Candidate for 2.1.1

[GallVp]

PR checklist

• Candidate for 2.1.1
• 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
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @GallVp,

It looks like this pull-request is has been made against the Plant-Food-Research-Open/assemblyqc main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the Plant-Food-Research-Open/assemblyqc dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 94f8150

+| ✅ 196 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 2.1.1
• schema_lint - Schema $id should be https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/nextflow_schema.json
  Found https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/nextflow_schema.json

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-assemblyqc_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-assemblyqc_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: assets/multiqc_config.yml
• files_exist - File is ignored: conf/igenomes.config
• 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 does not exist: .github/ISSUE_TEMPLATE/config.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 does not exist: assets/nf-core-assemblyqc_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/assemblyqc/assemblyqc/.github/workflows/awstest.yml
• template_strings - template_strings
• 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: 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: conf/base.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-assemblyqc_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/WorkflowAssemblyqc.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.outdir= ./results
• nextflow_config - Config default value correct: params.check_sequence_duplicates= true
• nextflow_config - Config default value correct: params.assemblathon_stats_n_limit= 100
• nextflow_config - Config default value correct: params.ncbi_fcs_adaptor_skip= true
• nextflow_config - Config default value correct: params.ncbi_fcs_gx_skip= true
• nextflow_config - Config default value correct: params.contamination_stops_pipeline= true
• nextflow_config - Config default value correct: params.busco_skip= true
• nextflow_config - Config default value correct: params.tidk_skip= true
• nextflow_config - Config default value correct: params.tidk_filter_size_bp= 1000000
• nextflow_config - Config default value correct: params.lai_skip= true
• nextflow_config - Config default value correct: params.kraken2_skip= true
• nextflow_config - Config default value correct: params.hic_fastp_ext_args= --qualified_quality_phred 20 --length_required 50
• nextflow_config - Config default value correct: params.synteny_skip= true
• nextflow_config - Config default value correct: params.synteny_mummer_skip= true
• nextflow_config - Config default value correct: params.synteny_plotsr_skip= true
• nextflow_config - Config default value correct: params.synteny_between_input_assemblies= true
• nextflow_config - Config default value correct: params.synteny_mummer_plot_type= both
• nextflow_config - Config default value correct: params.synteny_mummer_max_gap= 1000000
• nextflow_config - Config default value correct: params.synteny_mummer_min_bundle_size= 1000
• nextflow_config - Config default value correct: params.synteny_color_by_contig= true
• nextflow_config - Config default value correct: params.synteny_plotsr_seq_label= Chr
• nextflow_config - Config default value correct: params.merqury_skip= true
• nextflow_config - Config default value correct: params.merqury_kmer_length= 21
• nextflow_config - Config default value correct: params.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 512.GB
• nextflow_config - Config default value correct: params.max_time= 7.day
• 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.validate_params= true
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.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 - .gitignore matches the template
• files_unchanged - .prettierignore 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
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• pipeline_name_conventions - Name adheres to nf-core convention
• 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: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - NCBI_FCS_GX_SCREEN_SAMPLES found in conf/base.config and Nextflow scripts.
• base_config - KRAKEN2 found in conf/base.config and Nextflow scripts.
• base_config - BWA_MEM found in conf/base.config and Nextflow scripts.
• base_config - SAMBLASTER found in conf/base.config and Nextflow scripts.
• base_config - DNADIFF found in conf/base.config and Nextflow scripts.
• base_config - MERQURY_HAPMERS found in conf/base.config and Nextflow scripts.
• base_config - CREATEREPORT found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - SEQKIT_RMDUP found in conf/modules.config and Nextflow scripts.
• modules_config - ASSEMBLATHON_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - FCS_FCSADAPTOR found in conf/modules.config and Nextflow scripts.
• modules_config - NCBI_FCS_GX_SCREEN_SAMPLES found in conf/modules.config and Nextflow scripts.
• modules_config - NCBI_FCS_GX_KRONA_PLOT found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2_KRONA_PLOT found in conf/modules.config and Nextflow scripts.
• modules_config - CIRCOS found in conf/modules.config and Nextflow scripts.
• modules_config - LINEARSYNTENY found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_BY_LENGTH found in conf/modules.config and Nextflow scripts.
• modules_config - SORT_BY_LENGTH found in conf/modules.config and Nextflow scripts.
• modules_config - TIDK_EXPLORE found in conf/modules.config and Nextflow scripts.
• modules_config - TIDK_SEARCH_APRIORI found in conf/modules.config and Nextflow scripts.
• modules_config - TIDK_SEARCH_APOSTERIORI found in conf/modules.config and Nextflow scripts.
• modules_config - TIDK_PLOT_APRIORI found in conf/modules.config and Nextflow scripts.
• modules_config - TIDK_PLOT_APOSTERIORI found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_SHORTENFASTAIDS found in conf/modules.config and Nextflow scripts.
• modules_config - LTRHARVEST found in conf/modules.config and Nextflow scripts.
• modules_config - LTRFINDER found in conf/modules.config and Nextflow scripts.
• modules_config - LTRRETRIEVER_LTRRETRIEVER found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_RESTOREGFFIDS found in conf/modules.config and Nextflow scripts.
• modules_config - LTRRETRIEVER_LAI found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - SAMBLASTER found in conf/modules.config and Nextflow scripts.
• modules_config - AGP2ASSEMBLY found in conf/modules.config and Nextflow scripts.
• modules_config - ASSEMBLY2BEDPE found in conf/modules.config and Nextflow scripts.
• modules_config - HIC2HTML found in conf/modules.config and Nextflow scripts.
• modules_config - HICQC found in conf/modules.config and Nextflow scripts.
• modules_config - RUNASSEMBLYVISUALIZER found in conf/modules.config and Nextflow scripts.
• modules_config - TAG_ASSEMBLY found in conf/modules.config and Nextflow scripts.
• modules_config - MERQURY_MERQURY found in conf/modules.config and Nextflow scripts.
• modules_config - CREATEREPORT 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 2024-09-19 22:24:43