Release v1.1.0 #377

ramprasadn · 2023-07-17T14:28:43Z

PR checklist

This PR contains all the changes for release v1.1.0.

added check for case id

Gatkcnvcaller

Update schema, output.md, and remove unused parameters

update eklipse

Release prep v1.1.0

github-actions · 2023-07-17T14:30:56Z

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

Posted for pipeline commit 572bee2

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.0
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ 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-raredisease_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-raredisease_logo_light.png
files_exist - File found: docs/images/nf-core-raredisease_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/WorkflowRaredisease.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-raredisease_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.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
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/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-raredisease_logo_light.png matches the template
files_unchanged - docs/images/nf-core-raredisease_logo_light.png matches the template
files_unchanged - docs/images/nf-core-raredisease_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
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 (313 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: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 2023-07-21 09:22:24

maxulysse · 2023-07-18T09:46:38Z

CHANGELOG.md

@@ -3,7 +3,25 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

-## v1.0.0 - [2023-06-01]
+## v1.1.0 - Abu [xxxx-xx-xx]


Reminder to update date

conf/public_aws_ecr.config

nextflow.config

maxulysse

LGTM

ramprasadn · 2023-07-20T12:49:49Z

Thanks, @maxulysse!

sguizard

LGTM

JoseEspinosa

Nice job only some small suggestions! 🚀

CHANGELOG.md

JoseEspinosa · 2023-07-20T16:21:14Z

docs/output.md

@@ -296,7 +306,13 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support.

 #### vcfanno

-[vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder by default, and is passed to vep for further annotation.
+[vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder by default, and is passed to CADD and/or VEP for further annotation.


Suggested change

[vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder by default, and is passed to CADD and/or VEP for further annotation.

[vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple configuration file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder by default, and is passed to CADD and/or VEP for further annotation.

docs/output.md

lib/WorkflowRaredisease.groovy

JoseEspinosa · 2023-07-20T16:48:51Z

subworkflows/local/alignment/align_bwamem2.nf


        SAMTOOLS_INDEX_ALIGN ( BWAMEM2_MEM.out.bam )

        // Get stats for each demultiplexed read pair.
        bam_sorted_indexed = BWAMEM2_MEM.out.bam.join(SAMTOOLS_INDEX_ALIGN.out.bai, failOnMismatch:true, failOnDuplicate:true)
-        SAMTOOLS_STATS ( bam_sorted_indexed, [] )
+        SAMTOOLS_STATS ( bam_sorted_indexed, [[],[]] )


Suggested change

SAMTOOLS_STATS ( bam_sorted_indexed, [[],[]] )

SAMTOOLS_STATS ( bam_sorted_indexed, [[:],[]] )

JoseEspinosa · 2023-07-20T16:52:04Z

subworkflows/local/annotate_snvs.nf

+        CHROMOGRAPH_SITES([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_SITES.out.bed)
+        CHROMOGRAPH_REGIONS([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_REGIONS.out.bed, [[],[]])


I like to pass the empty map as [:] but up to you really 😉

Suggested change

CHROMOGRAPH_SITES([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_SITES.out.bed)

CHROMOGRAPH_REGIONS([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_REGIONS.out.bed, [[],[]])

CHROMOGRAPH_SITES([[:],[]], [[:],[]], [[:],[]], [[:],[]], [[:],[]], [[:],[]], UPD_SITES.out.bed)

CHROMOGRAPH_REGIONS([[:],[]], [[:],[]], [[:],[]], [[:],[]], [[:],[]], UPD_REGIONS.out.bed, [[:],[]])

JoseEspinosa · 2023-07-20T16:56:38Z

subworkflows/local/qc_bam.nf


        QUALIMAP_BAMQC (ch_bam, [])

-        TIDDIT_COV (ch_bam, []) // 2nd pos. arg is req. only for cram input
+        TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input


Suggested change

TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input

TIDDIT_COV (ch_bam, [[:],[]]) // 2nd pos. arg is req. only for cram input

JoseEspinosa · 2023-07-20T16:57:10Z

subworkflows/local/variant_calling/call_snv_deepvariant.nf

                        return [meta, bam, bai, []]
            }
            .set { ch_deepvar_in }

-        DEEPVARIANT ( ch_deepvar_in, ch_fasta, ch_fai, [] )
+        DEEPVARIANT ( ch_deepvar_in, ch_genome_fasta, ch_genome_fai, [[],[]] )


Suggested change

DEEPVARIANT ( ch_deepvar_in, ch_genome_fasta, ch_genome_fai, [[],[]] )

DEEPVARIANT ( ch_deepvar_in, ch_genome_fasta, ch_genome_fai, [[:],[]] )

workflows/raredisease.nf

JoseEspinosa

Awesome @ramprasadn 🚀

ramprasadn · 2023-07-21T13:56:24Z

Thanks @JoseEspinosa and @sguizard 🙏🏻

ryanjameskennedy and others added 30 commits November 17, 2022 16:23

Add Gatk4 GermlineCNVCaller module

e9cfd84

Merge branch 'dev' into add-gatk4-germlinecnvcaller

fe10e4e

GATK nightly bug fix

120a674

Merge dev changes into add-gatk4-germlinecnvcaller

edca36c

add cadd snv

4528288

add cadd subworkflow

e1fbab6

add bcftools annotate

d6cdfd4

update cadd subworkflow

364a25d

update annotate options

ce26305

update config

3357035

add to mt subworkflow

cf00edb

update when

988e3ea

add cadd nf-core

886c3b2

Merge branch 'dev' of github.com:nf-core/raredisease into cadd_indels

0ca6656

fix editorlint err

df3986d

update usage docs

92cabc7

update output

0df747c

update readme and output

4ea822e

Merge branch 'nf-core:dev' into add-gatk4-germlinecnvcaller

d8c7be8

Install nf-core modules

58d65ba

Update and add configs

02eaa84

Update and add subworkflows

349fc83

Update workflow

85b6825

Install & update modules

d1a8b8e

Fix formatting and structure

a5d6de2

Fix linting error

5be1daa

Update test_one_sample.config

3e20057

Add gatk params to rd main.nf

d18d4cd

Add meta to blacklist bed

6083b1b

Change germlinecnvcaller input channel

d0e8820

ramprasadn and others added 14 commits July 7, 2023 13:33

Merge branch 'dev' of github.com:nf-core/raredisease into gatkcnvcaller

2f83bbb

Merge pull request #357 from ClinicalGenomicsGBG/check_case_id

38e01e0

added check for case id

Merge branch 'dev' into gatkcnvcaller

007c5ee

Merge pull request #362 from genomic-medicine-sweden/gatkcnvcaller

06a9317

Gatkcnvcaller

update schema

2e97620

Merge branch 'dev' of github.com:nf-core/raredisease into fixes

59ab2e1

order

f14a62a

update module

f6f92da

Merge pull request #373 from genomic-medicine-sweden/fixes

a983256

Update schema, output.md, and remove unused parameters

Merge branch 'dev' into eklipse_update

0e2ca49

Merge pull request #374 from genomic-medicine-sweden/eklipse_update

3f09ab9

update eklipse

address warnings

8e9eb7b

bump version

253928f

Merge pull request #376 from genomic-medicine-sweden/release_prep

3d42ae9

Release prep v1.1.0

ramprasadn marked this pull request as ready for review July 18, 2023 07:52

maxulysse reviewed Jul 18, 2023

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remove ecr

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maxulysse approved these changes Jul 20, 2023

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sguizard approved these changes Jul 20, 2023

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JoseEspinosa requested changes Jul 20, 2023

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review suggestions

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JoseEspinosa approved these changes Jul 21, 2023

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update date

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ramprasadn merged commit 1a66422 into master Jul 21, 2023
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Release v1.1.0 #377

Release v1.1.0 #377

ramprasadn commented Jul 17, 2023 •

edited

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github-actions bot commented Jul 17, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse Jul 18, 2023

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ramprasadn commented Jul 20, 2023

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ramprasadn commented Jul 21, 2023

	SAMTOOLS_STATS ( bam_sorted_indexed, [[],[]] )
	SAMTOOLS_STATS ( bam_sorted_indexed, [[:],[]] )

		CHROMOGRAPH_SITES([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_SITES.out.bed)
		CHROMOGRAPH_REGIONS([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_REGIONS.out.bed, [[],[]])

	TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input
	TIDDIT_COV (ch_bam, [[:],[]]) // 2nd pos. arg is req. only for cram input

	DEEPVARIANT ( ch_deepvar_in, ch_genome_fasta, ch_genome_fai, [[],[]] )
	DEEPVARIANT ( ch_deepvar_in, ch_genome_fasta, ch_genome_fai, [[:],[]] )

Release v1.1.0 #377

Release v1.1.0 #377

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ramprasadn commented Jul 17, 2023 • edited Loading

PR checklist

github-actions bot commented Jul 17, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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ramprasadn commented Jul 21, 2023

ramprasadn commented Jul 17, 2023 •

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