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Important! Template update for nf-core/tools v3.0.2 #1095

Merged
merged 14 commits into from
Dec 13, 2024
Merged

Important! Template update for nf-core/tools v3.0.2 #1095

merged 14 commits into from
Dec 13, 2024

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nf-core-bot
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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.

@nf-core-bot nf-core-bot mentioned this pull request Oct 11, 2024
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@jfy133
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jfy133 commented Oct 25, 2024

@nf-core-bot fix linting

@github-actions GitHub Actions
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github-actions bot commented Oct 25, 2024 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit af80edd

+| ✅ 375 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_nothing.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_nothing.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_humanbam.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_humanbam.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.contamination_estimation_angsd_hapmap

✅ 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-eager_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-eager_logo_light.png
  • files_exist - File found: docs/images/nf-core-eager_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-eager_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/WorkflowEager.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: 3.0.0dev
  • 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.igenomes_base= s3://ngi-igenomes/igenomes/
  • nextflow_config - Config default value correct: params.fasta_circularmapper_elongationfactor= 500
  • 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/
  • nextflow_config - Config default value correct: params.sequencing_qc_tool= fastqc
  • nextflow_config - Config default value correct: params.preprocessing_tool= fastp
  • nextflow_config - Config default value correct: params.preprocessing_minlength= 25
  • nextflow_config - Config default value correct: params.preprocessing_trim5p= 0
  • nextflow_config - Config default value correct: params.preprocessing_trim3p= 0
  • nextflow_config - Config default value correct: params.preprocessing_fastp_complexityfilter_threshold= 10
  • nextflow_config - Config default value correct: params.preprocessing_adapterremoval_trimbasequalitymin= 20
  • nextflow_config - Config default value correct: params.preprocessing_adapterremoval_adapteroverlap= 1
  • nextflow_config - Config default value correct: params.preprocessing_adapterremoval_qualitymax= 41
  • nextflow_config - Config default value correct: params.fastq_shard_size= 1000000
  • nextflow_config - Config default value correct: params.mapping_tool= bwaaln
  • nextflow_config - Config default value correct: params.mapping_bwaaln_n= 0.01
  • nextflow_config - Config default value correct: params.mapping_bwaaln_k= 2
  • nextflow_config - Config default value correct: params.mapping_bwaaln_l= 1024
  • nextflow_config - Config default value correct: params.mapping_bwaaln_o= 2
  • nextflow_config - Config default value correct: params.mapping_bwamem_k= 19
  • nextflow_config - Config default value correct: params.mapping_bwamem_r= 1.5
  • nextflow_config - Config default value correct: params.mapping_bowtie2_alignmode= local
  • nextflow_config - Config default value correct: params.mapping_bowtie2_sensitivity= sensitive
  • nextflow_config - Config default value correct: params.mapping_bowtie2_n= 0
  • nextflow_config - Config default value correct: params.mapping_bowtie2_l= 20
  • nextflow_config - Config default value correct: params.mapping_bowtie2_trim5= 0
  • nextflow_config - Config default value correct: params.mapping_bowtie2_trim3= 0
  • nextflow_config - Config default value correct: params.mapping_bowtie2_maxins= 500
  • nextflow_config - Config default value correct: params.bamfiltering_minreadlength= 0
  • nextflow_config - Config default value correct: params.bamfiltering_mappingquality= 0
  • nextflow_config - Config default value correct: params.bamfilter_genomicbamfilterflag= 4
  • nextflow_config - Config default value correct: params.metagenomics_input= unmapped
  • nextflow_config - Config default value correct: params.metagenomics_complexity_tool= bbduk
  • nextflow_config - Config default value correct: params.metagenomics_complexity_entropy= 0.3
  • nextflow_config - Config default value correct: params.metagenomics_prinseq_mode= entropy
  • nextflow_config - Config default value correct: params.metagenomics_prinseq_dustscore= 0.5
  • nextflow_config - Config default value correct: params.metagenomics_krakenuniq_ramchunksize= 16G
  • nextflow_config - Config default value correct: params.metagenomics_malt_mode= BlastN
  • nextflow_config - Config default value correct: params.metagenomics_malt_alignmentmode= SemiGlobal
  • nextflow_config - Config default value correct: params.metagenomics_malt_minpercentidentity= 85
  • nextflow_config - Config default value correct: params.metagenomics_malt_toppercent= 1
  • nextflow_config - Config default value correct: params.metagenomics_malt_minsupportmode= percent
  • nextflow_config - Config default value correct: params.metagenomics_malt_minsupportpercent= 0.01
  • nextflow_config - Config default value correct: params.metagenomics_malt_minsupportreads= 1
  • nextflow_config - Config default value correct: params.metagenomics_malt_maxqueries= 100
  • nextflow_config - Config default value correct: params.metagenomics_malt_memorymode= load
  • nextflow_config - Config default value correct: params.metagenomics_malt_group_size= 0
  • nextflow_config - Config default value correct: params.metagenomics_maltextract_filter= def_anc
  • nextflow_config - Config default value correct: params.metagenomics_maltextract_toppercent= 0.01
  • nextflow_config - Config default value correct: params.metagenomics_maltextract_minpercentidentity= 85.0
  • nextflow_config - Config default value correct: params.deduplication_tool= markduplicates
  • nextflow_config - Config default value correct: params.damage_manipulation_rescale_seqlength= 12
  • nextflow_config - Config default value correct: params.damage_manipulation_rescale_length_5p= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_rescale_length_3p= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_pmdtools_threshold= 3
  • nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_none_udg_left= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_none_udg_right= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_half_udg_left= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_half_udg_right= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_none_udg_left= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_none_udg_right= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_half_udg_left= 0
  • nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_half_udg_right= 0
  • nextflow_config - Config default value correct: params.genotyping_reference_ploidy= 2
  • nextflow_config - Config default value correct: params.genotyping_pileupcaller_min_base_quality= 30
  • nextflow_config - Config default value correct: params.genotyping_pileupcaller_min_map_quality= 30
  • nextflow_config - Config default value correct: params.genotyping_pileupcaller_method= randomHaploid
  • nextflow_config - Config default value correct: params.genotyping_pileupcaller_transitions_mode= AllSites
  • nextflow_config - Config default value correct: params.genotyping_gatk_call_conf= 30
  • nextflow_config - Config default value correct: params.genotyping_gatk_ug_downsample= 250
  • nextflow_config - Config default value correct: params.genotyping_gatk_ug_out_mode= EMIT_VARIANTS_ONLY
  • nextflow_config - Config default value correct: params.genotyping_gatk_ug_genotype_mode= SNP
  • nextflow_config - Config default value correct: params.genotyping_gatk_ug_defaultbasequalities= -1
  • nextflow_config - Config default value correct: params.genotyping_gatk_hc_out_mode= EMIT_VARIANTS_ONLY
  • nextflow_config - Config default value correct: params.genotyping_gatk_hc_emitrefconf= GVCF
  • nextflow_config - Config default value correct: params.genotyping_freebayes_min_alternate_count= 1
  • nextflow_config - Config default value correct: params.genotyping_freebayes_skip_coverage= 0
  • nextflow_config - Config default value correct: params.genotyping_angsd_glmodel= samtools
  • nextflow_config - Config default value correct: params.genotyping_angsd_glformat= binary
  • nextflow_config - Config default value correct: params.mitochondrion_header= MT
  • nextflow_config - Config default value correct: params.mapstats_preseq_mode= c_curve
  • nextflow_config - Config default value correct: params.mapstats_preseq_stepsize= 1000
  • nextflow_config - Config default value correct: params.mapstats_preseq_terms= 100
  • nextflow_config - Config default value correct: params.mapstats_preseq_maxextrap= 10000000000
  • nextflow_config - Config default value correct: params.mapstats_preseq_bootstrap= 100
  • nextflow_config - Config default value correct: params.mapstats_preseq_cval= 0.95
  • nextflow_config - Config default value correct: params.damagecalculation_tool= damageprofiler
  • nextflow_config - Config default value correct: params.damagecalculation_yaxis= 0.3
  • nextflow_config - Config default value correct: params.damagecalculation_xaxis= 25
  • nextflow_config - Config default value correct: params.damagecalculation_damageprofiler_length= 100
  • nextflow_config - Config default value correct: params.damagecalculation_mapdamage_downsample= 0
  • nextflow_config - Config default value correct: params.host_removal_mode= remove
  • nextflow_config - Config default value correct: params.contamination_estimation_angsd_chrom_name= X
  • nextflow_config - Config default value correct: params.contamination_estimation_angsd_range_from= 5000000
  • nextflow_config - Config default value correct: params.contamination_estimation_angsd_range_to= 154900000
  • nextflow_config - Config default value correct: params.contamination_estimation_angsd_mapq= 30
  • nextflow_config - Config default value correct: params.contamination_estimation_angsd_minq= 30
  • 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-eager_logo_light.png matches the template
  • files_unchanged - docs/images/nf-core-eager_logo_light.png matches the template
  • files_unchanged - docs/images/nf-core-eager_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_ci - '.github/workflows/ci.yml' is triggered on expected events
  • actions_ci - '.github/workflows/ci.yml' checks minimum NF version
  • 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
  • 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.
  • modules_config - conf/modules.config found and not ignored.
  • modules_config - SAMTOOLS_CONVERT_BAM_INPUT found in conf/modules.config and Nextflow scripts.
  • modules_config - CAT_FASTQ_CONVERTED_BAM found in conf/modules.config and Nextflow scripts.
  • modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
  • modules_config - FASTQC_PROCESSED found in conf/modules.config and Nextflow scripts.
  • modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
  • modules_config - FALCO found in conf/modules.config and Nextflow scripts.
  • modules_config - FALCO_PROCESSED found in conf/modules.config and Nextflow scripts.
  • modules_config - FASTP_SINGLE found in conf/modules.config and Nextflow scripts.
  • modules_config - FASTP_PAIRED found in conf/modules.config and Nextflow scripts.
  • modules_config - ADAPTERREMOVAL_SINGLE found in conf/modules.config and Nextflow scripts.
  • modules_config - ADAPTERREMOVAL_PAIRED found in conf/modules.config and Nextflow scripts.
  • modules_config - CAT_FASTQ_ADAPTERREMOVAL found in conf/modules.config and Nextflow scripts.
  • modules_config - GUNZIP_FASTA found in conf/modules.config and Nextflow scripts.
  • modules_config - GUNZIP_PMDFASTA found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
  • modules_config - PICARD_CREATESEQUENCEDICTIONARY found in conf/modules.config and Nextflow scripts.
  • modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
  • modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
  • modules_config - GUNZIP_ELONGATED_FASTA found in conf/modules.config and Nextflow scripts.
  • modules_config - CIRCULARMAPPER_CIRCULARGENERATOR found in conf/modules.config and Nextflow scripts.
  • modules_config - BWA_INDEX_CIRCULARISED found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FLAGSTATS_BAM_INPUT found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_INDEX_BAM_INPUT found in conf/modules.config and Nextflow scripts.
  • modules_config - CAT_FASTQ_UNMAPPED found in conf/modules.config and Nextflow scripts.
  • modules_config - FILTER_BAM_FRAGMENT_LENGTH found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FASTQ_UNMAPPED found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_VIEW_BAM_FILTERING found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_LENGTH_FILTER_INDEX found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FASTQ_MAPPED found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FLAGSTAT_FILTERED found in conf/modules.config and Nextflow scripts.
  • modules_config - SEQKIT_SPLIT2 found in conf/modules.config and Nextflow scripts.
  • modules_config - BWA_ALN found in conf/modules.config and Nextflow scripts.
  • modules_config - BWA_SAMSE found in conf/modules.config and Nextflow scripts.
  • modules_config - ENDORSPY found in conf/modules.config and Nextflow scripts.
  • modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
  • modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_INDEX_MEM found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_MERGE_LANES found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_SORT_MERGED_LANES found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_INDEX_MERGED_LANES found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FLAGSTAT_MERGED_LANES found in conf/modules.config and Nextflow scripts.
  • modules_config - CIRCULARMAPPER_REALIGNSAMFILE found in conf/modules.config and Nextflow scripts.
  • modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
  • modules_config - DEDUP found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_MERGE_DEDUPPED found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_SORT_DEDUPPED found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_INDEX_DEDUPPED found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FLAGSTAT_DEDUPPED found in conf/modules.config and Nextflow scripts.
  • modules_config - HOST_REMOVAL found in conf/modules.config and Nextflow scripts.
  • modules_config - PRESEQ_CCURVE found in conf/modules.config and Nextflow scripts.
  • modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_VIEW_GENOME found in conf/modules.config and Nextflow scripts.
  • modules_config - BEDTOOLS_COVERAGE_DEPTH found in conf/modules.config and Nextflow scripts.
  • modules_config - BEDTOOLS_COVERAGE_BREADTH found in conf/modules.config and Nextflow scripts.
  • modules_config - BEDTOOLS_MASKFASTA found in conf/modules.config and Nextflow scripts.
  • modules_config - MAPDAMAGE2 found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_INDEX_DAMAGE_RESCALED found in conf/modules.config and Nextflow scripts.
  • modules_config - PMDTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_INDEX_DAMAGE_FILTERED found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FLAGSTAT_DAMAGE_FILTERED found in conf/modules.config and Nextflow scripts.
  • modules_config - BAMUTIL_TRIMBAM found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_INDEX_DAMAGE_TRIMMED found in conf/modules.config and Nextflow scripts.
  • modules_config - ANGSD_DOCOUNTS found in conf/modules.config and Nextflow scripts.
  • modules_config - ANGSD_CONTAMINATION found in conf/modules.config and Nextflow scripts.
  • modules_config - PRINT_CONTAMINATION_ANGSD found in conf/modules.config and Nextflow scripts.
  • modules_config - MTNUCRATIO found in conf/modules.config and Nextflow scripts.
  • modules_config - PRINSEQPLUSPLUS found in conf/modules.config and Nextflow scripts.
  • modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
  • modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
  • modules_config - CAT_CAT_MALT found in conf/modules.config and Nextflow scripts.
  • modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
  • modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
  • modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
  • modules_config - MALTEXTRACT found in conf/modules.config and Nextflow scripts.
  • modules_config - MEGAN_RMA2INFO found in conf/modules.config and Nextflow scripts.
  • modules_config - AMPS found in conf/modules.config and Nextflow scripts.
  • modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
  • modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
  • modules_config - QUALIMAP_BAMQC_WITHBED found in conf/modules.config and Nextflow scripts.
  • modules_config - DAMAGEPROFILER found in conf/modules.config and Nextflow scripts.
  • modules_config - CALCULATE_MAPDAMAGE2 found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_DEPTH_SEXDETERRMINE found in conf/modules.config and Nextflow scripts.
  • modules_config - SEXDETERRMINE found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_MPILEUP_PILEUPCALLER found in conf/modules.config and Nextflow scripts.
  • modules_config - SEQUENCETOOLS_PILEUPCALLER found in conf/modules.config and Nextflow scripts.
  • modules_config - COLLECT_GENOTYPES found in conf/modules.config and Nextflow scripts.
  • modules_config - EIGENSTRATDATABASETOOLS_EIGENSTRATSNPCOVERAGE found in conf/modules.config and Nextflow scripts.
  • modules_config - GATK_REALIGNERTARGETCREATOR found in conf/modules.config and Nextflow scripts.
  • modules_config - GATK_INDELREALIGNER found in conf/modules.config and Nextflow scripts.
  • modules_config - GATK_UNIFIEDGENOTYPER found in conf/modules.config and Nextflow scripts.
  • modules_config - BCFTOOLS_INDEX_UG found in conf/modules.config and Nextflow scripts.
  • modules_config - GATK4_HAPLOTYPECALLER found in conf/modules.config and Nextflow scripts.
  • modules_config - FREEBAYES found in conf/modules.config and Nextflow scripts.
  • modules_config - BCFTOOLS_INDEX_FREEBAYES found in conf/modules.config and Nextflow scripts.
  • modules_config - BCFTOOLS_STATS_GENOTYPING found in conf/modules.config and Nextflow scripts.
  • modules_config - ANGSD_GL 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 2024-12-13 10:17:58

jfy133
jfy133 approved these changes Nov 29, 2024
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Code wise I think this looks OK (the PR does include a lot of reformatting from the Nextflow formatter), I will do a few input samplesheet/reference sheet checks however to make sure the updated schema is working

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jfy133 commented Nov 29, 2024

Samplesheets against https://github.com/nf-core/test-datasets/tree/eager/testdata/broken have been tested and all gave expected errors

TODO next: test against all reference sheets

reference_sheet_multiref_test.zip

@TCLamnidis TCLamnidis mentioned this pull request Nov 29, 2024
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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 #1102

Please use #1102 to merge in the new changes from the nf-core template as soon as possible.

@jfy133 jfy133 reopened this Dec 12, 2024
@jfy133 jfy133 merged commit 1818975 into dev Dec 13, 2024
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@jfy133 jfy133 deleted the nf-core-template-merge-3.0.2 branch December 13, 2024 12:03
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@TCLamnidis TCLamnidis TCLamnidis approved these changes

@jfy133 jfy133 jfy133 approved these changes

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