pre-first release review - DO NOT MERGE #159

maxulysse · 2024-09-23T14:26:54Z

PR checklist

add msa mixin for KALIGN, LEARNMSA, MAFFT

add MAGUS

Some Docs

add MTMalign

Bump version

github-actions · 2024-09-23T14:28:31Z

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

Posted for pipeline commit 0df116a

+| ✅ 192 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
multiqc_config - multiqc_config

✅ 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: 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-multiplesequencealign_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-multiplesequencealign_logo_light.png
files_exist - File found: docs/images/nf-core-multiplesequencealign_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: main.nf
files_exist - File found: assets/multiqc_config.yml
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 found: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-multiplesequencealign_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowMultiplesequencealign.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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/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.html 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-multiplesequencealign_logo_light.png matches the template
files_unchanged - docs/images/nf-core-multiplesequencealign_logo_light.png matches the template
files_unchanged - docs/images/nf-core-multiplesequencealign_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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: 24.04.1, Config: 24.04.1
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (275 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
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - CALCULATE_SEQSTATS found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_SEQSTATS found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_PLDDT found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_PLDDT found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_SEQREFORMAT_SIM found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_SIMSTATS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_STATS found in conf/modules.config and Nextflow scripts.
modules_config - FAMSA_GUIDETREE found in conf/modules.config and Nextflow scripts.
modules_config - CLUSTALO_GUIDETREE found in conf/modules.config and Nextflow scripts.
modules_config - MAGUS_GUIDETREE found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_TCOFFEETEMPLATE found in conf/modules.config and Nextflow scripts.
modules_config - CLUSTALO_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - MTMALIGN_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - CONSENSUS found in conf/modules.config and Nextflow scripts.
modules_config - PIGZ_COMPRESS found in conf/modules.config and Nextflow scripts.
modules_config - PARSE_IRMSD found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_ALNCOMPARE_SP found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_ALNCOMPARE_TC found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_IRMSD found in conf/modules.config and Nextflow scripts.
modules_config - CALC_GAPS found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_IRMSD found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_GAPS found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_SP found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_TC found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_TCS found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_TCS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_EVAL found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_STATS_EVAL found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - PREPARE_SHINY found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-10-01 08:26:54

maxulysse · 2024-09-24T07:32:28Z

README.md

-The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
-
-On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/proteinfold/results).


you're missing this bit from the TEMPLATE

uh ups! added :)

README.md

maxulysse · 2024-09-24T07:36:05Z

docs/extending.md

@@ -0,0 +1,71 @@
+# Extending nf-core/multiplesequencealign


Isn't this covered by the Contributing Guidelines in .github/CONTRIBUTING.md?

Not completely - here it specifies precisely how to do it for this specific pipeline (which parts of the workflow to touch etc). I added now a pointer to CONTRIBUTING from the extending

maxulysse · 2024-09-24T07:36:50Z

docs/images/nf-core-msa_metro_map.png

The logo seems a bit off

upsi, updated

Update mtmalign

First release review

luisas · 2024-10-04T07:59:52Z

dev branch was merged with #158 .

I will close this one :)

lrauschning and others added 30 commits May 21, 2024 14:38

add msa mixin for KALIGN, LEARNMSA, MAFFT

bbe5b27

fix import for guidetree

85f9bd6

handle clustalo output a bit more elegantly

cffd25a

use maffts output name

36178d1

Merge pull request #128 from lrauschning/fixes

038234b

add msa mixin for KALIGN, LEARNMSA, MAFFT

Merge pull request #127 from lrauschning/magus

93f7138

add MAGUS

Merge pull request #125 from lrauschning/doc

3f1090e

Some Docs

bump nextflow version

6145a81

Merge branch 'dev' into mtmalign

b5704f0

Update align.nf

62b7ae0

Update README.md

78ec0f1

Update

77ef1c9

"Update readme"

f24c84e

Bump version again

ed40f43

update readme

a51d802

Merge pull request #126 from lrauschning/mtmalign

508c7ce

add MTMalign

Fix linting warnings

45c8f77

Improve parameter handling

1db22b5

compression handling fixe

0bda718

Update readme and fix compression

832c5c0

Ci tests

b3dd100

Update readme

97e2a9e

Update tcoffee and readme

dd7feb5

Update readme

a24de25

Update readme

599bdf0

Update

fd349bd

Update

ab06fe9

Update

919f107

Update

554ad5c

Update

859ae11

Merge pull request #157 from luisas/bump_version

b3540dc

Bump version

maxulysse changed the title ~~POC: pre-first release review - DO NOT MERGE~~ pre-first release review - DO NOT MERGE Sep 23, 2024

update

aa02e39

maxulysse commented Sep 24, 2024

View reviewed changes

README.md Outdated Show resolved Hide resolved

maxulysse commented Sep 24, 2024

View reviewed changes

luisas added 20 commits September 25, 2024 08:06

update

ab3005b

Merge pull request #160 from luisas/update_mtmalign

15c3126

Update mtmalign

add magus citation

6d1a5ea

fix version multiqc

c0fec41

add versions

8dd7ab2

update plugin

c96bc5f

remove custom

124fdcb

notes

f10da49

upate

2f54559

update diff

a94011e

update docs

7e06615

fix template readme

39160a0

Add files via upload

d6963c7

fix versions

7b8e4a1

update contribting

f70117b

revert contributing changes

ca26a7a

Add files via upload

b0105d1

Update contributing

38852b2

update contributing

5b51fcf

Merge pull request #161 from nf-core/first_release_review

0df116a

First release review

luisas closed this Oct 4, 2024

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pre-first release review - DO NOT MERGE #159

pre-first release review - DO NOT MERGE #159

maxulysse commented Sep 23, 2024

github-actions bot commented Sep 23, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse Sep 24, 2024

luisas Sep 25, 2024

maxulysse Sep 24, 2024

luisas Sep 25, 2024

maxulysse Sep 24, 2024

luisas Sep 25, 2024

luisas commented Oct 4, 2024

		The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

		On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/proteinfold/results).

pre-first release review - DO NOT MERGE #159

pre-first release review - DO NOT MERGE #159

Conversation

maxulysse commented Sep 23, 2024

PR checklist

github-actions bot commented Sep 23, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse Sep 24, 2024

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luisas Sep 25, 2024

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maxulysse Sep 24, 2024

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luisas Sep 25, 2024

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maxulysse Sep 24, 2024

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luisas Sep 25, 2024

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luisas commented Oct 4, 2024

github-actions bot commented Sep 23, 2024 •

edited

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