Add hicDetectLoops loop caller and visualization (part of #189) by samuelruizperez · Pull Request #237 · nf-core/hic

samuelruizperez · 2026-03-11T10:54:54Z

This pull request introduces a new loop calling feature (part of #189), using the hicDetectLoops tool:

Added a new LOOP_CALLING subworkflow in subworkflows/local/loop_calling/main.nf, which includes HICDETECTLOOPS for loop detection and HICPLOTMATRIX_LOOPS for loop visualization.

Tool modules for loop detection and visualization:

Added modules/local/hicexplorer/hicdetectloops/main.nf for running hicDetectLoops and outputting loop calls, and modules/local/hicexplorer/hicplotmatrix/main.nf for visualizing loops with hicPlotMatrix.

Configuration and parameter updates:

Updated nextflow.config and conf/test.config to add loop calling parameters.

Schema extension:

Added a new loop_calling section to nextflow_schema.json to describe loop calling parameters.

Balanced cooler output handling:

Updated subworkflows/local/cooler.nf and usages in workflows/hic.nf to ensure loop calling uses unbalanced matrix (see Clarifications of parameters deeptools/HiCExplorer#681)

PR checklist

github-actions · 2026-03-11T10:57:06Z

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

Posted for pipeline commit 98b31a1

+| ✅ 269 tests passed       |+
#| ❔   1 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

local_component_structure - split_cooler_dump.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - pairtools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - tads.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - compartments.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - cooler.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - hicpro.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - hicpro_mapping.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

schema_params - schema_params

❔ Tests fixed:

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

✅ Tests passed:

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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.processing= hicpro
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nextflow_config - Config default value correct: params.min_mapq= 10
nextflow_config - Config default value correct: params.bwt2_opts_end2end= --very-sensitive --end-to-end --reorder
nextflow_config - Config default value correct: params.bwt2_opts_trimmed= --very-sensitive --end-to-end --reorder
nextflow_config - Config default value correct: params.bwa_opts= -5SP -T0
nextflow_config - Config default value correct: params.pairtools_parse_opts= --walks-policy 5unique
nextflow_config - Config default value correct: params.bin_size= 1000000
nextflow_config - Config default value correct: params.ice_filter_low_count_perc= 0.02
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nextflow_config - Config default value correct: params.balancing_opts= --force
nextflow_config - Config default value correct: params.res_dist_decay= 250000
nextflow_config - Config default value correct: params.tads_caller= insulation
nextflow_config - Config default value correct: params.compartments_caller= cooltools
nextflow_config - Config default value correct: params.res_tads= 40000
nextflow_config - Config default value correct: params.res_compartments= 250000
nextflow_config - Config default value correct: params.loop_caller= hicexplorer
nextflow_config - Config default value correct: params.res_loops= 20000
nextflow_config - Config default value correct: params.maxloopdistance= 2000000
nextflow_config - Config default value correct: params.peakwidth= 2
nextflow_config - Config default value correct: params.windowsize= 5
nextflow_config - Config default value correct: params.pvaluepreselection= 0.1
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nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
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nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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modules_config - PAIRTOOLS_PARSE found in conf/modules.config and Nextflow scripts.
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modules_config - PAIRTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - PAIRTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
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modules_config - PAIRTOOLS_DEDUP found in conf/modules.config and Nextflow scripts.
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modules_config - PAIRIX found in conf/modules.config and Nextflow scripts.
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modules_config - COOLER_MAKEBINS found in conf/modules.config and Nextflow scripts.
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modules_config - SPLIT_COOLER_DUMP found in conf/modules.config and Nextflow scripts.
modules_config - COOLER_ZOOMIFY found in conf/modules.config and Nextflow scripts.
modules_config - COOLTOOLS_EIGSCIS found in conf/modules.config and Nextflow scripts.
modules_config - COOLTOOLS_INSULATION found in conf/modules.config and Nextflow scripts.
modules_config - HIC_FIND_TADS found in conf/modules.config and Nextflow scripts.
modules_config - HICDETECTLOOPS found in conf/modules.config and Nextflow scripts.
modules_config - HICPLOTMATRIX_LOOPS 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 2026-03-11 12:18:51

samuelruizperez · 2026-03-11T12:16:20Z

@nf-core-bot fix linting

samuelruizperez added 4 commits March 10, 2026 23:10

feat: add hicdetectloops

8c2bf8c

update docs

044c17f

update citations

f25760e

missing schema

efacb56

samuelruizperez self-assigned this Mar 11, 2026

samuelruizperez added the enhancement New feature or request label Mar 11, 2026

samuelruizperez added this to Hackathon March 2026 Mar 11, 2026

fix: res_loops in schema

b144c0d

[automated] Fix linting with Prettier

98b31a1

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Add hicDetectLoops loop caller and visualization (part of #189)#237

Add hicDetectLoops loop caller and visualization (part of #189)#237
samuelruizperez wants to merge 6 commits intonf-core:devfrom
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samuelruizperez commented Mar 11, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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