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verified publisher icon nf-core

Release PR for 2.0.0

Open jasmezz opened this issue 1 year ago • 1 comments

Added

  • #322 Updated all modules: introduce environment.yml files. (by @jasmezz)
  • #324 Removed separate DeepARG test profile because database download is now stable. (by @jasmezz)
  • #332 & #327 Merged pipeline template of nf-core/tools version 2.12.1 (by @jfy133, @jasmezz)
  • #338 Set --meta parameter to default for Bakta, with singlemode optional. (by @jasmezz)
  • #343 Added contig taxonomic classification using MMseqs2. (by @darcy220606)
  • #358 Improved RGI databases handling, users can supply their own CARD now. (by @jasmezz)
  • #375 Merged pipeline template of nf-core/tools version 2.14.1. (by @jfy133)
  • #381 Added support for supplying pre-annotated sequences to the pipeline. (by @jfy133, @jasmezz)
  • #382 Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. (by @jfy133, @darcy220606)
  • #366 Added nf-test on pipeline level. (by @jfy133, @Darcy220606, @jasmezz)
  • #403 Added antiSMASH parameters --pfam2go, --rre, and --tfbs. (reported by @Darcy220606, added by @jasmezz)
  • #405 Added argNorm to ARG subworkflow. (by @Vedanth-Ramji)

Fixed

  • #343 Standardized the resulting workflow summary tables to always start with 'sample_id\tcontig_id\t..'. Reformatted the output of hamronization/summarize module. (by @darcy220606)
  • #348 Updated samplesheet for pipeline tests to 'samplesheet_reduced.csv' with smaller datasets to reduce resource consumption. Updated prodigal module to fix pigz issue. Removed tests/ from .gitignore. (by @darcy220606)
  • #362 Save annotations from bakta in subdirectories per sample. (by @jasmezz)
  • #363 Removed warning from DeepBGC usage docs. (by @jasmezz)
  • #365 Fixed AMRFinderPlus module and usage docs for manual database download. (by @jasmezz)
  • #371 Fixed AMRFinderPlus parameter arg_amrfinderplus_name. (by @m3hdad)
  • #376 Fixed an occasional RGI process failure when certain files not produced. (❤️ to @amizeranschi for reporting, fix by @amizeranschi & @jfy133)
  • #386 Updated DeepBGC module to fix output file names, separate annotation step for all BGC tools, add warning if no BGCs found, fix MultiQC reporting of annotation workflow. (by @jfy133, @jasmezz)
  • #392 & #397 Fixed a docker/singularity only error appearing when running with conda. (❤️ to @ewissel for reporting, fix by @jfy33 & @jasmezz)
  • #394 Fixed BGC input channel: pre-annotated input is picked up correctly now. (by @jfy133, @jasmezz)
  • #391 Skip hmmmsearch by default to not crash pipeline if user provides no HMM files, updated docs. (by @jasmezz)
  • #391 Made all "database" parameter names consistent. (by @jasmezz)
  • #397 Removed deprecated AMPcombi module, fixed variable name in BGC workflow, updated minor parts in docs (usage, parameter schema). (by @jasmezz)
  • #402 Fixed BGC length calculation for antiSMASH hits by comBGC. (by @jasmezz)
  • #406 Fixed prediction tools not being executed if annotation workflow skipped. (by @jasmezz)
  • #407 Fixed comBGC bug when parsing multiple antiSMASH files. (by @jasmezz)
  • #409 Fixed argNorm overwriting its output for DeepARG. (by @jasmezz, @jfy133)

Dependencies

Tool Previous version New version
AMPcombi 0.1.7 0.2.2
AMPlify 1.1.0 2.0.0
AMRFinderPlus 3.11.18 3.12.8
antiSMASH 6.1.1 7.1.0
argNorm NA 0.5.0
bioawk 1.0 NA
comBGC 1.6.1 1.6.2
DeepARG 1.0.2 1.0.4
DeepBGC 0.1.30 0.1.31
GECCO 0.9.8 0.9.10
hAMRonization 1.1.1 1.1.4
HMMER 3.3.2 3.4
MMSeqs NA 2:15.6f452
MultiQC 1.15 1.23
Pyrodigal 2.1.0 3.3.0
RGI 5.2.1 6.0.3
seqkit NA 2.8.1
tabix/htslib 1.11 1.19.1

Deprecated

  • #384 Deprecated AMPcombi and exchanged it with full suite of AMPcombi2 submodules. (by @darcy220606)
  • #382 Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. Bioawk is replaced with seqkit. (by @jfy133, @darcy220606)

PR checklist

  • [x] This comment contains a description of changes (with reason).
  • [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • [ ] If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
  • [x] Make sure your code lints (nf-core lint).
  • [x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • [x] Usage Documentation in docs/usage.md is updated.
  • [x] Output Documentation in docs/output.md is updated.
  • [x] CHANGELOG.md is updated.
  • [x] README.md is updated (including new tool citations and authors/contributors).

jasmezz avatar Jul 29 '24 09:07 jasmezz

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 09f61d1

+| ✅ 333 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

:grey_question: Tests ignored:

:white_check_mark: 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: .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 - Config variable found: manifest.name
  • nextflow_config - Config variable found: manifest.nextflowVersion
  • nextflow_config - Config variable found: manifest.description
  • nextflow_config - Config variable found: manifest.version
  • nextflow_config - Config variable found: manifest.homePage
  • nextflow_config - Config variable found: timeline.enabled
  • nextflow_config - Config variable found: trace.enabled
  • nextflow_config - Config variable found: report.enabled
  • nextflow_config - Config variable found: dag.enabled
  • nextflow_config - Config variable found: process.cpus
  • nextflow_config - Config variable found: process.memory
  • nextflow_config - Config variable found: process.time
  • nextflow_config - Config variable found: params.outdir
  • nextflow_config - Config variable found: params.input
  • nextflow_config - Config variable found: params.validationShowHiddenParams
  • nextflow_config - Config variable found: params.validationSchemaIgnoreParams
  • nextflow_config - Config variable found: manifest.mainScript
  • nextflow_config - Config variable found: timeline.file
  • nextflow_config - Config variable found: trace.file
  • nextflow_config - Config variable found: report.file
  • nextflow_config - Config variable found: dag.file
  • nextflow_config - Config variable (correctly) not found: params.nf_required_version
  • nextflow_config - Config variable (correctly) not found: params.container
  • nextflow_config - Config variable (correctly) not found: params.singleEnd
  • nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
  • nextflow_config - Config variable (correctly) not found: params.name
  • nextflow_config - Config variable (correctly) not found: params.enable_conda
  • nextflow_config - Config timeline.enabled had correct value: true
  • nextflow_config - Config report.enabled had correct value: true
  • nextflow_config - Config trace.enabled had correct value: true
  • nextflow_config - Config dag.enabled had correct value: true
  • nextflow_config - Config manifest.name began with nf-core/
  • nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
  • nextflow_config - Config dag.file ended with .html
  • nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
  • nextflow_config - Config params.custom_config_version is set to master
  • nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
  • nextflow_config - Lines for loading custom profiles found
  • 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_parsetables_cutoff= 0.6
  • nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_aalength= 100
  • 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_pfam2go= false
  • nextflow_config - Config default value correct: params.bgc_antismash_rre= false
  • nextflow_config - Config default value correct: params.bgc_antismash_taxon= bacteria
  • nextflow_config - Config default value correct: params.bgc_antismash_tfbs= false
  • 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.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.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: 23.04.0, Config: 23.04.0
  • readme - README Zenodo placeholder was replaced with DOI.
  • pipeline_todos - No TODO strings found
  • pipeline_name_conventions - Name adheres to nf-core convention
  • template_strings - Did not find any Jinja template strings (389 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: branch.yml
  • actions_schema_validation - Workflow validation passed: fix-linting.yml
  • actions_schema_validation - Workflow validation passed: linting.yml
  • actions_schema_validation - Workflow validation passed: clean-up.yml
  • actions_schema_validation - Workflow validation passed: ci.yml
  • actions_schema_validation - Workflow validation passed: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: awsfulltest.yml
  • actions_schema_validation - Workflow validation passed: download_pipeline.yml
  • actions_schema_validation - Workflow validation passed: release-announcements.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 - DRAMP_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: 2.14.1

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-21 15:17:53

github-actions[bot] avatar Jul 29 '24 09:07 github-actions[bot]