nf-core/circdna update to v1.0.2 #46

DSchreyer · 2023-03-07T13:36:28Z

Nf-core/circdna Update to v.1.0.2

This pull requests contains:

bug fixes to current local modules
updates to nf-core modules
updates to local modules
Added new functionality to AmpliconArchitect branch
Updated to nf-core template 2.7.2
Fixed nextflow.config bugs
Updated README.md

PR checklist

[x ] This comment contains a description of changes (with reason).
[ x] If you've fixed a bug or added code that should be tested, add tests!
- If you've added a new tool - have you followed the pipeline conventions in the contribution docs
- If necessary, also make a PR on the nf-core/circdna branch on the nf-core/test-datasets repository.
[ x] Make sure your code lints (nf-core lint).
[x ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ x] Usage Documentation in docs/usage.md is updated.
[x ] Output Documentation in docs/output.md is updated.
[x ] CHANGELOG.md is updated.
[x ] README.md is updated (including new tool citations and authors/contributors).

…ocation

…move

github-actions · 2023-03-07T14:11:04Z

Python linting (`black`) is failing

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To fix this CI test, please run:

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Fix formatting errors in your pipeline: black .

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github-actions · 2023-03-07T14:31:14Z

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

Posted for pipeline commit 238312e

+| ✅ 154 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.0.2'
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

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_unchanged - File ignored due to lint config: assets/email_template.html

✅ 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-circdna_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-circdna_logo_light.png
files_exist - File found: docs/images/nf-core-circdna_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: 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/WorkflowCircdna.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-circdna_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.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-circdna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circdna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circdna_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_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: 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 (152 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 2023-03-09 10:13:38

…assifier and ampliconsimilarity stub

sguizard

Very clean code, nicely commented.
Some minor corrections needed, otherwise LGTM for me.

CHANGELOG.md

docs/usage.md

modules/local/getcircularreads.nf

subworkflows/local/bam_markduplicates_picard/meta.yml

Co-authored-by: Sébastien Guizard <[email protected]>

sguizard

OK for me.

sguizard · 2023-03-09T07:42:35Z

subworkflows/local/bam_markduplicates_picard/meta.yml

+    type: file
+    description: Reference genome fasta index file
+    pattern: "*.{fai}"


Suggested change

type: file

description: Reference genome fasta index file

pattern: "*.{fai}"

type: file

description: Reference genome fasta index file

pattern: "*.{fai}"

sguizard · 2023-03-09T07:43:01Z

subworkflows/local/bam_markduplicates_picard/meta.yml

+    type: file
+    description: BAM file with duplicate reads marked/removed
+    pattern: "*.{bam}"


Suggested change

type: file

description: BAM file with duplicate reads marked/removed

pattern: "*.{bam}"

type: file

description: BAM file with duplicate reads marked/removed

pattern: "*.{bam}"

yuukiiwa

Thanks, @DSchreyer! Looks good to me! Just a very small comment for CHANGELOG.md

yuukiiwa · 2023-03-09T08:56:19Z

CHANGELOG.md

+
+### `Added`
+
+- AmpliconClassifier MakeInput and MakeResultsTable process


It will be great if softwares/functions are indicated as code for clarity:

AmpliconClassifier MakeInput and MakeResultsTable process

DSchreyer and others added 30 commits March 24, 2022 14:43

Reset changes to nf-core 2.3.2 merge

bfdee09

Template update for nf-core/tools version 2.4

3a3a23e

Added channel version mix for each software

3090938

Removed amplified intervals copy

1b75adf

added container image

4e15c63

Minor line fixes

44805c3

Updated AC and AS

296b597

added ignoreUnmated for samblaster; changed markduplicates bai file l…

d8c33a0

…ocation

Added save parameters

660ed52

Added new parameters to save intermediate files

9d63458

Changed formatting; Added new parameters for intermediate file saving

121796d

Changed formatting

16ba748

Removed prefix

a9c8fc2

nf-core lint fix

d168bf0

Added Zenodo ID

f297574

Linting

c27c6b0

Prettier

16978e7

Added if statement to remove module warning

04194f2

Template update for nf-core/tools version 2.5

60762e0

Updated modules

52e8bad

Update to nf-core template 2.5

a27e20e

Black

93380a9

Template update for nf-core/tools version 2.5.1

c74061b

Template update for nf-core/tools version 2.6

2372b13

Added if clause to check wether ampliconclassifier files exist; Then …

d749acc

…move

Added cnvkit cnn file to essential inputs

16bc26a

update

fcb799f

Template update for nf-core/tools version 2.7.1

5bcaa63

Template update for nf-core/tools version 2.7.2

d4eaa0f

Updated

795fd12

modified samtools local modules

5a1fc5f

Prettier

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DSchreyer added 7 commits March 7, 2023 14:33

black

ffe2bbb

Added input_format parameter check, mentioned in the issue: #47

49a3f18

BWA Index pattern

bbf5778

Updated nextflow version

fd351cf

Added stub to BWA-MEM -> Moved it to local module; Updated ampliconcl…

8f61b31

…assifier and ampliconsimilarity stub

Updated bwa-mem module path to local

c58bcca

Samtools filter only printed header -> now includes the full file

de56ea3

sguizard requested changes Mar 8, 2023

View reviewed changes

DSchreyer and others added 8 commits March 8, 2023 14:14

Update CHANGELOG.md

eec00c3

Co-authored-by: Sébastien Guizard <[email protected]>

Update docs/usage.md

c567694

Co-authored-by: Sébastien Guizard <[email protected]>

Update docs/usage.md

2f09b7d

Co-authored-by: Sébastien Guizard <[email protected]>

Update modules/local/getcircularreads.nf

f169004

Co-authored-by: Sébastien Guizard <[email protected]>

Update docs/usage.md

a80b5bf

Co-authored-by: Sébastien Guizard <[email protected]>

Added bam output and fai input information

ec11484

Prettier

fcdfc2a

Added metrics output meta

4afab78

DSchreyer requested a review from sguizard March 8, 2023 14:25

sguizard approved these changes Mar 9, 2023

View reviewed changes

jfy133 assigned yuukiiwa Mar 9, 2023

yuukiiwa self-requested a review March 9, 2023 08:08

yuukiiwa approved these changes Mar 9, 2023

View reviewed changes

DSchreyer added 3 commits March 9, 2023 10:09

Added cnvkit and AmpliconClassifier citation

1bb5c21

Ampliconclassifier functions are more clear now!

0fefc80

Syntax

238312e

DSchreyer merged commit cce8473 into master Mar 9, 2023

jfy133 assigned sguizard Mar 9, 2023


		### `Added`

		- AmpliconClassifier MakeInput and MakeResultsTable process

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nf-core/circdna update to v1.0.2 #46

nf-core/circdna update to v1.0.2 #46

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DSchreyer commented Mar 7, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Nf-core/circdna Update to v.1.0.2

PR checklist

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github-actions bot commented Mar 7, 2023

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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DSchreyer commented Mar 7, 2023 •

edited

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Python linting (`black`) is failing

github-actions bot commented Mar 7, 2023 •

edited

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

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