updated docs

[mattheww95]

updated docs and readme.

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5ac0ceb

+| ✅ 225 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 0.4.2
• 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.override_allele_scheme=
• 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
• nextflow_config - Config default value correct: params.ec_opcov= 90
• nextflow_config - Config default value correct: params.ec_hpid= 95
• nextflow_config - Config default value correct: params.ec_hpcov= 50
• 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 (300 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: ci.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: doc.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: spellcheck.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'
• 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 - LOCIDEX_SELECT found in conf/modules.config and Nextflow scripts.
• modules_config - LOCIDEX_SUMMARIZE 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 - RASUSA 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 2024-10-03 19:50:35