Dsl2 sex determination #1035

jbv2 · 2023-12-08T10:48:49Z

PR checklist

This comment contains a description of changes (with reason).
- If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
- If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint .).
Ensure the test suite passes (nextflow run . -profile test,docker).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

github-actions · 2023-12-08T11:01:25Z

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

Posted for pipeline commit 624ba69

+| ✅ 247 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  22 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 main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
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 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 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 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.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_humanbam.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test_humanbam.config: Give any required params for the test so that command line flags are not needed
schema_description - No description provided in schema for parameter: skip_qualimap
schema_description - No description provided in schema for parameter: skip_damagecalculation

❔ Tests ignored:

nextflow_config - Config default ignored: params.contamination_estimation_angsd_hapmap

✅ 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: 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-eager_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-eager_logo_light.png
files_exist - File found: docs/images/nf-core-eager_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: 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: 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: pipeline_template.yml
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-eager_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: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowEager.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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: 3.0.0dev
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.sequencing_qc_tool= fastqc
nextflow_config - Config default value correct: params.preprocessing_tool= fastp
nextflow_config - Config default value correct: params.preprocessing_minlength= 25
nextflow_config - Config default value correct: params.preprocessing_trim5p= 0
nextflow_config - Config default value correct: params.preprocessing_trim3p= 0
nextflow_config - Config default value correct: params.preprocessing_fastp_complexityfilter_threshold= 10
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_trimbasequalitymin= 20
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_adapteroverlap= 1
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_qualitymax= 41
nextflow_config - Config default value correct: params.fastq_shard_size= 1000000
nextflow_config - Config default value correct: params.mapping_tool= bwaaln
nextflow_config - Config default value correct: params.mapping_bwaaln_n= 0.01
nextflow_config - Config default value correct: params.mapping_bwaaln_k= 2
nextflow_config - Config default value correct: params.mapping_bwaaln_l= 1024
nextflow_config - Config default value correct: params.mapping_bwaaln_o= 2
nextflow_config - Config default value correct: params.mapping_bwamem_k= 19
nextflow_config - Config default value correct: params.mapping_bwamem_r= 1.5
nextflow_config - Config default value correct: params.mapping_bowtie2_alignmode= local
nextflow_config - Config default value correct: params.mapping_bowtie2_sensitivity= sensitive
nextflow_config - Config default value correct: params.mapping_bowtie2_n= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_l= 20
nextflow_config - Config default value correct: params.mapping_bowtie2_trim5= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_trim3= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_maxins= 500
nextflow_config - Config default value correct: params.bamfiltering_minreadlength= 0
nextflow_config - Config default value correct: params.bamfiltering_mappingquality= 0
nextflow_config - Config default value correct: params.bamfilter_genomicbamfilterflag= 4
nextflow_config - Config default value correct: params.metagenomicscreening_input= unmapped
nextflow_config - Config default value correct: params.metagenomics_complexity_tool= bbduk
nextflow_config - Config default value correct: params.metagenomics_complexity_entropy= 0.3
nextflow_config - Config default value correct: params.metagenomics_prinseq_mode= entropy
nextflow_config - Config default value correct: params.metagenomics_prinseq_dustscore= 0.5
nextflow_config - Config default value correct: params.deduplication_tool= markduplicates
nextflow_config - Config default value correct: params.damage_manipulation_rescale_seqlength= 12
nextflow_config - Config default value correct: params.damage_manipulation_rescale_length_5p= 0
nextflow_config - Config default value correct: params.damage_manipulation_rescale_length_3p= 0
nextflow_config - Config default value correct: params.damage_manipulation_pmdtools_threshold= 3
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_none_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_none_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_half_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_half_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_none_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_none_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_half_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_half_udg_right= 0
nextflow_config - Config default value correct: params.genotyping_reference_ploidy= 2
nextflow_config - Config default value correct: params.genotyping_pileupcaller_min_base_quality= 30
nextflow_config - Config default value correct: params.genotyping_pileupcaller_min_map_quality= 30
nextflow_config - Config default value correct: params.genotyping_pileupcaller_method= randomHaploid
nextflow_config - Config default value correct: params.genotyping_pileupcaller_transitions_mode= AllSites
nextflow_config - Config default value correct: params.genotyping_gatk_call_conf= 30
nextflow_config - Config default value correct: params.genotyping_gatk_ug_downsample= 250
nextflow_config - Config default value correct: params.genotyping_gatk_ug_out_mode= EMIT_VARIANTS_ONLY
nextflow_config - Config default value correct: params.genotyping_gatk_ug_genotype_mode= SNP
nextflow_config - Config default value correct: params.genotyping_gatk_ug_defaultbasequalities= -1
nextflow_config - Config default value correct: params.genotyping_gatk_hc_out_mode= EMIT_VARIANTS_ONLY
nextflow_config - Config default value correct: params.genotyping_gatk_hc_emitrefconf= GVCF
nextflow_config - Config default value correct: params.genotyping_freebayes_min_alternate_count= 1
nextflow_config - Config default value correct: params.genotyping_freebayes_skip_coverage= 0
nextflow_config - Config default value correct: params.mitochondrion_header= MT
nextflow_config - Config default value correct: params.mapstats_preseq_mode= c_curve
nextflow_config - Config default value correct: params.mapstats_preseq_stepsize= 1000
nextflow_config - Config default value correct: params.mapstats_preseq_terms= 100
nextflow_config - Config default value correct: params.mapstats_preseq_maxextrap= 10000000000
nextflow_config - Config default value correct: params.mapstats_preseq_bootstrap= 100
nextflow_config - Config default value correct: params.mapstats_preseq_cval= 0.95
nextflow_config - Config default value correct: params.damagecalculation_tool= damageprofiler
nextflow_config - Config default value correct: params.damagecalculation_yaxis= 0.3
nextflow_config - Config default value correct: params.damagecalculation_xaxis= 25
nextflow_config - Config default value correct: params.damagecalculation_damageprofiler_length= 100
nextflow_config - Config default value correct: params.damagecalculation_mapdamage_downsample= 0
nextflow_config - Config default value correct: params.host_removal_mode= remove
nextflow_config - Config default value correct: params.contamination_estimation_angsd_chrom_name= X
nextflow_config - Config default value correct: params.contamination_estimation_angsd_range_from= 5000000
nextflow_config - Config default value correct: params.contamination_estimation_angsd_range_to= 154900000
nextflow_config - Config default value correct: params.contamination_estimation_angsd_mapq= 30
nextflow_config - Config default value correct: params.contamination_estimation_angsd_minq= 30
nextflow_config - Config default value correct: params.run_sexdeterrmine= false
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-eager_logo_light.png matches the template
files_unchanged - docs/images/nf-core-eager_logo_light.png matches the template
files_unchanged - docs/images/nf-core-eager_logo_dark.png matches the template
files_unchanged - docs/README.md 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 (292 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: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: 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' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
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 2.13.1
Run at 2024-03-20 10:40:14

TCLamnidis

The bedfile for sexdeterrmine should be read in via the REFERENCE_INDEXING SWF (see dev docs ).
Rename SAMTOOLS_DEPTH module to have a unique name (see code conventions )
ext.args for sexdeterrmine samtools depth
PublishDir name needs to match output.md.
Name of subworkflow(SWF) and its .nf file must match, AND be an imperative verb (i.e. DETERMINE_SEX), to keep in line with all other SWF (MAP, DEDUPLICATE, etc)
remove unnecessary channel ch_sexdeterrmine_samplelist
No local paths in test config files.

CITATIONS.md

conf/modules.config

conf/test_humanbam.config

docs/output.md

workflows/eager.nf

subworkflows/local/sex_determination.nf

conf/modules.config

docs/output.md

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

TCLamnidis

Couple of minor changes. Otherwise looks good! Good job!

conf/modules.config

.github/workflows/ci.yml

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

TCLamnidis

nf-core linting re-installed the dumpsoftwareversions module. Please remove it.

You need to delete the module files, and remove the module from modules.json. Additionally, it seems some nf-core subworkflows were removed from the modules.json. Try removing the entire subworkflow block rerunning linting to hopefully index them all.

TCLamnidis

dump software versions module is still there

nextflow.config

jbv2 added 8 commits October 6, 2023 12:02

adding base version

ce47f48

first draft of sex determination subworkflow

4dd74a3

missing adding parameters

14c1325

adding module configs

bedc01f

linting

4b12727

Adding sex determine subworfflow

7073bfe

Merge branch 'dev' into dsl2-sex_determination

f530965

rerunning prettier after merge

25c465e

TCLamnidis marked this pull request as draft December 8, 2023 10:56

fixing linting

24d0a88

jbv2 linked an issue Dec 8, 2023 that may be closed by this pull request

new subworkflow: DSL2 sex determination #1028

Closed

jbv2 self-assigned this Dec 8, 2023

jbv2 requested a review from a team December 8, 2023 11:19

jbv2 marked this pull request as ready for review January 12, 2024 09:29

TCLamnidis requested changes Jan 12, 2024

View reviewed changes

jbv2 and others added 14 commits January 26, 2024 10:05

Apply suggestions from code review

1c2cb37

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

adding parameters for samtools depth

b805c83

Header option

c9d4788

importing properly samtools module

4d1f765

trying to add bed from reference file

b36bc45

adding bed to reference index

839b81c

breaking inputs inside the module with the reference outputs

3dda4e1

linting changes

09e800f

Merge branch 'dev' into dsl2-sex_determination

38c1592

prettier

79f097e

linting

b35a487

removing tab

e78b791

fixing passing ids, bams as list

e1e8853

linting

cd3e744

jbv2 and others added 8 commits March 18, 2024 09:24

Apply suggestions from code review

7d908e0

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

Apply suggestions from code review

7f6b3cf

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

aligning comments

3aa9482

consistent naming of sexdeterrmine

f394152

Removing commented lines code

ef5fd44

Adding manual tests

c9fb55e

Adding sexdeterrmine to CI test

bc53f26

Matching current dev nf-core template

ade2cdb

jbv2 requested a review from a team March 18, 2024 10:47

TCLamnidis approved these changes Mar 18, 2024

View reviewed changes

conf/modules.config Outdated Show resolved Hide resolved

.github/workflows/ci.yml Outdated Show resolved Hide resolved

jbv2 and others added 4 commits March 18, 2024 12:50

Apply suggestions from code review

8a01c0c

Co-authored-by: Thiseas C. Lamnidis <[email protected]>

prettier

384bc90

Merge branch 'dev' into dsl2-sex_determination

47838c7

including "addNewMetaFromAttributes"

cabc09e

TCLamnidis requested changes Mar 20, 2024

View reviewed changes

jbv2 added 4 commits March 20, 2024 10:15

removing subworflows

ddb4d78

lint

6ebc965

lint

40c6237

fix linting

d03589b

jbv2 requested review from TCLamnidis and a team March 20, 2024 10:03

TCLamnidis reviewed Mar 20, 2024

View reviewed changes

TCLamnidis added 2 commits March 20, 2024 11:20

Merge branch 'dev' into dsl2-sex_determination

9f7f8a1

remove dumpsoftwareversions. linting

f66e0fd

TCLamnidis approved these changes Mar 20, 2024

View reviewed changes

nextflow.config Outdated Show resolved Hide resolved

Update nextflow.config

624ba69

TCLamnidis merged commit cb178b6 into dev Mar 20, 2024
18 checks passed

TCLamnidis deleted the dsl2-sex_determination branch March 20, 2024 11:20

jbv2 added this to the 3.0 Augsburg milestone Mar 20, 2024

scarlhoff mentioned this pull request Jul 5, 2024

DSL2: pop-gen #924

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Dsl2 sex determination #1035

Dsl2 sex determination #1035

jbv2 commented Dec 8, 2023 •

edited by TCLamnidis

Loading

github-actions bot commented Dec 8, 2023 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

TCLamnidis left a comment •

edited by jbv2

Loading

TCLamnidis left a comment

TCLamnidis left a comment

TCLamnidis left a comment

Dsl2 sex determination #1035

Dsl2 sex determination #1035

Conversation

jbv2 commented Dec 8, 2023 • edited by TCLamnidis Loading

PR checklist

github-actions bot commented Dec 8, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

TCLamnidis left a comment • edited by jbv2 Loading

Choose a reason for hiding this comment

TCLamnidis left a comment

Choose a reason for hiding this comment

TCLamnidis left a comment

Choose a reason for hiding this comment

TCLamnidis left a comment

Choose a reason for hiding this comment

jbv2 commented Dec 8, 2023 •

edited by TCLamnidis

Loading

github-actions bot commented Dec 8, 2023 •

edited

Loading

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

TCLamnidis left a comment •

edited by jbv2

Loading