DSL2 - Genotyping Input Updates #1126

ilight1542 · 2025-03-25T16:13:15Z

Main bulk of this adjustment relates to #1128.

Otherwise, this is a QOL improvement/update for post mapping inputs into genotyping and its interactions with damage manipulation. Ascurrently implemented, this is a bit inflexible and requires the user to have specific parameter combinations for saving damage_manipulation outputs.

goal for improvement:

Allow for library by library genotyping
Uncouple damage manipulation saving from genotyping input

Allow for multiple damage manipulation tool calls (currently allowed, but previously only one would be saved if used for genotyping input)

Removed overwriting of final_bams/raw by multiple calls of samtools merge

Expand parameter checks/warnings to guide end user through best practices

PR checklist

… test profile

…roblem with collection/name not working

…Dir (but not working - no md5swum?!)

…ability

…nk so

… name coll. + not correct wet-lab-wise)

… same file, but still)

…ol and consistent saving of files.

ilight1542 · 2025-03-25T16:15:22Z

Current issue, Read Group assignment is done at least in some cases to be consistent across all libraries of a given sample -- but this breaks mpiluep calling which expects each input file to have a unique Read Group Sample ID.

will check if it breaks everything to swap to libID read groups (possibly only in the case we are running genotyping on unmerged libs?) 🗡️

RG assigned:

bowtie2
bwa

RG not assigned (?):

circular mapper

github-actions · 2025-03-25T17:37:36Z

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

Posted for pipeline commit 426e4cd

+| ✅ 395 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  50 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 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: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in ro-crate-metadata.json: "description": "
\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-eager_logo_dark.png">\n <img alt="nf-core/eager" src="docs/images/nf-core-eager_logo_light.png">\n \n
\n\n\n \n\n\n\n\n\n\n\n\n \n\n## Introduction\n\nnf-core/eager is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/eager \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/eager was originally written by The nf-core/eager community.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #eager channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/eager for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
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 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_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_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 awsfulltest.yml: You can customise AWS full pipeline tests as required
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.
local_component_structure - samtools_view_genome.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - build_intervals.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - print_contamination_angsd.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - host_removal.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - collect_genotypes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - filter_bam_fragment_length.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - metagenomics_postprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - reference_indexing_multi.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - metagenomics_profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - genotype.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - metagenomics_complexityfilter.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - manipulate_damage.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - estimate_contamination.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - merge_lanes_inputbam.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - preprocessing_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - reference_indexing_single.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - circularmapper.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - elongate_reference.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - merge_libraries.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - bamfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - metagenomics.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - preprocessing_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - map.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - reference_indexing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - calculate_damage.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - run_sex_determination.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - deduplicate.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

nextflow_config - Config default ignored: params.contamination_estimation_angsd_hapmap

✅ Tests passed:

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nextflow_config - Found nf-schema plugin
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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.bamfiltering_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_source= raw
nextflow_config - Config default value correct: params.genotyping_use_unmerged_libraries= false
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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.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 - MULTIQC found in conf/modules.config and Nextflow scripts.
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 - 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_INDEX_BAM_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_MERGED_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_MERGED_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_MERGED_LANES_BAMINPUT 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_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_FLAGSTAT_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ_SAVEBAMFILTERINGREADS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ_METAGENOMICS found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ_METAGENOMICS 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 - 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 - ENDORSPY 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 - 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 - QUALIMAP_BAMQC_WITHBED 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 - 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 - 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 - UNTAR_METAGENOMICS 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 - PICARD_ADDORREPLACEREADGROUPS 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: 3.2.0

Run details

nf-core/tools version 3.2.0
Run at 2025-03-28 12:06:51

ilight1542 · 2025-03-28T11:01:10Z

Got a working implementation for redeclaring the Read Group ID's. Needs test with multiple ref genomes/multiple libs from same sample.

Then on to ANGSD

jfy133 and others added 30 commits April 26, 2024 10:56

Add general structure, and generate (not working!) snapshot for basic…

f7fceaf

… test profile

Try adding an ignore zip system, doesn't work atm though...

0778e58

Merge branch 'dev' into nf-test-conversionMerge in from dev

eb73ae6

Continue customisation

cc114f3

More debugging

37994df

Get working function

e07dc06

Get working function properly, and start integrating into snapshot: p…

c0f93d9

…roblem with collection/name not working

Extract names properly

de035ca

Remove unnecesary code

7890575

Get working string check function!

b795b9e

TODO

cac8152

Update MQC so works on gitpod, try to re-add original getAllFilesFrom…

a8dcd64

…Dir (but not working - no md5swum?!)

And get it back again

56cba0c

Sort output to ensure consistency

0f12b21

Sort file name only funciton

d41aad9

Start testing preprocessing

61c4d24

Merge branch 'dev' into nf-test-conversion

19db88c

Start adding preprocessing dir but diff not working so can't ser vari…

bcc3baf

…ability

Backing up TODO notes

0b58cf7

Final snapshots, need to double check all files are covered but I thi…

eb4824e

…nk so

Finalise first test

9ce930f

Merge branch 'dev' into nf-test-conversion

5598eec

Update tests to latest dev

6362fa3

Merge branch 'dev' into nf-test-conversion

61086b5

Merge branch 'dev' into nf-test-conversion

9a56d48

Start refactoring to use nft-utils

bb12ca1

fix qualimap output dir typo

87fafc5

no sampleid in qualimap outdir

ef71d3b

bump nft-utils version

a7fadc6

start refactoring to use nft-utils

4baefaf

TCLamnidis and others added 23 commits January 24, 2025 10:38

Fix test. and snapshot.

80007d7

Merge branch 'dsl2-restructure-output' into nf-test-conversion

21a3462

bump nft-bam version

024433e

Start over with new output directory structure

3091e4a

bump nft-bams to latest

8627928

remove premature snapshot

64106a6

WIP test reimplementation

44cda40

add all remaining sections. tests still fail.

466e999

Merge branch 'dev' into nf-test-conversion

6e17b72

Slightly improved docs phrasing and structure

757eae4

Add some TODOs

ddfd514

Add ebugging prints

70a1bcf

Fix var name

4e4dacb

Update test snapshot to exclude directories and contained files

a71ab62

Merge branch 'nf-test-conversion' into dsl2-test-namecollisions

3519aa2

added error catching for multiple udg treatment in single lib (causes…

b2b0394

… name coll. + not correct wet-lab-wise)

adjusted default behavior for bam saving to prevent overwriting (with…

3787542

… same file, but still)

unfinished config for testing for name collisions

34dd28c

partial implementation

ee05ad1

mild rewrite of DAMAGEMANIPULATION --> GENOTYPING for increased contr…

8b52233

…ol and consistent saving of files.

update validation, genotyping parameter consistency

e8e812b

removal of partial implementation of name collision config

021aea4

typo in parameter check

07d0a2d

ilight1542 added 3 commits March 26, 2025 10:35

fixed erroneous param combo check

b7ac6ed

update genotyping libraries splitting for process names and saving

6eb67c4

working RG removal branching for mpileupcaller

71f4510

module import for addreadgroups

426e4cd

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DSL2 - Genotyping Input Updates #1126

DSL2 - Genotyping Input Updates #1126

ilight1542 commented Mar 25, 2025 •

edited

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ilight1542 commented Mar 25, 2025 •

edited

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