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Merge pull request #910 from nf-core/hotfix
Release 3.1.2
2 parents 986579a + 64f0e90 commit 83f2699

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‎.github/workflows/nf-test.yml‎

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@@ -50,7 +50,7 @@ jobs:
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env:
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NFT_VER: ${{ env.NFT_VER }}
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with:
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max_shards: 20
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max_shards: 25
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- name: debug
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run: |

‎.nf-core.yml‎

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name: raredisease
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org: nf-core
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outdir: .
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version: 3.1.1
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version: 3.1.2

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## 3.1.2 - Princess Peach (patch) [2026-07-06]
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### `Fixed`
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- Fix `svdb/merge` mislabelling VCF caller tags by passing `sort_inputs = false` to `SVDB_MERGE` in `call_structural_variants`; the VCF list is already in the correct caller-priority order from the upstream `concat` chain, so in-module re-sorting by filename was causing tag misassignment [#910](https://github.com/nf-core/raredisease/pull/910)
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- Changed filter logic for merging mitochondrial snvs to report variants which pass filter in at least one sample [#915](https://github.com/nf-core/raredisease/pull/915)
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## 3.1.1 - Princess Peach (patch) [2026-06-24]
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### `Fixed`

‎assets/multiqc_config.yml‎

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@@ -2,7 +2,7 @@ custom_logo: "nf-core-raredisease_logo_light.png"
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custom_logo_url: https://github.com/nf-core/raredisease/
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custom_logo_title: "nf-core/raredisease"
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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/3.1.1" target="_blank">nf-core/raredisease</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/raredisease/3.1.1/docs/output" target="_blank">documentation</a>.
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This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/3.1.2" target="_blank">nf-core/raredisease</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/raredisease/3.1.2/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-raredisease-methods-description":

‎conf/modules/postprocess_MT_calls.config‎

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@@ -41,7 +41,7 @@ process {
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}
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withName: '.*POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT' {
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ext.args = '--output-type z --write-index=tbi'
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ext.args = '--output-type z --write-index=tbi --filter-logic x'
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ext.prefix = { "${meta.id}_split_rmdup_merged" }
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}
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‎nextflow.config‎

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@@ -485,7 +485,7 @@ manifest {
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mainScript = 'main.nf'
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defaultBranch = 'master'
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nextflowVersion = '!>=25.10.4'
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version = '3.1.1'
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version = '3.1.2'
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doi = '10.5281/zenodo.7995798'
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}
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‎ro-crate-metadata.json‎

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‎subworkflows/local/call_structural_variants/main.nf‎

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@@ -134,7 +134,7 @@ workflow CALL_STRUCTURAL_VARIANTS {
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ch_case_info
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.combine(ch_vcf_paths)
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.set { ch_merge_vcfs_in }
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SVDB_MERGE (ch_merge_vcfs_in, ch_svcaller_priority, true)
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SVDB_MERGE (ch_merge_vcfs_in, ch_svcaller_priority, false)
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TABIX_TABIX (SVDB_MERGE.out.vcf)
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ch_merged_svs = SVDB_MERGE.out.vcf

‎subworkflows/local/call_structural_variants/tests/main.nf.test‎

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@@ -10,10 +10,102 @@ nextflow_workflow {
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tag "call_sv_tiddit"
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tag "call_sv_germlinecnvcaller"
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tag "call_sv_cnvnator"
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tag "call_sv_mt"
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tag "bwa/index"
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tag "svdb/merge"
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tag "tabix/tabix"
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config "./nextflow.config"
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test("CALL_STRUCTURAL_VARIANTS - wgs") {
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setup {
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run("BWA_INDEX") {
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script "modules/nf-core/bwa/index/main.nf"
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process {
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"""
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input[0] = channel.of([
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[id:'genome'],
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file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)
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])
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"""
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}
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}
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}
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when {
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workflow {
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"""
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input[0] = BWA_INDEX.out.index.collect()
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input[1] = channel.of([id:'justhusky'])
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input[2] = channel.of([[id:'gcnvcaller'], []])
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input[3] = channel.of([
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[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
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file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)
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])
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input[4] = channel.of([
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[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
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file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)
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])
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input[5] = channel.of([
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[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
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file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true),
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file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)
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])
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input[6] = channel.from(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true))
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input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect()
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input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect()
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input[9] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect()
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input[10] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] }
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input[11] = channel.value([[], []])
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input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15])
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input[13] = channel.of([
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[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
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file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true),
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file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)
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])
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input[14] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect()
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input[15] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect()
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input[16] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] }
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input[17] = channel.of([[id:'ploidy'], []])
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input[18] = channel.of([[]])
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input[19] = channel.of([
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[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
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[
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file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true),
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file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)
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]
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])
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input[20] = channel.value(10000000)
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input[21] = channel.value(['manta', 'tiddit', 'cnvnator'])
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input[22] = true
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input[23] = true
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input[24] = 'wgs'
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input[25] = 407
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input[26] = 16081
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input[27] = 5763
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input[28] = 5730
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input[29] = 16569
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input[30] = 'MT'
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input[31] = 15
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input[32] = 0.01
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input[33] = true
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"""
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}
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}
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then {
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assertAll(
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{ assert workflow.success },
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{ assert snapshot(
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workflow.out.tbi.collect { meta, tbi -> file(tbi).name },
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path(workflow.out.vcf[0][1]).vcf.summary
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).match() }
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)
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}
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}
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test("CALL_STRUCTURAL_VARIANTS - wgs, stub") {
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options "-stub"

‎subworkflows/local/call_structural_variants/tests/main.nf.test.snap‎

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{
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"CALL_STRUCTURAL_VARIANTS - wgs": {
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"content": [
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[
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"justhusky_sv.vcf.gz.tbi"
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],
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"VcfFile [chromosomes=[MT, 21], sampleCount=1, variantCount=115, phased=false, phasedAutodetect=false]"
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],
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"timestamp": "2026-07-03T15:59:49.244712615",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.4"
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}
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},
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"CALL_STRUCTURAL_VARIANTS - wgs, stub": {
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"content": [
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[

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