Add BAGEL2 functionality #60

LaurenceKuhl · 2023-07-24T12:44:57Z

PR checklist

github-actions · 2023-07-24T12:46:49Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 4930690

+| ✅ 154 tests passed       |+
#| ❔  16 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

files_unchanged - CODE_OF_CONDUCT.md does not match the template
files_unchanged - .github/CONTRIBUTING.md does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template
files_unchanged - lib/NfcoreTemplate.groovy does not match the template

❗ Test warnings:

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 preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

files_exist - File is ignored: c
files_exist - File is ignored: o
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files_exist - File is ignored: /
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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

✅ 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
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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
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files_exist - File found: .github/workflows/linting_comment.yml
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files_exist - File found: assets/email_template.html
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files_exist - File found: assets/nf-core-crisprseq_logo_light.png
files_exist - File found: conf/modules.config
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files_exist - File found: docs/images/nf-core-crisprseq_logo_light.png
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files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
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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
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files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowCrisprseq.groovy
files_exist - File found: modules.json
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files_exist - File not found check: Singularity
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files_exist - File not found check: conf/aws.config
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files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
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files_exist - File not found check: docs/images/nf-core-crisprseq_logo.png
files_exist - File not found check: .markdownlint.yml
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files_exist - File not found check: lib/Checks.groovy
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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: 2.1.0dev
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 - 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 - 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 - .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
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (164 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: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest_screening.yml
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: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.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 2.10
Run at 2023-11-07 12:24:15

mirpedrol

In general, it would be good if we try to add the modules to nf-core, it will be easier for reviewers when we release the next version. But I think it's ok for now, maybe open an issue to track this and have it in mind in the future.

CHANGELOG.md

workflows/crisprseq_screening.nf

assets/CEGv2.txt

assets/NEGv1.txt

modules/local/bagel2/graph.nf

nextflow_schema.json

workflows/crisprseq_screening.nf

modules/nf-core/mageck/count/main.nf

workflows/crisprseq_screening.nf

Co-authored-by: Júlia Mir Pedrol <[email protected]>

… bump fix merge

Co-authored-by: Júlia Mir Pedrol <[email protected]>

LaurenceKuhl · 2023-08-16T14:03:14Z

Hi @mirpedrol, i think i had a look over your comments, thanks a lot :)

mirpedrol

I left two last comments, after addressing those OK for me to merge!

workflows/crisprseq_screening.nf

modules/local/bagel2/graph.nf

Co-authored-by: Júlia Mir Pedrol <[email protected]>

docs/output/screening.md

docs/usage/screening.md

modules/local/mageck/graphrra.nf

mirpedrol · 2023-10-25T07:00:47Z

modules/local/mageck/graphrra.nf

+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """


A license is missing in this script

I don't understand why i need to give a license when it's a script i wrote myself? I think it's a bit unclear to me in which case a license is needed or not :D

modules/local/bagel2/graph.nf

workflows/crisprseq_screening.nf

mirpedrol · 2023-10-25T07:08:25Z

conf/test_screening.config

@@ -25,4 +25,5 @@ params {
    crisprcleanr      = "Brunello_Library"
    mle_design_matrix = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/design_matrix.txt"
    library           = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/brunello_target_sequence.txt"
+    //rra_contrasts     = ""


Should be commented out?

I'm waiting for my PR nf-core/test-datasets#1032 to be accepted to then add the param :)

Co-authored-by: Júlia Mir Pedrol <[email protected]>

… bump

LaurenceKuhl · 2023-11-07T11:29:45Z

@nf-core-bot lint

LaurenceKuhl · 2023-11-07T11:31:24Z

@nf-core-bot fix linting

… bump

mirpedrol · 2023-11-07T11:53:35Z

@nf-core-bot fix linting

LaurenceKuhl added 4 commits July 14, 2023 11:00

Extra files from mageck count

8f6af2d

fix bug in rra

13181f0

Add bagel fold change

b66f7e5

Merge remote-tracking branch 'source_repo/dev' into bump

4faa210

LaurenceKuhl added 6 commits July 27, 2023 16:17

Trying to add BAGEL_BF

ac2ca2c

Adding bagel2_bf

8a88803

working modules of bagel

0bebd94

All of the bagel modules and output graphs

a6d4090

Bagel2

6ef05ac

Add new features in changelog

7030145

mirpedrol changed the title ~~Bump~~ Add BAGEL2 functionality Aug 8, 2023

mirpedrol reviewed Aug 8, 2023

View reviewed changes

Fixed paired-end

5be5815

mirpedrol reviewed Aug 8, 2023

View reviewed changes

mirpedrol and others added 15 commits August 8, 2023 15:11

Merge branch 'dev' into bump

1d2dff0

Update CHANGELOG.md

2519663

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update CHANGELOG.md

65c0f6f

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update workflows/crisprseq_screening.nf

2be7f3b

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update workflows/crisprseq_screening.nf

ea07b75

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update workflows/crisprseq_screening.nf

9278293

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update workflows/crisprseq_screening.nf

4cc4bba

Co-authored-by: Júlia Mir Pedrol <[email protected]>

formatting

d0b21d9

Merge branch 'bump' of https://github.com/LaurenceKuhl/crisprseq into…

ce6c7ee

… bump fix merge

test

6c8993b

Update workflows/crisprseq_screening.nf

29dc2bd

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Add doc

f8210a4

fix meta id

e21fc25

Ran nf-core modules patch

63f328a

Add license

90eb287

mirpedrol approved these changes Aug 17, 2023

View reviewed changes

workflows/crisprseq_screening.nf Outdated Show resolved Hide resolved

modules/local/bagel2/graph.nf Show resolved Hide resolved

LaurenceKuhl and others added 3 commits August 23, 2023 09:02

Update workflows/crisprseq_screening.nf

0d7aeb4

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Add license

6b75dd9

Merge branch 'dev' into bump

1bf922d

mirpedrol added this to the 2.1.0 milestone Sep 19, 2023

LaurenceKuhl added 3 commits October 2, 2023 14:22

Remove symlink issue

f2576c4

Update module config

5d343af

Add graphs for mageck rra

31a1103

mirpedrol reviewed Oct 25, 2023

View reviewed changes

LaurenceKuhl and others added 8 commits October 25, 2023 09:10

Update docs/usage/screening.md

fef0481

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update workflows/crisprseq_screening.nf

77f2509

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Modifications suggested by Julia

acd150d

merge branch 'bump' of https://github.com/LaurenceKuhl/crisprseq into…

0fefa45

… bump

Take comments into account add license

718ceaa

Add contrast file in the test

2a756b8

remove condition

4a95736

rollback on the condition in the samplesheet

9d67bd0

nf-core-bot and others added 4 commits November 7, 2023 11:31

[automated] Fix linting with Prettier

00d0d16

ran prettier

0049dde

Merge branch 'bump' of https://github.com/LaurenceKuhl/crisprseq into…

fdc1c2c

… bump

nf-core modules patch on mageck mle

e073518

mirpedrol added 2 commits November 7, 2023 13:06

run black

d5c59ab

fix left-padding spaces

4930690

LaurenceKuhl merged commit 98c85db into nf-core:dev Nov 7, 2023
9 of 10 checks passed

mirpedrol mentioned this pull request Nov 17, 2023

Integrate Bagel2 #59

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Add BAGEL2 functionality #60

Add BAGEL2 functionality #60

LaurenceKuhl commented Jul 24, 2023

github-actions bot commented Jul 24, 2023 •

edited

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❌ Test failures:

❗ Test warnings:

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✅ Tests passed:

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mirpedrol left a comment

LaurenceKuhl commented Aug 16, 2023

mirpedrol left a comment

mirpedrol Oct 25, 2023

LaurenceKuhl Oct 25, 2023

mirpedrol Oct 25, 2023

LaurenceKuhl Oct 25, 2023

LaurenceKuhl commented Nov 7, 2023

LaurenceKuhl commented Nov 7, 2023

mirpedrol commented Nov 7, 2023

Add BAGEL2 functionality #60

Add BAGEL2 functionality #60

Conversation

LaurenceKuhl commented Jul 24, 2023

PR checklist

github-actions bot commented Jul 24, 2023 • edited Loading

nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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LaurenceKuhl commented Aug 16, 2023

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LaurenceKuhl commented Nov 7, 2023

LaurenceKuhl commented Nov 7, 2023

mirpedrol commented Nov 7, 2023

github-actions bot commented Jul 24, 2023 •

edited

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`nf-core lint` overall result: Failed ❌