minimum version badge.
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below, 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: .github/markdownlint.yml
files_exist - File is ignored: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
files_unchanged - File does not exist: .github/markdownlint.yml
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/sendmail_template.txt
files_unchanged - File does not exist: bin/markdown_to_html.py
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
files_unchanged - File ignored due to lint config: .gitignore or foo
files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
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/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-bactmap_logo.png
files_exist - File found: docs/images/nf-core-bactmap_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: 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 - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml 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/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/nf-core-bactmap_logo.png matches the template
files_unchanged - docs/images/nf-core-bactmap_logo.png matches the template
files_unchanged - lib/nfcore_external_java_deps.jar 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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (132 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: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.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 1.14
Run at 2021-06-18 11:26:14

thanhleviet

LGTM

drpatelh

Absolutely awesome effort guys 🙇🏽 🥳

drpatelh · 2021-06-17T12:42:25Z

PS: Don't forget to change the date in the CHANGELOG!

ggabernet

Great work, I'll be really happy to see this released 😄

antunderwood and others added 30 commits June 25, 2019 10:43

add enaBrowserTools to conda env

5fd0f91

install nf-core tools from dev branch

95ae8ea

install nf-core tools from dev branch revised URL

36cfbf4

Merge pull request #1 from aunderwo/master

fca8cab

Updates with latest boilerplate code from nf-core create

Delete everything 🔥

e3ca2e0

nf-core create with dsl2_template branch

a61d997

Initial dsl2 template commit

43b4f11

Merge branch 'TEMPLATE' into dsl2

c3da8fc

adding gubbins module

9553912

adding snp-sites module

c6e6111

created mash_sketch module to count number of reads and estimate geno…

af1a24d

…me size

adding snp-sites module

055aafa

updated CHANGELOG.md, CITATIONS.md, README.md

d171e6b

corrected nf-core format error CITATIONS.md

1a6367d

adding iqtree module

41959cb

removed pipeline summary clashing with markdown linting

9a4c1ce

adding fasttree module

5bf6180

move utility functions

a3c6c40

Merge pull request #16 from alexandregilardet/dsl2

3a6377c

Dsl2 mash sketch

Merge remote-tracking branch 'avantonder/dsl2' into dsl2

93d88c4

add test inout files and samplesheet

fc98ded

Add functions to create inputs from samplesheet

57dc55c

make the requirements a bit more sane

11f880e

add fastp nf-core module

5e79380

add optional path for adapter fasta file

f3c2c8c

get basic inputs enetering workflow

03d90c2

add fastp with optional adapter sequence file

13cfd59

add options for fastp

2ebe373

remove unnecessary genome checks

8c125e7

add default workflow params

68026ab

antunderwood and others added 17 commits June 7, 2021 17:25

Fix linting issues

bad6c78

Merge pull request #38 from drpatelh/fixes

8bbe33e

Pre-release fixes and syncing with latest DSL2 pipeline template

remove unnecessary module param

dd0fe68

move find_genome_size to WorkflowBactMap

2851b49

Added some more detail to the output markdown

eefc054

fix whitespace

9eab94d

Couple more linting fixes

fa1491a

One more lint fix

efe722e

Update main.nf

f5bb392

Update main.nf

7276abe

Merge pull request #39 from nf-core/fixes

fa18945

Fixes

prepare for release

bdad426

auto lint fixing

100532e

add new line to config

0a4163a

ignore some linting issues

bd73aaa

software versions output is a tsv

852830c

Merge pull request #40 from nf-core/preparing_for_release

717a052

Preparing for release

antunderwood requested a review from ewels June 16, 2021 19:37

antunderwood requested review from avantonder, drpatelh and ggabernet June 16, 2021 19:38

avantonder approved these changes Jun 16, 2021

View reviewed changes

thanhleviet approved these changes Jun 16, 2021

View reviewed changes

drpatelh approved these changes Jun 16, 2021

View reviewed changes

ggabernet approved these changes Jun 17, 2021

View reviewed changes

antunderwood added 2 commits June 18, 2021 09:55

Update date for release

6810d7f

add codename

06483f5

antunderwood merged commit 834642d into master Jun 18, 2021

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v1.0.0 #41

v1.0.0 #41

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antunderwood commented Jun 16, 2021

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github-actions bot commented Jun 16, 2021 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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drpatelh commented Jun 17, 2021

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v1.0.0 #41

v1.0.0 #41

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antunderwood commented Jun 16, 2021

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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drpatelh commented Jun 17, 2021

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github-actions bot commented Jun 16, 2021 •

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