Dev #78

apetkau · 2024-05-14T14:28:48Z

Release 0.2.0 PR of dev into main

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
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).

…idex

Co-authored-by: dpbastedo <45338596+dpbastedo@users.noreply.github.com>

updated documentation and parameters.

added locidex test data

…idex

…rameters updated ext.containers to ext.parameters

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

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.

Locidex Integration

Update/staramr

…ication-and-running-staramr-pipeline-fails 69 when skipping species classification and running staramr pipeline fails

Release/0.2.0

github-actions · 2024-05-14T14:30:10Z

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

Posted for pipeline commit 90ce217

+| ✅ 220 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 0.2.0
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
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 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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-mikrokondo_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowMikrokondo.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
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.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.ec_opid= 90.0
nextflow_config - Config default value correct: params.ec_opcov= 90.0
nextflow_config - Config default value correct: params.ec_hpid= 95.0
nextflow_config - Config default value correct: params.ec_hpcov= 50.0
nextflow_config - Config default value correct: params.ec_enable_verification= true
nextflow_config - Config default value correct: params.sr_full_cgmlst= 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
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
nextflow_config - Config default value correct: params.lx_report_max_stop= 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 (232 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.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
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - PUBLISH_FINAL_READS found in conf/modules.config and Nextflow scripts.
modules_config - PUBLISH_FINAL_ASSEMBLIES found in conf/modules.config and Nextflow scripts.
modules_config - LOCIDEX_EXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - LOCIDEX_SEARCH found in conf/modules.config and Nextflow scripts.
modules_config - LOCIDEX_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - REPORT found in conf/modules.config and Nextflow scripts.
modules_config - IDENTIFY_POINTDB found in conf/modules.config and Nextflow scripts.
modules_config - REPORT_AGGREGATE found in conf/modules.config and Nextflow scripts.
modules_config - BIN_KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_DATA found in conf/modules.config and Nextflow scripts.
modules_config - GZIP_FILES found in conf/modules.config and Nextflow scripts.
modules_config - CHECK_ONT found in conf/modules.config and Nextflow scripts.
modules_config - PARSE_MASH found in conf/modules.config and Nextflow scripts.
modules_config - PARSE_KRAKEN found in conf/modules.config and Nextflow scripts.
modules_config - READ_SCAN found in conf/modules.config and Nextflow scripts.
modules_config - PARSE_FASTP found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_STATS found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_SIZE found in conf/modules.config and Nextflow scripts.
modules_config - QUAST found in conf/modules.config and Nextflow scripts.
modules_config - CHECKM_LINEAGEWF found in conf/modules.config and Nextflow scripts.
modules_config - BANDAGE_IMAGE found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN found in conf/modules.config and Nextflow scripts.
modules_config - MASH_ESTIMATE found in conf/modules.config and Nextflow scripts.
modules_config - MLST found in conf/modules.config and Nextflow scripts.
modules_config - STARAMR found in conf/modules.config and Nextflow scripts.
modules_config - MOBSUITE_RECON found in conf/modules.config and Nextflow scripts.
modules_config - MASH_SKETCH found in conf/modules.config and Nextflow scripts.
modules_config - MASH_PASTE found in conf/modules.config and Nextflow scripts.
modules_config - MASH_SCREEN found in conf/modules.config and Nextflow scripts.
modules_config - REMOVE_CONTAMINANTS found in conf/modules.config and Nextflow scripts.
modules_config - FLYE_ASSEMBLE found in conf/modules.config and Nextflow scripts.
modules_config - SPADES_ASSEMBLE found in conf/modules.config and Nextflow scripts.
modules_config - UNICYCLER_ASSEMBLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_MAP found in conf/modules.config and Nextflow scripts.
modules_config - SAM_TO_BAM found in conf/modules.config and Nextflow scripts.
modules_config - RACON_POLISH found in conf/modules.config and Nextflow scripts.
modules_config - PILON_ITER found in conf/modules.config and Nextflow scripts.
modules_config - MEDAKA_POLISH found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_DB_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_ANNOTATE found in conf/modules.config and Nextflow scripts.
modules_config - ABRICATE found in conf/modules.config and Nextflow scripts.
modules_config - ECTYPER found in conf/modules.config and Nextflow scripts.
modules_config - KLEBORATE found in conf/modules.config and Nextflow scripts.
modules_config - SPATYPER found in conf/modules.config and Nextflow scripts.
modules_config - SISTR found in conf/modules.config and Nextflow scripts.
modules_config - LISSERO found in conf/modules.config and Nextflow scripts.
modules_config - SHIGEIFINDER found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-05-14 20:11:13

modules/local/locidex_search.nf

mattheww95

PR looks good, just reviewing the parameter changes to locidex.

If locidex receives a fasta that has been processed with extract it no longer needs to be annotated with pyrodigal as the sample has been blasted against the database to extract relevent hits. To verify that results generated in locidex match what is tested, this is the preferred route forward. However as databases will get larger in may be more cost effective pass in a genbank file or just annotate the fasta directly, however this relies on bakta working...

removed annotate from locidex search parameters

mattheww95 and others added 30 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

updated doc params, fixed Patrick's recommendations

9859ec8

updated changelog

d1e3b96

Update docs/usage/tool_params.md

859f6e6

Co-authored-by: dpbastedo <45338596+dpbastedo@users.noreply.github.com>

Update docs/usage/tool_params.md

9e9bf14

Co-authored-by: dpbastedo <45338596+dpbastedo@users.noreply.github.com>

Update docs/usage/usage.md

be70b6b

Co-authored-by: dpbastedo <45338596+dpbastedo@users.noreply.github.com>

Update docs/usage/usage.md

dd0b7c9

Co-authored-by: dpbastedo <45338596+dpbastedo@users.noreply.github.com>

Merge pull request #56 from phac-nml/update/docs

85efc07

updated documentation and parameters.

added locidex test data

94f206c

Merge pull request #61 from phac-nml/tests/locidex_data

f0f55a4

added locidex test data

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

148ebd5

…idex

updated tests

fc52e8c

updated config

68de4c1

updated config params

c0467b7

updated locidex modules to gzip output files

be8cd5b

updated output tests

30cb619

added test allele profiles

e0e90a8

updated schema params for locidex

48bca05

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

updated pr comments

c8e0c8a

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

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

Merge pull request #62 from phac-nml/locidex

f3a27ca

Locidex Integration

Renaming some metadata fields

b0d56a4

apetkau and others added 16 commits May 13, 2024 11:33

Updated staramr to version 0.10.0

90f1805

Added CGE Predicted Phenotype

fe9df6e

merged when skipping species classification

4fee3e9

Fixed up one test

aad32ff

Merge pull request #75 from phac-nml/update/staramr

041d269

Update/staramr

resolved pr comments

4ec2383

removed starAMR db version dump

e2a8603

fixed linting issues

005a9c8

Merge pull request #74 from phac-nml/69-when-skipping-species-classif…

f833152

…ication-and-running-staramr-pipeline-fails 69 when skipping species classification and running staramr pipeline fails

Merge branch 'dev' into release/0.2.0

7db53e2

Cleaned up changelog

1c12dd2

A few fixes for the nextflow schema

40dbc5d

Added additional pattern to nanopore_chemistry

e9e9d75

Added nf-core version

000395a

Added another changelog statement

f740bfc

Merge pull request #77 from phac-nml/release/0.2.0

c2eba04

Release/0.2.0

apetkau marked this pull request as ready for review May 14, 2024 15:16

apetkau requested a review from mattheww95 May 14, 2024 15:28

mattheww95 reviewed May 14, 2024

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mattheww95 reviewed May 14, 2024

View reviewed changes

mattheww95 and others added 8 commits May 14, 2024 11:04

updated changelog

2f2aeab

updated locidex search gzipping

1c196b9

updated removed log printing

8c3a6f5

updated locidex test data

aedd4c8

updated test information

3f8c810

removed changelog update

2931bb5

Merge pull request #79 from phac-nml/update/lx_search

90ce217

removed annotate from locidex search parameters

mattheww95 merged commit f1efb35 into main May 14, 2024
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Dev #78

Dev #78

apetkau commented May 14, 2024 •

edited

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github-actions bot commented May 14, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mattheww95 left a comment

Dev #78

Dev #78

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apetkau commented May 14, 2024 • edited Loading

PR checklist

github-actions bot commented May 14, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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apetkau commented May 14, 2024 •

edited

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github-actions bot commented May 14, 2024 •

edited

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