Important! Template update for nf-core/tools v3.0.2 #421

nf-core-bot · 2024-10-11T12:34:17Z

Version 3.0.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.0.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.0.2 release page.

github-actions · 2024-10-23T11:10:19Z

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

Posted for pipeline commit b4e74bb

+| ✅ 344 tests passed       |+
#| ❔   1 tests were ignored |#

❔ Tests ignored:

actions_ci - actions_ci

✅ 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-funcscan_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-funcscan_logo_light.png
files_exist - File found: docs/images/nf-core-funcscan_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: conf/igenomes_ignored.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 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-funcscan_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/WorkflowFuncscan.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 - Found nf-schema plugin
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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: 2.1.0dev
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.taxa_classification_tool= mmseqs2
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_db_id= Kalamari
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_searchtype= 2
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_lcaranks= kingdom,phylum,class,order,family,genus,species
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_taxlineage= 1
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_sensitivity= 5.0
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_orffilters= 2.0
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_lcamode= 3
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_votemode= 1
nextflow_config - Config default value correct: params.annotation_tool= pyrodigal
nextflow_config - Config default value correct: params.annotation_bakta_db_downloadtype= full
nextflow_config - Config default value correct: params.annotation_bakta_mincontiglen= 1
nextflow_config - Config default value correct: params.annotation_bakta_translationtable= 11
nextflow_config - Config default value correct: params.annotation_bakta_gram= ?
nextflow_config - Config default value correct: params.annotation_prokka_kingdom= Bacteria
nextflow_config - Config default value correct: params.annotation_prokka_gcode= 11
nextflow_config - Config default value correct: params.annotation_prokka_mincontiglen= 1
nextflow_config - Config default value correct: params.annotation_prokka_evalue= 1e-06
nextflow_config - Config default value correct: params.annotation_prokka_coverage= 80
nextflow_config - Config default value correct: params.annotation_prokka_compliant= true
nextflow_config - Config default value correct: params.annotation_prodigal_transtable= 11
nextflow_config - Config default value correct: params.annotation_pyrodigal_transtable= 11
nextflow_config - Config default value correct: params.amp_ampir_model= precursor
nextflow_config - Config default value correct: params.amp_ampir_minlength= 10
nextflow_config - Config default value correct: params.amp_ampcombi_db_id= DRAMP
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_cutoff= 0.6
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_aalength= 120
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_dbevalue= 5.0
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_hmmevalue= 0.06
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_windowstopcodon= 60
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_windowtransport= 11
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_ampir= .ampir.tsv
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_amplify= .amplify.tsv
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_macrel= .macrel.prediction
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_hmmsearch= .hmmer_hmmsearch.txt
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_covmode= 0.0
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_sensitivity= 4.0
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_minmembers= 0
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_mode= 1.0
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_coverage= 0.8
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_seqid= 0.4
nextflow_config - Config default value correct: params.arg_amrfinderplus_identmin= -1.0
nextflow_config - Config default value correct: params.arg_amrfinderplus_coveragemin= 0.5
nextflow_config - Config default value correct: params.arg_amrfinderplus_translationtable= 11
nextflow_config - Config default value correct: params.arg_deeparg_db_version= 2
nextflow_config - Config default value correct: params.arg_deeparg_model= LS
nextflow_config - Config default value correct: params.arg_deeparg_minprob= 0.8
nextflow_config - Config default value correct: params.arg_deeparg_alignmentevalue= 1e-10
nextflow_config - Config default value correct: params.arg_deeparg_alignmentidentity= 50
nextflow_config - Config default value correct: params.arg_deeparg_alignmentoverlap= 0.8
nextflow_config - Config default value correct: params.arg_deeparg_numalignmentsperentry= 1000
nextflow_config - Config default value correct: params.arg_fargene_hmmmodel= class_a,class_b_1_2,class_b_3,class_c,class_d_1,class_d_2,qnr,tet_efflux,tet_rpg,tet_enzyme
nextflow_config - Config default value correct: params.arg_fargene_minorflength= 90
nextflow_config - Config default value correct: params.arg_fargene_translationformat= pearson
nextflow_config - Config default value correct: params.arg_rgi_alignmenttool= BLAST
nextflow_config - Config default value correct: params.arg_rgi_data= NA
nextflow_config - Config default value correct: params.arg_rgi_split_prodigal_jobs= true
nextflow_config - Config default value correct: params.arg_abricate_db_id= ncbi
nextflow_config - Config default value correct: params.arg_abricate_minid= 80
nextflow_config - Config default value correct: params.arg_abricate_mincov= 80
nextflow_config - Config default value correct: params.arg_hamronization_summarizeformat= tsv
nextflow_config - Config default value correct: params.bgc_mincontiglength= 3000
nextflow_config - Config default value correct: params.bgc_antismash_contigminlength= 3000
nextflow_config - Config default value correct: params.bgc_antismash_hmmdetectionstrictness= relaxed
nextflow_config - Config default value correct: params.bgc_antismash_taxon= bacteria
nextflow_config - Config default value correct: params.bgc_deepbgc_score= 0.5
nextflow_config - Config default value correct: params.bgc_deepbgc_mergemaxproteingap= 0
nextflow_config - Config default value correct: params.bgc_deepbgc_mergemaxnuclgap= 0
nextflow_config - Config default value correct: params.bgc_deepbgc_minnucl= 1
nextflow_config - Config default value correct: params.bgc_deepbgc_minproteins= 1
nextflow_config - Config default value correct: params.bgc_deepbgc_mindomains= 1
nextflow_config - Config default value correct: params.bgc_deepbgc_minbiodomains= 0
nextflow_config - Config default value correct: params.bgc_deepbgc_classifierscore= 0.5
nextflow_config - Config default value correct: params.bgc_gecco_cds= 3
nextflow_config - Config default value correct: params.bgc_gecco_pfilter= 1e-09
nextflow_config - Config default value correct: params.bgc_gecco_threshold= 0.8
nextflow_config - Config default value correct: params.bgc_gecco_edgedistance= 0
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.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.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_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
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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 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: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.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 found and not ignored.
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'
base_config - conf/base.config found and not ignored.
base_config - GUNZIP found in conf/base.config and Nextflow scripts.
base_config - UNTAR found in conf/base.config and Nextflow scripts.
base_config - PROKKA found in conf/base.config and Nextflow scripts.
base_config - PRODIGAL_GBK found in conf/base.config and Nextflow scripts.
base_config - BAKTA_BAKTA found in conf/base.config and Nextflow scripts.
base_config - ABRICATE_RUN found in conf/base.config and Nextflow scripts.
base_config - AMRFINDERPLUS_RUN found in conf/base.config and Nextflow scripts.
base_config - DEEPARG_DOWNLOADDATA found in conf/base.config and Nextflow scripts.
base_config - DEEPARG_PREDICT found in conf/base.config and Nextflow scripts.
base_config - FARGENE found in conf/base.config and Nextflow scripts.
base_config - RGI_MAIN found in conf/base.config and Nextflow scripts.
base_config - AMPIR found in conf/base.config and Nextflow scripts.
base_config - AMPLIFY_PREDICT found in conf/base.config and Nextflow scripts.
base_config - AMP_HMMER_HMMSEARCH found in conf/base.config and Nextflow scripts.
base_config - MACREL_CONTIGS found in conf/base.config and Nextflow scripts.
base_config - BGC_HMMER_HMMSEARCH found in conf/base.config and Nextflow scripts.
base_config - ANTISMASH_ANTISMASHLITE found in conf/base.config and Nextflow scripts.
base_config - ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES found in conf/base.config and Nextflow scripts.
base_config - DEEPBGC_DOWNLOAD found in conf/base.config and Nextflow scripts.
base_config - DEEPBGC_PIPELINE found in conf/base.config and Nextflow scripts.
base_config - GECCO_RUN found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_ABRICATE found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_AMRFINDERPLUS found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_DEEPARG found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_RGI found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_FARGENE found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_SUMMARIZE found in conf/base.config and Nextflow scripts.
base_config - ARGNORM_DEEPARG found in conf/base.config and Nextflow scripts.
base_config - ARGNORM_ABRICATE found in conf/base.config and Nextflow scripts.
base_config - ARGNORM_AMRFINDERPLUS found in conf/base.config and Nextflow scripts.
base_config - AMPCOMBI2_PARSETABLES found in conf/base.config and Nextflow scripts.
base_config - AMPCOMBI2_CLUSTER found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
modules_config - MMSEQS_DATABASES found in conf/modules.config and Nextflow scripts.
modules_config - MMSEQS_CREATEDB found in conf/modules.config and Nextflow scripts.
modules_config - MMSEQS_TAXONOMY found in conf/modules.config and Nextflow scripts.
modules_config - MMSEQS_CREATETSV found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SEQ found in conf/modules.config and Nextflow scripts.
modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_BAKTADBDOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_BAKTA found in conf/modules.config and Nextflow scripts.
modules_config - PRODIGAL found in conf/modules.config and Nextflow scripts.
modules_config - PYRODIGAL found in conf/modules.config and Nextflow scripts.
modules_config - ABRICATE_RUN found in conf/modules.config and Nextflow scripts.
modules_config - AMRFINDERPLUS_UPDATE found in conf/modules.config and Nextflow scripts.
modules_config - AMRFINDERPLUS_RUN found in conf/modules.config and Nextflow scripts.
modules_config - DEEPARG_DOWNLOADDATA found in conf/modules.config and Nextflow scripts.
modules_config - DEEPARG_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - FARGENE found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_CARD found in conf/modules.config and Nextflow scripts.
modules_config - RGI_CARDANNOTATION found in conf/modules.config and Nextflow scripts.
modules_config - RGI_MAIN found in conf/modules.config and Nextflow scripts.
modules_config - AMPIR found in conf/modules.config and Nextflow scripts.
modules_config - AMPLIFY_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - AMP_HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
modules_config - MACREL_CONTIGS found in conf/modules.config and Nextflow scripts.
modules_config - BGC_HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
modules_config - ANTISMASH_ANTISMASHLITE found in conf/modules.config and Nextflow scripts.
modules_config - ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES found in conf/modules.config and Nextflow scripts.
modules_config - DEEPBGC_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - DEEPBGC_PIPELINE found in conf/modules.config and Nextflow scripts.
modules_config - GECCO_RUN found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_ABRICATE found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_AMRFINDERPLUS found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_DEEPARG found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_RGI found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_FARGENE found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_SUMMARIZE found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_TAXONOMY_HAMRONIZATION found in conf/modules.config and Nextflow scripts.
modules_config - ARG_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
modules_config - AMPCOMBI2_PARSETABLES found in conf/modules.config and Nextflow scripts.
modules_config - AMPCOMBI2_COMPLETE found in conf/modules.config and Nextflow scripts.
modules_config - AMPCOMBI2_CLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_TAXONOMY_AMPCOMBI found in conf/modules.config and Nextflow scripts.
modules_config - AMP_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
modules_config - COMBGC found in conf/modules.config and Nextflow scripts.
modules_config - ARGNORM_ABRICATE found in conf/modules.config and Nextflow scripts.
modules_config - ARGNORM_AMRFINDERPLUS found in conf/modules.config and Nextflow scripts.
modules_config - ARGNORM_DEEPARG found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_TAXONOMY_COMBGC found in conf/modules.config and Nextflow scripts.
modules_config - BGC_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
modules_config - AMP_DATABASE_DOWNLOAD 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: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2024-12-18 12:52:39

.nf-core.yml

conf/modules.config

conf/test.config

modules/nf-core/macrel/contigs/main.nf

modules/nf-core/multiqc/main.nf

nextflow.config

subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf

pinin4fjords

Looks fairly uncontroversial, but I don't understand the CI errors. Ping me when those are resolved and I'll approve.

jasmezz · 2024-10-23T14:21:40Z

The CI errors all come from a (recent) faulty database update for one tool of the AMP workflow described in #423. Thus, only those CI tests without the AMP workflow succeed atm. All others will fail until either

we update how we deal with the faulty database or
the database maintainers fix it (tried to contact them again today)

For template update purposes I am not sure if the database issue is required to be solved first?

.nf-core.yml

conf/test.config

jfy133 · 2024-11-19T11:04:35Z

@nf-core-bot fix linting

jfy133 · 2024-11-29T09:57:02Z

Current status, waiting for new AMPcombi modules to be merged in from @Darcy220606 so we can get the tests to poass

jfy133 · 2024-12-11T09:01:08Z

Status update, waiting on:

First: Update ampcombi 2.0.1 modules#7142
Then: Add ampcombi 2.0.1 #427

nf-core-bot · 2024-12-12T11:23:56Z

Version 3.1.0 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of #429

Please use #429 to merge in the new changes from the nf-core template as soon as possible.

Add ampcombi 2.0.1

…cscan into nf-core-template-merge-3.0.2

jfy133 · 2024-12-18T10:52:22Z

@nf-core-bot fix linting

docs/output.md

nf-core-bot added 3 commits October 8, 2024 12:31

Template update for nf-core/tools version 3.0.0

62d7538

Template update for nf-core/tools version 3.0.1

01c5e49

Template update for nf-core/tools version 3.0.2

10b698e

nf-core-bot mentioned this pull request Oct 11, 2024

Important! Template update for nf-core/tools v3.0.1 #420

Closed

jfy133 added 4 commits October 23, 2024 11:30

Merge branch 'dev' into nf-core-template-merge-3.0.2

e321cba

Skip igenomes and fastqc becuase no reads nor reference genome

b5e346e

Remove max_ params for all other profiles

57762a7

Fix linting errors

d744c99

jfy133 added 5 commits October 23, 2024 13:13

Fix schema linting errors

d6d38f9

Update all modules

0f893df

Remove check_max and max_ parameters

c762ac9

Update missing module

d739f41

Fix schema

ba2fc82

jasmezz reviewed Oct 23, 2024

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pinin4fjords reviewed Oct 23, 2024

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jfy133 reviewed Nov 19, 2024

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.nf-core.yml Outdated Show resolved Hide resolved

conf/test.config Show resolved Hide resolved

Update .nf-core.yml

f4e13b3

Darcy220606 and others added 9 commits December 3, 2024 08:59

update the amp db download script

06852e9

update to use ampcombi 2.0.1

3aac84a

fix parametrs

d8f1f57

Update nf_schema

e670a3c

fix schema values

892b43d

update the docs

2d7758c

[automated] Fix code linting

9dc0d0f

add review suggestions

15a4429

[automated] Fix code linting

5c8144a

update nextflow.config

a69830a

maxulysse deleted the branch dev December 10, 2024 14:42

maxulysse closed this Dec 10, 2024

jasmezz reopened this Dec 10, 2024

nf-core-bot closed this Dec 12, 2024

jfy133 reopened this Dec 12, 2024

Darcy220606 and others added 8 commits December 12, 2024 13:55

update ampcombi2 2.0.1

35e7178

fix the ampcombi inputs

be89885

fix error strategy

8e1da95

Merge pull request #427 from nf-core/add_ampcombi_2.0.1

c8ce54a

Add ampcombi 2.0.1

Add AMPcombi to 2.0.1

75f1bc9

Add darkmode diagram

137f4dd

Merge branch 'nf-core-template-merge-3.0.2' of github.com:nf-core/fun…

a98783a

…cscan into nf-core-template-merge-3.0.2

Update snapshots due to new macrel and ampcombi versions

daf6a96

jfy133 added 3 commits December 18, 2024 12:13

Merge branch 'dev' into nf-core-template-merge-3.0.2

cf68706

Fix precommit and missing prokka snapshot

09a1018

Fix ARG tool variability

44c132c

jfy133 self-requested a review December 18, 2024 12:48

jfy133 approved these changes Dec 18, 2024

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Update docs/output.md

b4e74bb

jfy133 merged commit 75ff75a into dev Dec 18, 2024
27 checks passed

jfy133 deleted the nf-core-template-merge-3.0.2 branch December 18, 2024 12:51

jasmezz mentioned this pull request Feb 13, 2025

Release PR for 2.1.0 #456

Merged

11 tasks

Important! Template update for nf-core/tools v3.0.2 #421

Important! Template update for nf-core/tools v3.0.2 #421

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github-actions bot commented Oct 23, 2024 •

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