DSL2: Starting subworkflow for circularmapper #1076

jbv2 · 2024-06-14T09:51:43Z

Closes #1033
Linked to #921

PR checklist

github-actions · 2024-06-14T09:53:57Z

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

Posted for pipeline commit 81784cb

+| ✅ 342 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  22 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 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 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 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 ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
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 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 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_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_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

❔ 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: .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 - 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 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.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/
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.metagenomicscreening_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.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: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (307 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.
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 - PRINSEQPLUSPLUS found in conf/modules.config and Nextflow scripts.
modules_config - MTNUCRATIO 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_MERGE_LIBRARIES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_MERGED_LIBRARIES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_MERGED_LIBRARIES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_MERGED_LIBRARIES 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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-08-16 08:13:41

… workflow

This reverts commit 3fac93d.

Add elongated fasta and fai input for circularmapper

TCLamnidis · 2024-08-02T13:43:06Z

TODO:

Add CM filter to modules.config for module.

TCLamnidis · 2024-08-02T13:47:16Z

@nf-core-bot fix linting

TCLamnidis · 2024-08-05T13:45:16Z

❎ Adding the circularfilter parameter causes length filtering in the BAM_FILTERING step to fail. unsure what that is about.

Also: Due to how the CIRCULARMAPPER_CIRCULARGENERATOR module is set up, it can currently only handle fasta files with the fasta suffix, while fa, and gzipped variants fail. (Unclear if gz should be allowed in the module to begin with, but fa should definitely work.

TCLamnidis · 2024-08-05T15:35:33Z

I attempted to tweak bin/filter_bam_fragment_length.py to deactivate the check for @SQ tags in the header of the input. This creates errors downstream, since the @SQ tag does not get reintroduced, and is required for the NFCORE_EAGER:EAGER:SAMTOOLS_VIEW_GENOME process. >.<

UPDATE: Found the problem. RealignSAMFile implicitly requires an additional input file that is a list of the circularised chromosomes. This is output by CircularGenerator, but was not picked up by the module. Need to update both modules to account for this extra file. In the presence of this file, RealignSAMFile will remove all @SQ entries in the header EXCEPT those in the file.
nf-core/modules#6131

TCLamnidis · 2024-08-09T09:51:47Z

Updated to the new CM modules, and added passing of the elongated chromosome list to RealignSAMFile.

New problem: When the extended reference is provided, CircularGenerator is not run, so no elongated chromosome list exists to go into mapping...
Need to generate that from the circulartarget and pass it on. Alternatively, adding an ifEmpty{ [] } to the RealignSAMFile channel would work, but would break when circularfilter is used, as before.

TCLamnidis · 2024-08-10T09:31:17Z

random thought: Check that Circularmapper does what it's supposed to in the absence of the elongated chromosome file

TCLamnidis · 2024-08-12T12:49:38Z

Added some channel magic to create a file with the circular target info required by RealignSAMFile if an elongated reference is required.
To go with the above, made a circular target required for CM, regardless of if an elongated fasta was provided.

apeltzer

Looks good to me. Other option would be to edit CircularMapper, but I've given up on the development as no time/different work these days.

jfy133

I don't see anything major

jfy133 · 2024-08-13T08:50:11Z

nextflow_schema.json

+                },
+                "fasta_circularmapper_elongatedfasta": {
+                    "type": "string",
+                    "description": "Specify an elongated reference FASTA to be used for circularmapper.",


Is this in addition to or instead of --fasta?

Ok this is just docs, can be fixed later if it becomes an issue

nextflow_schema.json

subworkflows/local/reference_indexing.nf

subworkflows/local/utils_nfcore_eager_pipeline/main.nf

nextflow_schema.json

Starting subworkflow for circularmapper

010ffcd

jbv2 added the WIP Work in progress label Jun 14, 2024

jbv2 added this to the 3.0 Augsburg milestone Jun 14, 2024

jbv2 and others added 6 commits June 21, 2024 11:58

adding parameters and outputs. Missing to add subworkflow to the main…

3bbb28c

… workflow

Merge branch 'dev' into circularmapper

74b620e

adding circularmapper to map.nf

25ec1da

removing local path

68f7243

Merge branch 'dev' into circularmapper

1a5a148

fixing schema

3fac93d

jbv2 requested a review from a team July 3, 2024 12:34

TCLamnidis and others added 19 commits July 5, 2024 10:29

Revert "fixing schema"

ed9e948

This reverts commit 3fac93d.

fix schema

050acfd

WIP

d7a2d92

fix swf emissions

6caacef

add elongate_reference swf

670771d

wip n CM mapping

21093ac

add elongated fasta and fai input

a6a145a

attempt to add CM SWF

cd86749

index output bams

e05cc42

add validation and address comments

1764505

Merge branch 'circularmapper' into dsl2_circularmappe_refsheet

530cf7f

Merge pull request #2 from scarlhoff/dsl2_circularmappe_refsheet

203b9e5

Add elongated fasta and fai input for circularmapper

update CM modules

dff6208

updates to reference elongation SWF

c140062

Add unzipping in ELONGATE_REFERENCE SWF

4cd7a19

unzip, elongate and index reference when CM is used

de747de

add original reference input

ff2ad9a

i broke something Q_Q

b48e80f

bracket swap

7e311f4

Add suggestions from review

3b3d1d0

linting

d03b7c7

TCLamnidis added 3 commits August 5, 2024 15:45

rename elongated ref channel for clarity with its purpose

f72531b

add mapping_circularmapper_circularfilter option

8fe564b

update manual tests

2a98bd9

TCLamnidis added 3 commits August 9, 2024 10:29

update CM modules

6a076c2

add elongated chromosome list needed for circularmapper filtering

81d79f8

start adding manual chrom_list creation

f901063

TCLamnidis added 5 commits August 12, 2024 11:37

create elongated_chr_list from circular target

0b0bcf1

Circular target required regardless of elongated fasta

7063fd2

remove dumps

5d8476f

update manual tests

302acf3

fix module configuration application

c89ef24

update parameter name in CI

32fa8b1

TCLamnidis requested review from jfy133 and a team August 12, 2024 13:21

apeltzer approved these changes Aug 12, 2024

View reviewed changes

TCLamnidis removed the WIP Work in progress label Aug 13, 2024

jfy133 approved these changes Aug 13, 2024

View reviewed changes

Apply suggestions from code review

753994c

jfy133 reviewed Aug 16, 2024

View reviewed changes

nextflow_schema.json Outdated Show resolved Hide resolved

Fix linting

81784cb

jfy133 merged commit d63da95 into nf-core:dev Aug 16, 2024
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DSL2: Starting subworkflow for circularmapper #1076

DSL2: Starting subworkflow for circularmapper #1076

jbv2 commented Jun 14, 2024 •

edited by TCLamnidis

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DSL2: Starting subworkflow for circularmapper #1076

DSL2: Starting subworkflow for circularmapper #1076

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nf-core lint overall result: Passed ✅ ⚠️

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jbv2 commented Jun 14, 2024 •

edited by TCLamnidis

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

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