Fix bam filtering

[TCLamnidis]

While testing CircularMapper, I found out that providing --fasta_largeref caused half the pipeline to not execute. The reason was that BAM filtering once accounts for the BAI indices, so I made changes so the CSI indices are also picked if necessary.

A similar bug was also identified in the nf-core SWF BAM_SPLIT_BY_REGION, so I deactivated the -c option for SAMTOOLS_INDEX in that SWF, to avoid issues. The swf will need an upstream fix, but since we don;t publish these indices, it makes little difference here.

Also fixed the same issue when running flagstat on input bams

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
  • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• 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]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7765f16

+| ✅ 337 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 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 nextflow.config: Specify your pipeline's command line flags
• 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.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 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 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 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
• pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run 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: .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.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 (299 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: fix-linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.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: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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 - 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_MAPPED 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 2024-07-25 12:21:32