Locidex Integration #62

mattheww95 · 2024-04-10T18:55:40Z

Initial integration of locidex into mikrokondo

…idex

github-actions · 2024-04-10T18:59:41Z

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

Posted for pipeline commit a87bc3b

+| ✅ 161 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 0.1.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/mikrokondo/master/nextflow_schema.json
Found https://raw.githubusercontent.com/phac-nml/mikrokondo/main/nextflow_schema.json

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-mikrokondo_logo_light.png
files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_light.png
files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: docs/output.md
files_exist - File is ignored: docs/README.md
files_exist - File is ignored: docs/usage.md
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-mikrokondo_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_dark.png
files_unchanged - File does not exist: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mikrokondo/mikrokondo/.github/workflows/awstest.yml
multiqc_config - multiqc_config

✅ 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: 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/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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: 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-mikrokondo_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/WorkflowMikrokondo.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.platform= illumina
nextflow_config - Config default value correct: params.long_read_opt= nanopore
nextflow_config - Config default value correct: params.dehosting_idx= ./databases/PhiPacHum_m2.idx
nextflow_config - Config default value correct: params.mash_sketch= ./databases/GTDBSketch_20231003.msh
nextflow_config - Config default value correct: params.bakta_db= ./databases/db-light
nextflow_config - Config default value correct: params.kraken2_db= ./databases/k2_standard_20220607/
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= 2000.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.validate_params= true
nextflow_config - Config default value correct: params.tracedir= null/pipeline_info
nextflow_config - Config default value correct: params.stage_in_mode= symlink
nextflow_config - Config default value correct: params.validationS3PathCheck= true
nextflow_config - Config default value correct: params.skip_bakta= true
nextflow_config - Config default value correct: params.skip_ont_header_cleaning= true
nextflow_config - Config default value correct: params.fp_average_quality= 25
nextflow_config - Config default value correct: params.fp_cut_tail_mean_quality= 15
nextflow_config - Config default value correct: params.fp_cut_tail_window_size= 4
nextflow_config - Config default value correct: params.fp_complexity_threshold= 20
nextflow_config - Config default value correct: params.fp_qualified_phred= 15
nextflow_config - Config default value correct: params.fp_unqualified_percent_limit= 40
nextflow_config - Config default value correct: params.fp_polyg_min_len= 10
nextflow_config - Config default value correct: params.fp_polyx_min_len= 10
nextflow_config - Config default value correct: params.fp_illumina_length_min= 35
nextflow_config - Config default value correct: params.fp_illumina_length_max= 400
nextflow_config - Config default value correct: params.fp_single_end_length_min= 1000
nextflow_config - Config default value correct: params.lx_min_evalue= 0.0001
nextflow_config - Config default value correct: params.lx_min_dna_len= 1
nextflow_config - Config default value correct: params.lx_min_aa_len= 1
nextflow_config - Config default value correct: params.lx_max_dna_len= 10000000
nextflow_config - Config default value correct: params.lx_max_aa_len= 10000000
nextflow_config - Config default value correct: params.lx_min_dna_ident= 80.0
nextflow_config - Config default value correct: params.lx_min_aa_ident= 80.0
nextflow_config - Config default value correct: params.lx_min_dna_match_cov= 80.0
nextflow_config - Config default value correct: params.lx_min_aa_match_cov= 80.0
nextflow_config - Config default value correct: params.lx_max_target_seqs= 10.0
nextflow_config - Config default value correct: params.lx_extraction_mode= raw
nextflow_config - Config default value correct: params.lx_report_mode= normal
nextflow_config - Config default value correct: params.lx_report_prop= locus_name
nextflow_config - Config default value correct: params.lx_report_max_ambig= 0.0
nextflow_config - Config default value correct: params.lx_report_max_stop= 0.0
nextflow_config - Config default value correct: params.target_depth= 100
nextflow_config - Config default value correct: params.min_reads= 1000
nextflow_config - Config default value correct: params.ba_min_contig_length= 200
nextflow_config - Config default value correct: params.qt_min_contig_length= 1000
nextflow_config - Config default value correct: params.mh_min_kmer= 10
nextflow_config - Config default value correct: params.flye_read_type= hq
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (222 files)
schema_lint - Schema 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: doc.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.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
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13.1
Run at 2024-04-12 21:05:22

mattheww95 · 2024-04-10T19:52:18Z

Initial integration of locidex along, all tests passed. Only one test was added for locidex mainly, that it runs without throwing an error.

apetkau

Thanks so much for the awesome work @mattheww95 😄 . I have a few comments for you.

conf/modules.config

modules/local/locidex_extract.nf

modules/local/locidex_report.nf

modules/local/locidex_search.nf

modules/local/locidex_report.nf

subworkflows/local/locidex.nf

tests/pipelines/main.from_assemblies.nf.test

workflows/PostAssembly.nf

conf/modules.config

modules/local/locidex_extract.nf

modules/local/locidex_search.nf

nextflow_schema.json

subworkflows/local/locidex.nf

…rameters updated ext.containers to ext.parameters

apetkau

This is amazing @mattheww95 . Thanks so much for addressing all those issues 😄. I do have some more comments (sorry I didn't get to these until the second round of reviewing).

modules/local/locidex_report.nf

subworkflows/local/locidex.nf

modules/local/locidex_search.nf

nextflow_schema.json

Fixed the elvis expression, updated the schema and added a regex to validation strings in the locidex command.

subworkflows/local/locidex.nf

nextflow_schema.json

set the return value to null for an erroneous allele scheme specification. Additionally I updated the schema json regex for lx_report_prop to specify allowed characters.

mattheww95 added 8 commits March 22, 2024 10:08

waiting for containers

26b8413

waiting for containers

03fb6e1

waiting for containers

66dd20e

initially integrated locidex

9b59c0c

Merge branch 'dev' of https://github.com/phac-nml/mikrokondo into loc…

ac65b7a

…idex

updated report suffix

f02e471

Merge branch 'dev' of https://github.com/phac-nml/mikrokondo into loc…

148ebd5

…idex

updated tests

fc52e8c

mattheww95 added 2 commits April 10, 2024 14:30

updated config

68de4c1

updated config params

c0467b7

mattheww95 requested review from apetkau and emarinier April 10, 2024 19:52

apetkau requested changes Apr 10, 2024

View reviewed changes

emarinier requested changes Apr 11, 2024

View reviewed changes

mattheww95 added 3 commits April 11, 2024 10:34

updated locidex modules to gzip output files

be8cd5b

updated output tests

30cb619

added test allele profiles

e0e90a8

mattheww95 mentioned this pull request Apr 11, 2024

Rename ext.containers to ext.parameters #63

Closed

updated schema params for locidex

48bca05

mattheww95 requested review from emarinier and apetkau April 11, 2024 17:31

mattheww95 marked this pull request as ready for review April 11, 2024 17:31

mattheww95 and others added 2 commits April 11, 2024 12:42

updated ext.containers to ext.parameters

df497f8

Merge pull request #64 from phac-nml/63-rename-extcontainers-to-extpa…

e668c33

…rameters updated ext.containers to ext.parameters

mattheww95 linked an issue Apr 11, 2024 that may be closed by this pull request

Rename ext.containers to ext.parameters #63

Closed

mattheww95 added this to the Add an Allele Caller milestone Apr 11, 2024

apetkau requested changes Apr 11, 2024

View reviewed changes

updated pr comments

c8e0c8a

Fixed the elvis expression, updated the schema and added a regex to validation strings in the locidex command.

apetkau reviewed Apr 12, 2024

View reviewed changes

subworkflows/local/locidex.nf Outdated Show resolved Hide resolved

apetkau reviewed Apr 12, 2024

View reviewed changes

nextflow_schema.json Outdated Show resolved Hide resolved

mattheww95 added 2 commits April 12, 2024 15:56

updated pr comments

8aaba2b

set the return value to null for an erroneous allele scheme specification. Additionally I updated the schema json regex for lx_report_prop to specify allowed characters.

updated typos

a87bc3b

emarinier approved these changes Apr 12, 2024

View reviewed changes

apetkau approved these changes Apr 12, 2024

View reviewed changes

mattheww95 merged commit f3a27ca into dev Apr 12, 2024
4 checks passed

mattheww95 deleted the locidex branch April 12, 2024 21:17

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Locidex Integration #62

Locidex Integration #62

mattheww95 commented Apr 10, 2024

github-actions bot commented Apr 10, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mattheww95 commented Apr 10, 2024

apetkau left a comment

apetkau left a comment

Locidex Integration #62

Locidex Integration #62

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mattheww95 commented Apr 10, 2024

github-actions bot commented Apr 10, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mattheww95 commented Apr 10, 2024

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github-actions bot commented Apr 10, 2024 •

edited

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