Adding functional genomics #22

LaurenceKuhl · 2023-05-03T13:48:46Z

This runs 3-4 modules related to functional genomics

… mle results

github-actions · 2023-05-03T14:05:00Z

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

Posted for pipeline commit 4a1ebc9

+| ✅ 153 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.0'
pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered 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

❔ Tests ignored:

files_exist - File is ignored: c
files_exist - File is ignored: o
files_exist - File is ignored: n
files_exist - File is ignored: f
files_exist - File is ignored: /
files_exist - File is ignored: t
files_exist - File is ignored: e
files_exist - File is ignored: s
files_exist - File is ignored: t
files_exist - File is ignored: .
files_exist - File is ignored: c
files_exist - File is ignored: o
files_exist - File is ignored: n
files_exist - File is ignored: f
files_exist - File is ignored: i
files_exist - File is ignored: g
actions_ci - actions_ci

✅ 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-crisprseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-crisprseq_logo_light.png
files_exist - File found: docs/images/nf-core-crisprseq_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: 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/WorkflowCrisprseq.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-crisprseq_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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.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.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
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-crisprseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-crisprseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-crisprseq_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
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
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: 22.10.1, Config: 22.10.1
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (130 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
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 2.7.2
Run at 2023-05-25 07:24:13

mirpedrol

It already looks very good! 🥳
Most of my comments are regarding formatting.

As a reminder that came to my mind while reviewing, we will need to modify the GHA and profile.test to run tests with this workflow

conf/modules.config

lib/WorkflowMain.groovy

main.nf

nextflow_schema.json

workflows/crisprseq_screening.nf

nextflow_schema.json

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

mirpedrol

LGTM if tests pass :)

LaurenceKuhl added 6 commits February 23, 2023 11:23

Fastqc and first mageck module

8f3a4b0

Added mageck test and mageck count

6e9139f

First version of the screening subworkflow and working

848b2f2

Added a line in the modules.config so it's sample separated in mageck…

4efe4c3

… mle results

Functioning complete pipeline

4b9d825

Fully functionning pipeline

90b6ea6

LaurenceKuhl added 5 commits May 4, 2023 08:54

remove input param as mandatory

c4deab4

Removed the mandatory input param in the json schema

240895d

removed the check param for input

0c0c4f3

still trying to figure out this mandatory input

368f2e4

remove mandatory input

288579c

mirpedrol reviewed May 5, 2023

View reviewed changes

LaurenceKuhl and others added 17 commits May 15, 2023 11:15

Ran nf-core modules patch

bbbcec0

Update conf/modules.config

3e97cb4

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

Update main.nf

a7fa77d

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

Update workflows/crisprseq_screening.nf

3b7e205

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

Update workflows/crisprseq_screening.nf

989bc1b

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

put ch_input and fix linting spaces

1173cd5

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

db81db3

Fix nextflow schema

f503887

Try to fix the schema json

edace6c

Reput the comma and updated the description of the params

c923bc7

Remove the skip alignment param

f85974e

Ran prettier

ffc515e

fix indentation

98185ae

add CI for screening tests

523907a

rename crisprseq_edition to crisprseq_targeted

9d87e4b

nf-core modules patch command and modify the ci yml to add tests

7df393d

turned the library in to a channel

0893da1

skip linting check for test.config

b9ea007

mirpedrol approved these changes May 24, 2023

View reviewed changes

mirpedrol added 3 commits May 25, 2023 06:59

run prettier

cb63bdb

ignore actions_ci test

3c296a5

Merge branch 'screening' into master

4a1ebc9

LaurenceKuhl merged commit 0545af4 into nf-core:screening May 25, 2023

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Adding functional genomics #22

Adding functional genomics #22

LaurenceKuhl commented May 3, 2023

github-actions bot commented May 3, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mirpedrol left a comment

mirpedrol left a comment

Adding functional genomics #22

Adding functional genomics #22

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LaurenceKuhl commented May 3, 2023

github-actions bot commented May 3, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mirpedrol left a comment

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mirpedrol left a comment

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github-actions bot commented May 3, 2023 •

edited

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