Update modules to nf-core ( clustalo and famsa) #40

luisas · 2023-08-17T14:55:52Z

Move modules of famsa and clustalo to nf-core modules.
Update corresponding subworkflows.

conf/test.config

assets/samplesheet.csv

conf/modules.config

maxulysse · 2023-09-08T10:26:56Z

assets/samplesheet.csv

+seatoxin-ref,../test-dataset/setoxin-ref.fa,/home/luisasantus/Desktop/crg_cluster/projects/multiplesequencealign/test-dataset/setoxin.ref,/home/luisasantus/Desktop/crg_cluster/projects/multiplesequencealign/test-dataset/structures/setoxin-ref
+toxin-ref,../test-dataset/toxin-ref.fa,/home/luisasantus/Desktop/crg_cluster/projects/multiplesequencealign/test-dataset/toxin.ref,


you still have some local paths leftovers

oh ok, yes i have those files in the repo. I imagine this is not supposed to happen then? Should i add it to the nf-core test datasets instead?

github-actions · 2023-09-12T08:23:56Z

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

Posted for pipeline commit ae302d6

+| ✅ 156 tests passed       |+
!| ❗  18 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
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 README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
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
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

✅ 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: 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: lib/nfcore_external_java_deps.jar
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/WorkflowMultiplesequencealign.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
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-multiplesequencealign_logo.png
files_exist - File not found check: .markdownlint.yml
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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/Workflow.groovy
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 manifest.version ends in dev: 0.1.0dev
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.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 - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (119 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: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci.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
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'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.9
Run at 2023-09-13 08:58:05

JoseEspinosa

Just some small comments to be addressed.
Also, local modules will need to have their own container even if they are running python scripts so this might need to be updated in a new PR also the test data should not be local, but this is something that also could be solve in a different PR.

LICENSE

assets/multiqc_config.yml

nextflow.config

subworkflows/local/align.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

…quencealign into update_modules

JoseEspinosa

LGTM! Let's merge this one and work in the remaining fixes in follow up PRs
Will also close #49

LICENSE

luisas added 3 commits August 11, 2023 14:55

Update famsa modules, change subworkflow align structure to accomodate.

3666a2a

Add clustalo as nf-core module. Add test run - (assets/toolsheet)

c71b616

Add mafft ( also add support for tools not requiring trees )

7bbb2c8

JoseEspinosa reviewed Sep 8, 2023

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Fix indent

8160373

maxulysse reviewed Sep 8, 2023

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JoseEspinosa reviewed Sep 8, 2023

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JoseEspinosa and others added 4 commits September 8, 2023 11:34

Fix indent

b7c6250

First round of linting fixes

b2425a9

merging fixes

f9bad25

Linting fixes

c701e9a

maxulysse reviewed Sep 8, 2023

View reviewed changes

luisas added 17 commits September 8, 2023 12:33

lint fixes

9749941

fixes

4c8c995

Other fixes

515238e

small fixes

0ddf880

linting

42f8897

patch

b9f3ae2

fix

515664f

mod template

eff77d2

add version

1cf3249

test

b0d17f2

remve docs

116019a

prettier

f0fec45

fix name

4e6c76c

fix data path

c9b0c8c

fix last local pathss

e24fc03

linting fix

146d45e

Update sample sheet

68f1121

luisas added 2 commits September 12, 2023 12:50

Fix dataset for test - sequence only for now

8fc1b6d

Linting fix

f3964b6

JoseEspinosa requested changes Sep 12, 2023

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luisas and others added 10 commits September 13, 2023 08:23

Update nextflow.config

2695c84

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Update assets/multiqc_config.yml

5377bdc

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Update subworkflows/local/align.nf

d22acbb

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Update subworkflows/local/align.nf

e0c9fd6

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Update LICENSE

5a2ac58

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Add fixes for PR

c5385fd

Fix license lint

315679f

Make prettier happy

654f2fa

Fix final linting

5253928

Merge branch 'update_modules' of https://github.com/luisas/multiplese…

ae302d6

…quencealign into update_modules

JoseEspinosa mentioned this pull request Sep 13, 2023

Update LICENSE #49

Closed

JoseEspinosa approved these changes Sep 13, 2023

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luisas merged commit fd8c671 into nf-core:dev Sep 13, 2023
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This was referenced Sep 14, 2023

NF-CORE MODULE: MAFFT #42

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NF-CORE MODULE - CLUSTALO #51

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NF-CORE-MODULE: FAMSA_ALIGN #29

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NF-CORE-MODULE: FAMSA_GUIDETREE #38

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Update modules to nf-core ( clustalo and famsa) #40

Update modules to nf-core ( clustalo and famsa) #40

luisas commented Aug 17, 2023

maxulysse Sep 8, 2023

luisas Sep 8, 2023

github-actions bot commented Sep 12, 2023 •

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❗ Test warnings:

✅ Tests passed:

Run details

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		seatoxin-ref,../test-dataset/setoxin-ref.fa,/home/luisasantus/Desktop/crg_cluster/projects/multiplesequencealign/test-dataset/setoxin.ref,/home/luisasantus/Desktop/crg_cluster/projects/multiplesequencealign/test-dataset/structures/setoxin-ref
		toxin-ref,../test-dataset/toxin-ref.fa,/home/luisasantus/Desktop/crg_cluster/projects/multiplesequencealign/test-dataset/toxin.ref,

Update modules to nf-core ( clustalo and famsa) #40

Update modules to nf-core ( clustalo and famsa) #40

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luisas commented Aug 17, 2023

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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

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