DSL2: Bam deduplication without jobsplit by ilight1542 · Pull Request #1169 · nf-core/eager

ilight1542 · 2026-02-13T11:05:44Z

This is an implementation of an optional flag of running dedupliaction across the full bam at once rather than contig-by-contig, leading to slowdowns for job scheduling when using poor quality reference genomes with many contigs.

Test-microbial now uses this parameter, and the snapshot has been updated.

PR checklist

…out_jobsplit

github-actions · 2026-02-20T09:47:14Z

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

Posted for pipeline commit a1145e4

+| ✅ 271 tests passed       |+
#| ❔   2 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  45 tests had warnings |!

Details

❗ Test warnings:

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 nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
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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!
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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 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_minimal.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test_minimal.config: Give any required params for the test so that command line flags are not needed
local_component_structure - samtools_view_genome.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 - build_intervals.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 - print_contamination_angsd.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 - deduplicate.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 - genotype.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 - manipulate_damage.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 - metagenomics_postprocessing.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 - merge_libraries.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 - preprocessing_adapterremoval.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 - metagenomics_complexityfilter.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 - reference_indexing_multi.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 - bamfiltering.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 - map.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 - elongate_reference.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

nextflow_config - nextflow_config
schema_params - schema_params

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

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files_exist - File not found check: parameters.settings.json
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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
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plugin_includes - No wrong validation plugin imports have been found
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schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
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system_exit - No System.exit calls found
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actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awstest.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
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modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
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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 - MAPAD_INDEX 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.
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modules_config - MAPAD_MAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_MAPAD 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.
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modules_config - ANGSD_DOCOUNTS found in conf/modules.config and Nextflow scripts.
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modules_config - PRINT_CONTAMINATION_ANGSD found in conf/modules.config and Nextflow scripts.
modules_config - MTNUCRATIO found in conf/modules.config and Nextflow scripts.
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modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
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modules_config - MALTEXTRACT found in conf/modules.config and Nextflow scripts.
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modules_config - AMPS found in conf/modules.config and Nextflow scripts.
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modules_config - DAMAGEPROFILER found in conf/modules.config and Nextflow scripts.
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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 - 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: 3.5.1
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-04-17 08:27:16

TCLamnidis

Generally this looks great! My only issue is the parameter name, and documentation.

The proposed name deduplication_mergejobs makes it sounds like additional work is done to merge bams, while in fact the opposite is the case. I also think that "jobs" is a bit of an under-the-hood, but that's maybe just a preference.

Please rename the parameter to something more intuitive. Suggestion: deduplication_skipregionsplit?
Please add a help_text section in the schema that explains the intended use case for the param.

ilight1542 · 2026-03-27T14:30:15Z

done :)

ilight1542 · 2026-04-17T09:21:45Z

@TCLamnidis should be all set now

ilight1542 added 6 commits January 30, 2026 10:49

successful implementation

b685274

Merge remote-tracking branch 'origin/dev' into bam_deduplication_with…

e2f86db

…out_jobsplit

updated snapshot

e4cef64

linting fix

82c4e1b

fix line space formatting

998cbe4

rollback of out of date linting

d62d8b9

ilight1542 requested a review from TCLamnidis February 20, 2026 11:27

TCLamnidis reviewed Mar 17, 2026

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adjusted paramet names and help text, per review

3cdec0a

extra space removal

acf82a3

TCLamnidis linked an issue Apr 10, 2026 that may be closed by this pull request

DSL2: #1167

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TCLamnidis mentioned this pull request Apr 17, 2026

DSL2: Pre-Release Checklist #1172

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DSL2: Bam deduplication without jobsplit#1169

DSL2: Bam deduplication without jobsplit#1169
ilight1542 wants to merge 9 commits intodevfrom
bam_deduplication_without_jobsplit

ilight1542 commented Feb 13, 2026 •

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ilight1542 commented Mar 27, 2026

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

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