From 10f54af8932d5e8cf925cbd160e9abb856ca678c Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 27 May 2026 14:49:27 +0000 Subject: [PATCH 01/19] Adding in fusionreport updates --- modules.json | 4 +- .../fusionreport/detect/environment.yml | 14 +- modules/nf-core/fusionreport/detect/main.nf | 25 ++- modules/nf-core/fusionreport/detect/meta.yml | 81 +++++----- .../fusionreport/detect/tests/main.nf.test | 83 ++++------ .../detect/tests/main.nf.test.snap | 146 +++++++----------- .../fusionreport/download/environment.yml | 24 +-- modules/nf-core/fusionreport/download/main.nf | 43 ++---- .../nf-core/fusionreport/download/meta.yml | 52 +++++-- .../fusionreport/download/tests/main.nf.test | 19 +-- .../download/tests/main.nf.test.snap | 63 ++++---- .../download/tests/nextflow.config | 2 +- 12 files changed, 252 insertions(+), 304 deletions(-) diff --git a/modules.json b/modules.json index 265f58c19..3c9ed8bf6 100644 --- a/modules.json +++ b/modules.json @@ -75,12 +75,12 @@ }, "fusionreport/detect": { "branch": "master", - "git_sha": "2737fcc61a0379e6f130de9069cadf77bc8e97ff", + "git_sha": "76dfaba27ac4eacd80cdac5ba28985ee2646b0bd", "installed_by": ["modules"] }, "fusionreport/download": { "branch": "master", - "git_sha": "df4b662dae05afb695a4326fc172178b5a7a48ce", + "git_sha": "76dfaba27ac4eacd80cdac5ba28985ee2646b0bd", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { diff --git a/modules/nf-core/fusionreport/detect/environment.yml b/modules/nf-core/fusionreport/detect/environment.yml index f14a523ea..d5575fa42 100644 --- a/modules/nf-core/fusionreport/detect/environment.yml +++ b/modules/nf-core/fusionreport/detect/environment.yml @@ -2,5 +2,17 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fusion-report=4.0.1 + - bioconda::fusion-report=4.1.0 + - conda-forge::beautifulsoup4=4.14.3 + - conda-forge::click=8.4.0 + - conda-forge::colorlog=6.10.1 + - conda-forge::jinja2=3.1.6 + - conda-forge::markupsafe=3.0.3 + - conda-forge::numpy=2.4.6 - conda-forge::openpyxl=3.1.5 + - conda-forge::pandas=3.0.3 + - conda-forge::pyyaml=6.0.3 + - conda-forge::requests=2.34.2 + - conda-forge::tabulate=0.10.0 + - conda-forge::tqdm=4.67.3 + - conda-forge::xlrd=2.0.2 diff --git a/modules/nf-core/fusionreport/detect/main.nf b/modules/nf-core/fusionreport/detect/main.nf index 618c14504..9b07af85e 100644 --- a/modules/nf-core/fusionreport/detect/main.nf +++ b/modules/nf-core/fusionreport/detect/main.nf @@ -3,9 +3,9 @@ process FUSIONREPORT_DETECT { label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/ed32f46746a5b33a1b5d597cfe2f62d3b1cfa54638f57cadc5d5158d6a4959d2/data' : - 'community.wave.seqera.io/library/fusion-report_beautifulsoup4_click_colorlog_pruned:78488bd99166aa9a'}" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73d08e3edb2f4c51bb65c3b43d751f8ddb4c92f49c45659a4a43a3f5e008f937/data' : + 'community.wave.seqera.io/library/fusion-report_beautifulsoup4_click_colorlog_pruned:5d32bf6f226660f1'}" input: tuple val(meta), path(arriba_fusions), path(starfusion_fusions), path(fusioncatcher_fusions) @@ -19,7 +19,7 @@ process FUSIONREPORT_DETECT { tuple val(meta), path("*_*.html") , emit: html , optional:true tuple val(meta), path("*.csv") , emit: csv , optional:true tuple val(meta), path("*.json") , emit: json , optional:true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('fusion_report'), eval("fusion_report --version |& sed 's/fusion-report //'"), topic: versions, emit: versions_fusionreport when: task.ext.when == null || task.ext.when @@ -32,19 +32,17 @@ process FUSIONREPORT_DETECT { tools += fusioncatcher_fusions ? "--fusioncatcher ${fusioncatcher_fusions} " : '' def prefix = task.ext.prefix ?: "${meta.id}" """ - fusion_report run $meta.id . $fusionreport_ref $tools --allow-multiple-gene-symbols --tool-cutoff $tools_cutoff $args $args2 + fusion_report run ${prefix} . \\ + ${fusionreport_ref} ${tools} \\ + --allow-multiple-gene-symbols \\ + --tool-cutoff ${tools_cutoff} \\ + ${args} ${args2} mv fusion_list.tsv ${prefix}.fusionreport.tsv mv fusion_list_filtered.tsv ${prefix}.fusionreport_filtered.tsv mv index.html ${prefix}_fusionreport_index.html [ ! -f fusions.csv ] || mv fusions.csv ${prefix}.fusions.csv [ ! -f fusions.json ] || mv fusions.json ${prefix}.fusions.json - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fusion_report: \$(fusion_report --version | sed 's/fusion-report //') - fusion_report DB retrieval: \$(cat $fusionreport_ref/DB-timestamp.txt) - END_VERSIONS """ stub: @@ -56,10 +54,5 @@ process FUSIONREPORT_DETECT { touch AAA_BBB.html touch ${prefix}.fusions.csv touch ${prefix}.fusions.json - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fusion_report: \$(fusion_report --version | sed 's/fusion-report //') - END_VERSIONS """ } diff --git a/modules/nf-core/fusionreport/detect/meta.yml b/modules/nf-core/fusionreport/detect/meta.yml index dc87feed9..13031b778 100644 --- a/modules/nf-core/fusionreport/detect/meta.yml +++ b/modules/nf-core/fusionreport/detect/meta.yml @@ -11,9 +11,9 @@ tools: homepage: https://github.com/Clinical-Genomics/fusion-report documentation: https://matq007.github.io/fusion-report/#/ doi: "10.1101/011650" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" - input: - - meta: type: map @@ -43,25 +43,22 @@ input: Groovy Map containing sample information - fusionreport_ref: type: directory - description: File + description: directory containing the genome resource files required for fusioncatcher pattern: "fusion_report_db" - tools_cutoff: type: integer - description: Discard fusions detected by less than $tools_cutoff tools both for display in fusionreport html index and to consider in fusioninspector. - + description: Discard fusions detected by less than $tools_cutoff tools both + for display in fusionreport html index and to consider in fusioninspector. output: fusion_list: - - meta: type: map description: | Groovy Map containing sample information - pattern: "*.tsv" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV - "*fusionreport.tsv": - type: map + type: file description: | - Groovy Map containing sample information + Fusion report pattern: "*.tsv" ontologies: - edam: http://edamontology.org/format_3475 # TSV @@ -70,13 +67,10 @@ output: type: map description: | Groovy Map containing sample information - pattern: "*.tsv" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV - "*fusionreport_filtered.tsv": - type: map + type: file description: | - Groovy Map containing sample information + Filtered fusion report pattern: "*.tsv" ontologies: - edam: http://edamontology.org/format_3475 # TSV @@ -85,13 +79,10 @@ output: type: map description: | Groovy Map containing sample information - pattern: "*.index.html" - ontologies: - - edam: "http://edamontology.org/format_2331" # HTML - "*index.html": - type: map + type: file description: | - Groovy Map containing sample information + Interactive HTML report pattern: "*.index.html" ontologies: - edam: "http://edamontology.org/format_2331" # HTML @@ -100,13 +91,10 @@ output: type: map description: | Groovy Map containing sample information - pattern: "*_*.html" - ontologies: - - edam: "http://edamontology.org/format_2331" # HTML - "*_*.html": type: map description: | - Groovy Map containing sample information + All HTML report files pattern: "*_*.html" ontologies: - edam: "http://edamontology.org/format_2331" # HTML @@ -115,13 +103,10 @@ output: type: map description: | Groovy Map containing sample information - pattern: "*.csv" - ontologies: - - edam: "http://edamontology.org/format_3752" # CSV - "*.csv": - type: map + type: file description: | - Groovy Map containing sample information + Report in CSV format pattern: "*.csv" ontologies: - edam: "http://edamontology.org/format_3752" # CSV @@ -130,22 +115,34 @@ output: type: map description: | Groovy Map containing sample information - pattern: "*.json" - ontologies: - - edam: "http://edamontology.org/format_3464" # JSON - "*.json": - type: map + type: file description: | - Groovy Map containing sample information + Report in JSON format pattern: "*.json" ontologies: - - edam: "http://edamontology.org/format_3464" # JSON + - edam: "http://edamontology.org/format_3464" + versions_fusionreport: + - - ${task.process}: + type: string + description: The name of the process + - fusion_report: + type: string + description: The name of the tool + - fusion_report --version |& sed 's/fusion-report //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - fusion_report: + type: string + description: The name of the tool + - fusion_report --version |& sed 's/fusion-report //': + type: eval + description: The expression to obtain the version of the tool authors: - - "@praveenraj2018, @rannick" + - "@praveenraj2018" + - "@rannick" diff --git a/modules/nf-core/fusionreport/detect/tests/main.nf.test b/modules/nf-core/fusionreport/detect/tests/main.nf.test index baf1ce12f..c208266bf 100644 --- a/modules/nf-core/fusionreport/detect/tests/main.nf.test +++ b/modules/nf-core/fusionreport/detect/tests/main.nf.test @@ -2,7 +2,9 @@ nextflow_process { name "Test Process FUSIONREPORT_DETECT" script "../main.nf" + config './nextflow.config' process "FUSIONREPORT_DETECT" + tag "modules" tag "modules_local" tag "fusionreport" @@ -10,25 +12,29 @@ nextflow_process { tag "modules_nfcore" tag "fusionreport/download" - - test("FUSIONREPORT - arriba - starfusion - fusioncatcher") { - config './nextflow.config' - - setup { - run("FUSIONREPORT_DOWNLOAD") { - script "../../../fusionreport/download/main.nf" - process { - """ - """ - } + setup { + run("FUSIONREPORT_DOWNLOAD") { + script "../../../fusionreport/download/main.nf" + process { + """ + input[0] = [id: 'fusion_report_db'] + """ } } + } + + test("FUSIONREPORT - arriba - starfusion - fusioncatcher") { when { + params { + fusionreport_download_args = "--no-cosmic" + fusionreport_detect_args = "--no-cosmic" + fusionreport_detect_args2 = "--export csv" + } process { """ input[0] = [ - [ id:'test_sample' ], // meta map + [ id:'test_sample' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/arriba.tsv', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/starfusion.tsv', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/fusioncatcher.txt', checkIfExists: true) @@ -37,55 +43,30 @@ nextflow_process { input[2] = 1 """ } - params { - arriba = true - starfusion = true - fusioncatcher = true - no_cosmic = true - outdir = "$outputDir" - fusionreport_download_args = '--no-cosmic' - fusionreport_detect_args = {params.no_cosmic} ? "--no-cosmic" : "" - fusionreport_detect_args2 = "--export csv" - } } then { assertAll( { assert process.success }, - { assert snapshot( - process.out.fusion_list, - process.out.fusion_list_filtered, - process.out.csv, - file(process.out.report[0][1]).name, - process.out.html[0][1].collect { file(it).name }, - process.out.json, - process.out.versions.flatten().first().toString().split('/')[-1] // md5sum not stable as versions contains DB timestamp - ).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["report", "html"])).match() } ) } } test("FUSIONREPORT - arriba - starfusion - fusioncatcher - stub") { - config './nextflow.config' - - setup { - run("FUSIONREPORT_DOWNLOAD") { - script "../../../fusionreport/download/main.nf" - process { - """ - """ - } - } - } - options "-stub" when { + params { + fusionreport_download_args = "--no-cosmic" + fusionreport_detect_args = "--no-cosmic" + fusionreport_detect_args2 = "--export csv" + } process { """ input[0] = [ - [ id:'test_sample' ], // meta map + [ id:'test_sample' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/arriba.tsv', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/starfusion.tsv', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/fusioncatcher.txt', checkIfExists: true) @@ -94,23 +75,13 @@ nextflow_process { input[2] = 1 """ } - params { - arriba = true - starfusion = true - fusioncatcher = true - no_cosmic = true - outdir = "$outputDir" - fusionreport_download_args = '--no-cosmic' - fusionreport_detect_args = {params.no_cosmic} ? "--no-cosmic" : "" - fusionreport_detect_args2 = "--export csv" - } } then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/fusionreport/detect/tests/main.nf.test.snap b/modules/nf-core/fusionreport/detect/tests/main.nf.test.snap index 7b71aa358..3abfd6e21 100644 --- a/modules/nf-core/fusionreport/detect/tests/main.nf.test.snap +++ b/modules/nf-core/fusionreport/detect/tests/main.nf.test.snap @@ -1,126 +1,94 @@ { "FUSIONREPORT - arriba - starfusion - fusioncatcher": { - "content": [ - [ - [ - { - "id": "test_sample" - }, - "test_sample.fusionreport.tsv:md5,3593b7021f26cc5427fdc96f0d1c72f0" - ] - ], - [ - [ - { - "id": "test_sample" - }, - "test_sample.fusionreport_filtered.tsv:md5,3593b7021f26cc5427fdc96f0d1c72f0" - ] - ], - [ - [ - { - "id": "test_sample" - }, - "test_sample.fusions.csv:md5,ee6c6838110d68bc75a13c19dca0a321" - ] - ], - "test_sample_fusionreport_index.html", - [ - "AKAP9_BRAF.html", - "BRD4-1_NUTM1.html", - "BRD4_NUTM1.html", - "CD74_AL132671.2.html", - "CD74_ROS1.html", - "CIC_DUX4.html", - "DUX4_IGH@.html", - "EML4_ALK.html", - "ETV6_NTRK3.html", - "EWSR1_ATF1.html", - "EWSR1_FLI1.html", - "FGFR3_TACC3.html", - "FIP1L1_PDGFRA.html", - "GOPC_ROS1.html", - "HOOK3_RET.html", - "IGH@_CRLF2.html", - "MALT1_IGH@.html", - "NPM1_ALK.html", - "TMPRSS2_ETV1.html", - "test_sample_fusionreport_index.html" - ], - [ - [ - { - "id": "test_sample" - }, - "fusion_genes_mqc.json:md5,b196dc8d064a47d17fd3a032b8fbed4f" - ] - ], - "versions.yml" - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.4" - }, - "timestamp": "2025-06-26T16:15:03.892288278" - }, - "FUSIONREPORT - arriba - starfusion - fusioncatcher - stub": { "content": [ { - "0": [ + "csv": [ [ { "id": "test_sample" }, - "test_sample.fusionreport.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sample.fusions.csv:md5,ee6c6838110d68bc75a13c19dca0a321" ] ], - "1": [ + "fusion_list": [ [ { "id": "test_sample" }, - "test_sample.fusionreport_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sample.fusionreport.tsv:md5,3593b7021f26cc5427fdc96f0d1c72f0" ] ], - "2": [ + "fusion_list_filtered": [ [ { "id": "test_sample" }, - "test_sample_fusionreport_index.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sample.fusionreport_filtered.tsv:md5,3593b7021f26cc5427fdc96f0d1c72f0" ] ], - "3": [ + "html": [ [ { "id": "test_sample" }, [ - "AAA_BBB.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "test_sample_fusionreport_index.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "AKAP9_BRAF.html", + "BRD4-1_NUTM1.html", + "BRD4_NUTM1.html", + "CD74_AL132671.2.html", + "CD74_ROS1.html", + "CIC_DUX4.html", + "DUX4_IGH@.html", + "EML4_ALK.html", + "ETV6_NTRK3.html", + "EWSR1_ATF1.html", + "EWSR1_FLI1.html", + "FGFR3_TACC3.html", + "FIP1L1_PDGFRA.html", + "GOPC_ROS1.html", + "HOOK3_RET.html", + "IGH@_CRLF2.html", + "MALT1_IGH@.html", + "NPM1_ALK.html", + "TMPRSS2_ETV1.html", + "test_sample_fusionreport_index.html" ] ] ], - "4": [ + "json": [ [ { "id": "test_sample" }, - "test_sample.fusions.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + "fusion_genes_mqc.json:md5,b196dc8d064a47d17fd3a032b8fbed4f" ] ], - "5": [ + "report": [ [ { "id": "test_sample" }, - "test_sample.fusions.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sample_fusionreport_index.html" ] ], - "6": [ - "versions.yml:md5,947ac2c0ed1623930f951f4f4ee3501e" - ], + "versions_fusionreport": [ + [ + "FUSIONREPORT_DETECT", + "fusion_report", + "4.0.1" + ] + ] + } + ], + "timestamp": "2026-05-27T14:07:24.513061495", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.2" + } + }, + "FUSIONREPORT - arriba - starfusion - fusioncatcher - stub": { + "content": [ + { "csv": [ [ { @@ -172,15 +140,19 @@ "test_sample_fusionreport_index.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,947ac2c0ed1623930f951f4f4ee3501e" + "versions_fusionreport": [ + [ + "FUSIONREPORT_DETECT", + "fusion_report", + "4.0.1" + ] ] } ], + "timestamp": "2026-05-27T14:08:24.497257039", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.4" - }, - "timestamp": "2025-07-01T14:42:59.809164059" + "nf-test": "0.9.5", + "nextflow": "26.04.2" + } } } \ No newline at end of file diff --git a/modules/nf-core/fusionreport/download/environment.yml b/modules/nf-core/fusionreport/download/environment.yml index ae86909d1..ca37d8403 100644 --- a/modules/nf-core/fusionreport/download/environment.yml +++ b/modules/nf-core/fusionreport/download/environment.yml @@ -2,17 +2,17 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fusion-report=4.0.1 - - conda-forge::beautifulsoup4=4.13.4 - - conda-forge::click=8.2.1 - - conda-forge::colorlog=6.9.0 + - bioconda::fusion-report=4.1.0 + - conda-forge::beautifulsoup4=4.14.3 + - conda-forge::click=8.4.0 + - conda-forge::colorlog=6.10.1 - conda-forge::jinja2=3.1.6 - - conda-forge::markupsafe=3.0.2 - - conda-forge::numpy=2.3.0 + - conda-forge::markupsafe=3.0.3 + - conda-forge::numpy=2.4.6 - conda-forge::openpyxl=3.1.5 - - conda-forge::pandas=2.3.0 - - conda-forge::pyyaml=6.0.2 - - conda-forge::requests=2.32.4 - - conda-forge::tabulate=0.9.0 - - conda-forge::tqdm=4.67.1 - - conda-forge::xlrd=2.0.1 + - conda-forge::pandas=3.0.1 + - conda-forge::pyyaml=6.0.3 + - conda-forge::requests=2.34.2 + - conda-forge::tabulate=0.10.0 + - conda-forge::tqdm=4.67.3 + - conda-forge::xlrd=2.0.2 diff --git a/modules/nf-core/fusionreport/download/main.nf b/modules/nf-core/fusionreport/download/main.nf index 3fd7ada4a..db6c134b7 100644 --- a/modules/nf-core/fusionreport/download/main.nf +++ b/modules/nf-core/fusionreport/download/main.nf @@ -3,44 +3,35 @@ process FUSIONREPORT_DOWNLOAD { label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/ed32f46746a5b33a1b5d597cfe2f62d3b1cfa54638f57cadc5d5158d6a4959d2/data' : - 'community.wave.seqera.io/library/fusion-report_beautifulsoup4_click_colorlog_pruned:78488bd99166aa9a'}" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73d08e3edb2f4c51bb65c3b43d751f8ddb4c92f49c45659a4a43a3f5e008f937/data' : + 'community.wave.seqera.io/library/fusion-report_beautifulsoup4_click_colorlog_pruned:5d32bf6f226660f1'}" + + input: + val(meta) output: - tuple val(meta), path("fusion_report_db"), emit: fusionreport_ref - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}"), emit: fusionreport_ref + tuple val("${task.process}"), val('fusion_report'), eval("fusion_report --version |& sed 's/fusion-report //'"), topic: versions, emit: versions_fusionreport when: task.ext.when == null || task.ext.when script: - meta = [id: 'fusion_report_db'] def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" """ - fusion_report download $args ./ - mkdir fusion_report_db - mv *.txt *.log *.db fusion_report_db/ - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fusion_report: \$(fusion_report --version | sed 's/fusion-report //') - END_VERSIONS + fusion_report download ${args} ${prefix} """ stub: - meta = [id: 'fusion_report_db'] + prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir fusion_report_db - touch fusion_report_db/cosmic.db - touch fusion_report_db/fusiongdb2.db - touch fusion_report_db/mitelman.db - touch fusion_report_db/DB-timestamp.txt - touch fusion_report_db/fusion_report.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fusion_report: \$(fusion_report --version | sed 's/fusion-report //') - END_VERSIONS + mkdir ${prefix} + touch ${prefix}/cosmic.db + touch ${prefix}/fusiongdb2.db + touch ${prefix}/mitelman.db + touch ${prefix}/DB-timestamp.txt + touch ${prefix}/fusion_report.log """ } diff --git a/modules/nf-core/fusionreport/download/meta.yml b/modules/nf-core/fusionreport/download/meta.yml index 8922d7549..3da15cb8c 100644 --- a/modules/nf-core/fusionreport/download/meta.yml +++ b/modules/nf-core/fusionreport/download/meta.yml @@ -7,30 +7,50 @@ keywords: - download tools: - fusionreport: - description: Generate an interactive summary report from fusion detection tools. + description: Generate an interactive summary report from fusion detection + tools. homepage: https://github.com/Clinical-Genomics/fusion-report documentation: https://github.com/Clinical-Genomics/fusion-report/blob/master/README.md tool_dev_url: https://github.com/Clinical-Genomics/fusion-report - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" - +input: + - meta: + type: map + description: | + Groovy Map containing database information output: fusionreport_ref: - - meta: - type: string - description: directory containing the genome resource files required for fusioncatcher - pattern: "fusion_report_db" - - fusion_report_db: + type: map + description: | + Groovy Map containing database information + - ${prefix}: type: directory - description: directory containing the genome resource files required for fusioncatcher - pattern: "fusion_report_db" - + description: directory containing the genome resource files required for + fusioncatcher + pattern: "${prefix}" + versions_fusionreport: + - - ${task.process}: + type: string + description: The name of the process + - fusion_report: + type: string + description: The name of the tool + - fusion_report --version |& sed 's/fusion-report //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - fusion_report: + type: string + description: The name of the tool + - fusion_report --version |& sed 's/fusion-report //': + type: eval + description: The expression to obtain the version of the tool authors: - "@praveenraj2018" diff --git a/modules/nf-core/fusionreport/download/tests/main.nf.test b/modules/nf-core/fusionreport/download/tests/main.nf.test index f05728932..f0d0160cc 100644 --- a/modules/nf-core/fusionreport/download/tests/main.nf.test +++ b/modules/nf-core/fusionreport/download/tests/main.nf.test @@ -3,13 +3,14 @@ nextflow_process { name "Test Process FUSIONREPORT_DOWNLOAD" script "../main.nf" process "FUSIONREPORT_DOWNLOAD" + config './nextflow.config' + tag "modules" tag "modules_nfcore" tag "fusionreport" tag "fusionreport/download" test("Download fusionreport databases") { - config './nextflow.config' when { params { @@ -17,7 +18,7 @@ nextflow_process { } process { """ - // This process doesn't have any inputs + input[0] = [id: 'fusion_report_db'] """ } } @@ -25,13 +26,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - path(process.out.fusionreport_ref[0][1]).resolve("fusiongdb2.db"), - path(process.out.fusionreport_ref[0][1]).resolve("mitelman.db"), - path(process.out.fusionreport_ref[0][1]).resolve("DB-timestamp.txt").exists(), - path(process.out.fusionreport_ref[0][1]).resolve("fusion_report.log").exists(), - process.out.versions - ).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["fusionreport_ref"])).match() } ) } } @@ -46,7 +41,7 @@ nextflow_process { } process { """ - // This process doesn't have any inputs + input[0] = [id: 'fusion_report_db'] """ } } @@ -54,8 +49,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/fusionreport/download/tests/main.nf.test.snap b/modules/nf-core/fusionreport/download/tests/main.nf.test.snap index ae2d0bc85..b246f73c8 100644 --- a/modules/nf-core/fusionreport/download/tests/main.nf.test.snap +++ b/modules/nf-core/fusionreport/download/tests/main.nf.test.snap @@ -1,40 +1,33 @@ { "Download fusionreport databases": { - "content": [ - "fusiongdb2.db:md5,9dec75bfc146f56b36e5a84358f9e515", - "mitelman.db:md5,c271894c1cd62ba2735a060411c16dea", - true, - true, - [ - "versions.yml:md5,620c6e01391800a7e7b717d7a3024003" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-07-15T18:56:45.064154384" - }, - "Create stub files": { "content": [ { - "0": [ + "fusionreport_ref": [ [ { "id": "fusion_report_db" }, - [ - "DB-timestamp.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "cosmic.db:md5,d41d8cd98f00b204e9800998ecf8427e", - "fusion_report.log:md5,d41d8cd98f00b204e9800998ecf8427e", - "fusiongdb2.db:md5,d41d8cd98f00b204e9800998ecf8427e", - "mitelman.db:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "fusion_report_db" ] ], - "1": [ - "versions.yml:md5,620c6e01391800a7e7b717d7a3024003" - ], + "versions_fusionreport": [ + [ + "FUSIONREPORT_DOWNLOAD", + "fusion_report", + "4.0.1" + ] + ] + } + ], + "timestamp": "2026-05-27T14:05:13.933196201", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.2" + } + }, + "Create stub files": { + "content": [ + { "fusionreport_ref": [ [ { @@ -49,15 +42,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,620c6e01391800a7e7b717d7a3024003" + "versions_fusionreport": [ + [ + "FUSIONREPORT_DOWNLOAD", + "fusion_report", + "4.0.1" + ] ] } ], + "timestamp": "2026-05-27T14:05:51.666843744", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.4" - }, - "timestamp": "2025-06-27T19:34:10.41756869" + "nf-test": "0.9.5", + "nextflow": "26.04.2" + } } } \ No newline at end of file diff --git a/modules/nf-core/fusionreport/download/tests/nextflow.config b/modules/nf-core/fusionreport/download/tests/nextflow.config index 505233327..ef35395c5 100644 --- a/modules/nf-core/fusionreport/download/tests/nextflow.config +++ b/modules/nf-core/fusionreport/download/tests/nextflow.config @@ -1,5 +1,5 @@ process { withName: 'FUSIONREPORT_DOWNLOAD' { - ext.args = params.module_args + ext.args = params.module_args } } From 490c2ad2b64dc983c1c04ab21555e83f0c5dca5e Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 27 May 2026 15:03:49 +0000 Subject: [PATCH 02/19] Fix versions channel topics after module updates --- subworkflows/local/build_references/main.nf | 1 - workflows/rnafusion.nf | 1 - 2 files changed, 2 deletions(-) diff --git a/subworkflows/local/build_references/main.nf b/subworkflows/local/build_references/main.nf index f2b6d2cf9..2ef9fa439 100644 --- a/subworkflows/local/build_references/main.nf +++ b/subworkflows/local/build_references/main.nf @@ -198,7 +198,6 @@ workflow BUILD_REFERENCES { error('COSMIC username and/or password missing, this is needed to download the fusionreport reference') } FUSIONREPORT_DOWNLOAD() - ch_versions = ch_versions.mix(FUSIONREPORT_DOWNLOAD.out.versions) ch_fusionreport_ref = FUSIONREPORT_DOWNLOAD.out.fusionreport_ref } else { ch_fusionreport_ref = channel.fromPath(params.fusionreport_ref).map { that -> [[id:that.Name], that] } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index b4ff6217f..c4de7c5d3 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -355,7 +355,6 @@ workflow RNAFUSION { params.tools_cutoff ) - ch_versions = ch_versions.mix(FUSIONREPORT_DETECT.out.versions) ch_fusion_list = FUSIONREPORT_DETECT.out.fusion_list ch_fusion_list_filtered = FUSIONREPORT_DETECT.out.fusion_list_filtered ch_fusionreport_report = FUSIONREPORT_DETECT.out.report From cd31f2ad4b936010b0f312f0f173f23723e3d612 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 06:42:21 +0000 Subject: [PATCH 03/19] Fix modules for fusionreport --- modules.json | 4 ++-- modules/nf-core/fusionreport/detect/environment.yml | 2 +- modules/nf-core/fusionreport/detect/main.nf | 4 ++-- modules/nf-core/fusionreport/detect/tests/main.nf.test.snap | 4 ++-- modules/nf-core/fusionreport/download/environment.yml | 2 +- modules/nf-core/fusionreport/download/main.nf | 4 ++-- modules/nf-core/fusionreport/download/tests/main.nf.test.snap | 4 ++-- subworkflows/local/build_references/main.nf | 2 +- 8 files changed, 13 insertions(+), 13 deletions(-) diff --git a/modules.json b/modules.json index 3c9ed8bf6..45c7f3e66 100644 --- a/modules.json +++ b/modules.json @@ -75,12 +75,12 @@ }, "fusionreport/detect": { "branch": "master", - "git_sha": "76dfaba27ac4eacd80cdac5ba28985ee2646b0bd", + "git_sha": "6ed53ffdb0d6be9a34de52b9472693397994e6d0", "installed_by": ["modules"] }, "fusionreport/download": { "branch": "master", - "git_sha": "76dfaba27ac4eacd80cdac5ba28985ee2646b0bd", + "git_sha": "6ed53ffdb0d6be9a34de52b9472693397994e6d0", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { diff --git a/modules/nf-core/fusionreport/detect/environment.yml b/modules/nf-core/fusionreport/detect/environment.yml index d5575fa42..28eaa4895 100644 --- a/modules/nf-core/fusionreport/detect/environment.yml +++ b/modules/nf-core/fusionreport/detect/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fusion-report=4.1.0 + - bioconda::fusion-report=4.1.1 - conda-forge::beautifulsoup4=4.14.3 - conda-forge::click=8.4.0 - conda-forge::colorlog=6.10.1 diff --git a/modules/nf-core/fusionreport/detect/main.nf b/modules/nf-core/fusionreport/detect/main.nf index 9b07af85e..cdd9b28ba 100644 --- a/modules/nf-core/fusionreport/detect/main.nf +++ b/modules/nf-core/fusionreport/detect/main.nf @@ -4,8 +4,8 @@ process FUSIONREPORT_DETECT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73d08e3edb2f4c51bb65c3b43d751f8ddb4c92f49c45659a4a43a3f5e008f937/data' : - 'community.wave.seqera.io/library/fusion-report_beautifulsoup4_click_colorlog_pruned:5d32bf6f226660f1'}" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a4/a41e89223340438d7cebca8af469cef9189d177bb44373b1bcb010c8e441a444/data' : + 'community.wave.seqera.io/library/fusion-report_beautifulsoup4_click_colorlog_pruned:4aeac839f8a4fc86'}" input: tuple val(meta), path(arriba_fusions), path(starfusion_fusions), path(fusioncatcher_fusions) diff --git a/modules/nf-core/fusionreport/detect/tests/main.nf.test.snap b/modules/nf-core/fusionreport/detect/tests/main.nf.test.snap index 3abfd6e21..784eb57b4 100644 --- a/modules/nf-core/fusionreport/detect/tests/main.nf.test.snap +++ b/modules/nf-core/fusionreport/detect/tests/main.nf.test.snap @@ -75,7 +75,7 @@ [ "FUSIONREPORT_DETECT", "fusion_report", - "4.0.1" + "4.1.1" ] ] } @@ -144,7 +144,7 @@ [ "FUSIONREPORT_DETECT", "fusion_report", - "4.0.1" + "4.1.1" ] ] } diff --git a/modules/nf-core/fusionreport/download/environment.yml b/modules/nf-core/fusionreport/download/environment.yml index ca37d8403..317365310 100644 --- a/modules/nf-core/fusionreport/download/environment.yml +++ b/modules/nf-core/fusionreport/download/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fusion-report=4.1.0 + - bioconda::fusion-report=4.1.1 - conda-forge::beautifulsoup4=4.14.3 - conda-forge::click=8.4.0 - conda-forge::colorlog=6.10.1 diff --git a/modules/nf-core/fusionreport/download/main.nf b/modules/nf-core/fusionreport/download/main.nf index db6c134b7..e1e39a6ca 100644 --- a/modules/nf-core/fusionreport/download/main.nf +++ b/modules/nf-core/fusionreport/download/main.nf @@ -4,8 +4,8 @@ process FUSIONREPORT_DOWNLOAD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73d08e3edb2f4c51bb65c3b43d751f8ddb4c92f49c45659a4a43a3f5e008f937/data' : - 'community.wave.seqera.io/library/fusion-report_beautifulsoup4_click_colorlog_pruned:5d32bf6f226660f1'}" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a4/a41e89223340438d7cebca8af469cef9189d177bb44373b1bcb010c8e441a444/data' : + 'community.wave.seqera.io/library/fusion-report_beautifulsoup4_click_colorlog_pruned:4aeac839f8a4fc86'}" input: val(meta) diff --git a/modules/nf-core/fusionreport/download/tests/main.nf.test.snap b/modules/nf-core/fusionreport/download/tests/main.nf.test.snap index b246f73c8..5e5ccd4ac 100644 --- a/modules/nf-core/fusionreport/download/tests/main.nf.test.snap +++ b/modules/nf-core/fusionreport/download/tests/main.nf.test.snap @@ -14,7 +14,7 @@ [ "FUSIONREPORT_DOWNLOAD", "fusion_report", - "4.0.1" + "4.1.1" ] ] } @@ -46,7 +46,7 @@ [ "FUSIONREPORT_DOWNLOAD", "fusion_report", - "4.0.1" + "4.1.1" ] ] } diff --git a/subworkflows/local/build_references/main.nf b/subworkflows/local/build_references/main.nf index 2ef9fa439..bc47c55bd 100644 --- a/subworkflows/local/build_references/main.nf +++ b/subworkflows/local/build_references/main.nf @@ -197,7 +197,7 @@ workflow BUILD_REFERENCES { if (!params.no_cosmic && (!params.cosmic_username || !params.cosmic_passwd)) { error('COSMIC username and/or password missing, this is needed to download the fusionreport reference') } - FUSIONREPORT_DOWNLOAD() + FUSIONREPORT_DOWNLOAD([[id: 'fusionreport']]) ch_fusionreport_ref = FUSIONREPORT_DOWNLOAD.out.fusionreport_ref } else { ch_fusionreport_ref = channel.fromPath(params.fusionreport_ref).map { that -> [[id:that.Name], that] } From 3433349c2a044882e1ae28849c8674e540dc9d0d Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 06:45:07 +0000 Subject: [PATCH 04/19] Add changelog --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7028f5b5e..8a7017485 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v4.1.3dev - [2026-05-28] + +### Added + +### Fixed + +- Fixed issues with FusionReport and COSMIC [#797](https://github.com/nf-core/rnafusion/issues/797) + ## v4.1.2 - [2026-05-20] ### Added From 2cd5fee1d253f1b2b2c8afd0ef221d4d5461f4a5 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 06:50:03 +0000 Subject: [PATCH 05/19] Fix snaps --- tests/test_build.nf.test.snap | 2 +- tests/test_stub.nf.test.snap | 12 ++++++------ tests/test_stub_bam.nf.test.snap | 16 ++++++++-------- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap index 23836cbb7..3d51ed292 100644 --- a/tests/test_build.nf.test.snap +++ b/tests/test_build.nf.test.snap @@ -13,7 +13,7 @@ "ctatsplicing": "0.0.2" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap index 98eb14df8..461536603 100644 --- a/tests/test_stub.nf.test.snap +++ b/tests/test_stub.nf.test.snap @@ -581,10 +581,10 @@ "fusion-inspector": "2.11.5" }, "FUSIONREPORT_DETECT": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" @@ -1211,10 +1211,10 @@ "fusioncatcher": "1.35" }, "FUSIONREPORT_DETECT": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" @@ -1735,10 +1735,10 @@ "fusion-inspector": "2.11.5" }, "FUSIONREPORT_DETECT": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" diff --git a/tests/test_stub_bam.nf.test.snap b/tests/test_stub_bam.nf.test.snap index 2df4f56be..8b609e681 100644 --- a/tests/test_stub_bam.nf.test.snap +++ b/tests/test_stub_bam.nf.test.snap @@ -449,10 +449,10 @@ "fusion-inspector": "2.11.5" }, "FUSIONREPORT_DETECT": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" @@ -1014,10 +1014,10 @@ "fusioncatcher": "1.35" }, "FUSIONREPORT_DETECT": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" @@ -1449,10 +1449,10 @@ "fusion-inspector": "2.11.5" }, "FUSIONREPORT_DETECT": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" @@ -1779,10 +1779,10 @@ "fusion-inspector": "2.11.5" }, "FUSIONREPORT_DETECT": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.0.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" From 0a269458373cfc3d4a518967b15e95eecf4c475e Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 06:57:14 +0000 Subject: [PATCH 06/19] Fix for fusitest --- subworkflows/local/fusioninspector_workflow/tests/main.nf.test | 2 ++ 1 file changed, 2 insertions(+) diff --git a/subworkflows/local/fusioninspector_workflow/tests/main.nf.test b/subworkflows/local/fusioninspector_workflow/tests/main.nf.test index 37034d577..e9148e27f 100644 --- a/subworkflows/local/fusioninspector_workflow/tests/main.nf.test +++ b/subworkflows/local/fusioninspector_workflow/tests/main.nf.test @@ -50,6 +50,8 @@ nextflow_workflow { script "../../../../modules/nf-core/fusionreport/download/main.nf" process { """ + input[0] = [ + [ id:'fusionreport' ] """ } } From 61bae8de155303d159d8977e668b93db50efc80f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 07:03:44 +0000 Subject: [PATCH 07/19] Fix fusion test --- .../local/fusioninspector_workflow/tests/main.nf.test | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/subworkflows/local/fusioninspector_workflow/tests/main.nf.test b/subworkflows/local/fusioninspector_workflow/tests/main.nf.test index e9148e27f..e3045c4ec 100644 --- a/subworkflows/local/fusioninspector_workflow/tests/main.nf.test +++ b/subworkflows/local/fusioninspector_workflow/tests/main.nf.test @@ -52,6 +52,7 @@ nextflow_workflow { """ input[0] = [ [ id:'fusionreport' ] + ] """ } } @@ -159,6 +160,9 @@ nextflow_workflow { script "../../../../modules/nf-core/fusionreport/download/main.nf" process { """ + input[0] = [ + [ id:'fusionreport' ] + ] """ } } From aa353f75529ac15803d8015666fdaa5f297cac99 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 08:43:53 +0000 Subject: [PATCH 08/19] That should do --- modules.json | 2 +- modules/nf-core/fusionreport/download/main.nf | 1 + .../local/fusioninspector_workflow/tests/main.nf.test | 8 ++------ 3 files changed, 4 insertions(+), 7 deletions(-) diff --git a/modules.json b/modules.json index 45c7f3e66..cf27152c1 100644 --- a/modules.json +++ b/modules.json @@ -80,7 +80,7 @@ }, "fusionreport/download": { "branch": "master", - "git_sha": "6ed53ffdb0d6be9a34de52b9472693397994e6d0", + "git_sha": "b871d05e5c8aab73132a41ede89c40910726df74", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { diff --git a/modules/nf-core/fusionreport/download/main.nf b/modules/nf-core/fusionreport/download/main.nf index e1e39a6ca..6dddb7814 100644 --- a/modules/nf-core/fusionreport/download/main.nf +++ b/modules/nf-core/fusionreport/download/main.nf @@ -21,6 +21,7 @@ process FUSIONREPORT_DOWNLOAD { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ + mkdir -p ${prefix} fusion_report download ${args} ${prefix} """ diff --git a/subworkflows/local/fusioninspector_workflow/tests/main.nf.test b/subworkflows/local/fusioninspector_workflow/tests/main.nf.test index e3045c4ec..205d27d69 100644 --- a/subworkflows/local/fusioninspector_workflow/tests/main.nf.test +++ b/subworkflows/local/fusioninspector_workflow/tests/main.nf.test @@ -50,9 +50,7 @@ nextflow_workflow { script "../../../../modules/nf-core/fusionreport/download/main.nf" process { """ - input[0] = [ - [ id:'fusionreport' ] - ] + input[0] = [ id:'fusionreport' ] """ } } @@ -160,9 +158,7 @@ nextflow_workflow { script "../../../../modules/nf-core/fusionreport/download/main.nf" process { """ - input[0] = [ - [ id:'fusionreport' ] - ] + input[0] = [ id:'fusionreport' ] """ } } From 97c083c3a458d74ff727bd442906dbfe222ad9f0 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 09:00:12 +0000 Subject: [PATCH 09/19] Hopefully finding it now ;-) --- subworkflows/local/build_references/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/build_references/main.nf b/subworkflows/local/build_references/main.nf index bc47c55bd..87182fc8b 100644 --- a/subworkflows/local/build_references/main.nf +++ b/subworkflows/local/build_references/main.nf @@ -197,7 +197,7 @@ workflow BUILD_REFERENCES { if (!params.no_cosmic && (!params.cosmic_username || !params.cosmic_passwd)) { error('COSMIC username and/or password missing, this is needed to download the fusionreport reference') } - FUSIONREPORT_DOWNLOAD([[id: 'fusionreport']]) + FUSIONREPORT_DOWNLOAD([id: 'fusionreport']) ch_fusionreport_ref = FUSIONREPORT_DOWNLOAD.out.fusionreport_ref } else { ch_fusionreport_ref = channel.fromPath(params.fusionreport_ref).map { that -> [[id:that.Name], that] } From 0155f258ea5f6275a6e3722315f31cc5deb2e323 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 09:14:55 +0000 Subject: [PATCH 10/19] Fix build snaps --- tests/test_build.nf.test.snap | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap index 3d51ed292..f0411b1a4 100644 --- a/tests/test_build.nf.test.snap +++ b/tests/test_build.nf.test.snap @@ -59,11 +59,10 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report_db", - "references/GRCh38/fusion_report_db/DB-timestamp.txt", - "references/GRCh38/fusion_report_db/fusion_report.log", - "references/GRCh38/fusion_report_db/fusiongdb2.db", - "references/GRCh38/fusion_report_db/mitelman.db", + "references/GRCh38/fusion_report", + "references/GRCh38/fusion_report/DB-timestamp.txt", + "references/GRCh38/fusion_report/fusiongdb2.db", + "references/GRCh38/fusion_report/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/minigenome.dict", @@ -193,7 +192,9 @@ [ "minigenome.gtf.bed:md5,d41d8cd98f00b204e9800998ecf8427e", "minigenome.gtf_rrna.gtf.gz:md5,fb03ec66f68bc4becc71c299ed38b62d", - "fusion_report.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "DB-timestamp.txt:md5,4440427bdb435a0becd8ceb94dc8a42d", + "fusiongdb2.db:md5,f249e3759b1556932f472919384d88be", + "mitelman.db:md5,0de51547910cd60fde4d262924714706", "minigenome.dict:md5,f2dfb8df1d1f860050fc0dba1399fd9e", "minigenome.fa.fai:md5,e3f74a27219b33ae80fd5de5cbeaf32b", "minigenome.gtf.fasta:md5,349d42b5dbd73e163cdbad3453d8cd3a", From 08c5ed2da3bbbd4a3b8ba17dd57dbe858ab807ad Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 09:18:30 +0000 Subject: [PATCH 11/19] Snap it --- tests/test_stub.nf.test.snap | 33 +++++++++++------------- tests/test_stub_bam.nf.test.snap | 44 +++++++++++++++----------------- 2 files changed, 35 insertions(+), 42 deletions(-) diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap index 461536603..703e12206 100644 --- a/tests/test_stub.nf.test.snap +++ b/tests/test_stub.nf.test.snap @@ -695,12 +695,11 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report_db", - "references/GRCh38/fusion_report_db/DB-timestamp.txt", - "references/GRCh38/fusion_report_db/cosmic.db", - "references/GRCh38/fusion_report_db/fusion_report.log", - "references/GRCh38/fusion_report_db/fusiongdb2.db", - "references/GRCh38/fusion_report_db/mitelman.db", + "references/GRCh38/fusion_report", + "references/GRCh38/fusion_report/DB-timestamp.txt", + "references/GRCh38/fusion_report/cosmic.db", + "references/GRCh38/fusion_report/fusiongdb2.db", + "references/GRCh38/fusion_report/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1319,12 +1318,11 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report_db", - "references/GRCh38/fusion_report_db/DB-timestamp.txt", - "references/GRCh38/fusion_report_db/cosmic.db", - "references/GRCh38/fusion_report_db/fusion_report.log", - "references/GRCh38/fusion_report_db/fusiongdb2.db", - "references/GRCh38/fusion_report_db/mitelman.db", + "references/GRCh38/fusion_report", + "references/GRCh38/fusion_report/DB-timestamp.txt", + "references/GRCh38/fusion_report/cosmic.db", + "references/GRCh38/fusion_report/fusiongdb2.db", + "references/GRCh38/fusion_report/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1892,12 +1890,11 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report_db", - "references/GRCh38/fusion_report_db/DB-timestamp.txt", - "references/GRCh38/fusion_report_db/cosmic.db", - "references/GRCh38/fusion_report_db/fusion_report.log", - "references/GRCh38/fusion_report_db/fusiongdb2.db", - "references/GRCh38/fusion_report_db/mitelman.db", + "references/GRCh38/fusion_report", + "references/GRCh38/fusion_report/DB-timestamp.txt", + "references/GRCh38/fusion_report/cosmic.db", + "references/GRCh38/fusion_report/fusiongdb2.db", + "references/GRCh38/fusion_report/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", diff --git a/tests/test_stub_bam.nf.test.snap b/tests/test_stub_bam.nf.test.snap index 8b609e681..44b795ee1 100644 --- a/tests/test_stub_bam.nf.test.snap +++ b/tests/test_stub_bam.nf.test.snap @@ -543,12 +543,11 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report_db", - "references/GRCh38/fusion_report_db/DB-timestamp.txt", - "references/GRCh38/fusion_report_db/cosmic.db", - "references/GRCh38/fusion_report_db/fusion_report.log", - "references/GRCh38/fusion_report_db/fusiongdb2.db", - "references/GRCh38/fusion_report_db/mitelman.db", + "references/GRCh38/fusion_report", + "references/GRCh38/fusion_report/DB-timestamp.txt", + "references/GRCh38/fusion_report/cosmic.db", + "references/GRCh38/fusion_report/fusiongdb2.db", + "references/GRCh38/fusion_report/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1102,12 +1101,11 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report_db", - "references/GRCh38/fusion_report_db/DB-timestamp.txt", - "references/GRCh38/fusion_report_db/cosmic.db", - "references/GRCh38/fusion_report_db/fusion_report.log", - "references/GRCh38/fusion_report_db/fusiongdb2.db", - "references/GRCh38/fusion_report_db/mitelman.db", + "references/GRCh38/fusion_report", + "references/GRCh38/fusion_report/DB-timestamp.txt", + "references/GRCh38/fusion_report/cosmic.db", + "references/GRCh38/fusion_report/fusiongdb2.db", + "references/GRCh38/fusion_report/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1586,12 +1584,11 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report_db", - "references/GRCh38/fusion_report_db/DB-timestamp.txt", - "references/GRCh38/fusion_report_db/cosmic.db", - "references/GRCh38/fusion_report_db/fusion_report.log", - "references/GRCh38/fusion_report_db/fusiongdb2.db", - "references/GRCh38/fusion_report_db/mitelman.db", + "references/GRCh38/fusion_report", + "references/GRCh38/fusion_report/DB-timestamp.txt", + "references/GRCh38/fusion_report/cosmic.db", + "references/GRCh38/fusion_report/fusiongdb2.db", + "references/GRCh38/fusion_report/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1919,12 +1916,11 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report_db", - "references/GRCh38/fusion_report_db/DB-timestamp.txt", - "references/GRCh38/fusion_report_db/cosmic.db", - "references/GRCh38/fusion_report_db/fusion_report.log", - "references/GRCh38/fusion_report_db/fusiongdb2.db", - "references/GRCh38/fusion_report_db/mitelman.db", + "references/GRCh38/fusion_report", + "references/GRCh38/fusion_report/DB-timestamp.txt", + "references/GRCh38/fusion_report/cosmic.db", + "references/GRCh38/fusion_report/fusiongdb2.db", + "references/GRCh38/fusion_report/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", From f28eff7aa10eff08ba10382ce2f5db0cc8f95571 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 09:35:24 +0000 Subject: [PATCH 12/19] BUmp versions everywhere --- .nf-core.yml | 2 +- assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 28 ++++++++++++++-------------- tests/test_build.nf.test.snap | 2 +- tests/test_stub.nf.test.snap | 22 +++++++++++----------- tests/test_stub_bam.nf.test.snap | 22 +++++++++++----------- 7 files changed, 40 insertions(+), 40 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 8fa8266cf..5a960caaa 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -16,4 +16,4 @@ template: name: rnafusion org: nf-core outdir: . - version: 4.1.2 + version: 4.1.3dev diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 4c276219b..bbe68fc4a 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: nf-core-rnafusion-methods-description: diff --git a/nextflow.config b/nextflow.config index 8b7408b03..78809a9e8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -372,7 +372,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '4.1.2' + version = '4.1.3dev' doi = '10.5281/zenodo.17641566' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 8efd3e8e9..eb15cc704 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2026-05-20T09:51:42+00:00", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-05-28T09:25:34+00:00", "description": "

\n \n \n \"nf-core/rnafusion\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/rnafusion)\n[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.2565517-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.2565517)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnafusion)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnafusion-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnafusion)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from fusion callers tools (STAR-Fusion, arriba and FusionCatcher) are created, and are also aggregated, most notably in a pdf visualisation document, a vcf data collection file, and html and tsv reports. In parallel StringTie and CTAT-Splicing collect additional information on splicing events.\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results).\n\nIn rnafusion the full-sized test includes reference building and fusion detection. The test dataset is taken from [here](https://github.com/nf-core/test-datasets/tree/rnafusion/testdata/human).\n\n## Pipeline summary\n\n![nf-core/rnafusion metro map](docs/images/nf-core-rnafusion_metro_map.png)\n\n### References\n\nThe references for the pipeline can be downloaded from the nf-core AWS megatests S3 bucket using the following command for the [AWS CLI tool](https://github.com/aws/aws-cli):\n\n```bash\naws --no-sign-request s3 sync s3://nf-core-awsmegatests/rnafusion/references/ \n```\n\nThe path to the downloaded references can then be provided to the pipeline with the `--genomes_base` parameter.\n\n⚠️ **Please note that the references are large and can take a long time to download, so it is recommended to download them once and use them for all future runs of the pipeline.**\n\nThe pipeline is also able to build the references in case files from a specific gencode version are missing (Note: only gencode 46 is available for fusioncatcher). This is done automatically when the expected references are not found and these files will be automatically published in the directory specified by the `--genomes_base` parameter. Use the `--references_only` parameter to trigger the reference building workflow only, without running the rest of the pipeline.\n\n1. Download gencode fasta and gtf files\n2. Download the HGNC nomenclature file\n3. Create files needed for QC (Sequence Dictionary and RRNA intervals)\n4. Convert the gtf file to a refflat file\n5. Create the [Salmon](https://salmon.readthedocs.io/en/latest/) index\n6. Create [STAR](https://github.com/alexdobin/STAR) index\n7. Build [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) and [CTAT-SPLICING](https://github.com/TrinityCTAT/CTAT-SPLICING) references\n8. Download [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) DBs\n\n> [!WARNING]\n> References for Fusioncatcher and Arriba cannot be automatically created by the pipeline and should be downloaded from the S3 bucket or another source. See the [References](#references) section for more information.\n\n#### Main workflow\n\n1. Input samplesheet check\n2. Reads quality control ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Optional trimming with [fastp](https://github.com/OpenGene/fastp)\n4. Align FASTQs to BAM with [STAR](https://github.com/alexdobin/STAR)\n5. Run fusion detection with [Arriba](https://github.com/suhrig/arriba)\n6. Run fusion detection with [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion)\n 7a. Optional trimming of 3' end with [fastp](https://github.com/OpenGene/fastp) to feed into fusioncatcher (other tools not affected)\n 7b. Run fusion detection with [FusionCatcher](https://github.com/ndaniel/fusioncatcher)\n7. Run transcript assembly and quantification with [StringTie](https://ccb.jhu.edu/software/stringtie/)\n8. Run cancer splicing aberrations detection with [CTAT-SPLICING](https://github.com/TrinityCTAT/CTAT-SPLICING)\n9. Merge all fusions detected by the selected tools with [Fusion-report](https://github.com/Clinical-Genomics/fusion-report)\n10. Post-processing and analysis of data\n - [FusionInspector](https://github.com/FusionInspector/FusionInspector)\n - Summarize information into a VCF file\n - [Arriba](https://github.com/suhrig/arriba) visualisation\n - Collect metrics ([`picard CollectRnaSeqMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard-)), [`picard CollectInsertSizeMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037055772-CollectInsertSizeMetrics-Picard-) and ([`GATK MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-))\n11. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n12. Compress bam files to cram with [samtools view](http://www.htslib.org/)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nAs the reference building is computationally heavy (> 24h on HPC), we had to use dummy reference files in the test profile. Therefore, it is recommended to run the test profile with the `-stub` option.\n\n```bash\nnextflow run nf-core/rnafusion \\\n -profile test, \\\n --outdir \\\n -stub\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](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n> **Notes:**\n>\n> - Conda is not currently supported; run with singularity or docker.\n> - Paths need to be absolute.\n> - GRCh38 is the only supported reference.\n> - Single-end reads are to be used as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp.\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnafusion/usage) and the [parameter documentation](https://nf-co.re/rnafusion/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnafusion/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnafusion/output).\n\n## Credits\n\nnf-core/rnafusion was written by Martin Proks ([@matq007](https://github.com/matq007)), Maxime Garcia ([@maxulysse](https://github.com/maxulysse)) and Annick Renevey ([@rannick](https://github.com/rannick))\n\n## We thank the following people for their help in the development of this pipeline\n\n- [Phil Ewels](https://github.com/ewels)\n- [Rickard Hammarén](https://github.com/Hammarn)\n- [Alexander Peltzer](https://github.com/apeltzer)\n- [Praveen Raj](https://github.com/praveenraj2018)\n- [Anabella Trigila](https://github.com/atrigila)\n- [Nicolas Vannieuwkerke](https://github.com/nvnieuwk)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnafusion` channel](https://nfcore.slack.com/channels/rnafusion) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/rnafusion for your analysis, please cite it using the following doi: [10.5281/zenodo.3946477](https://doi.org/10.5281/zenodo.3946477)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](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](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -108,7 +108,7 @@ }, "mentions": [ { - "@id": "#1429fcfc-1ec1-46c5-a62e-70e97cf33a65" + "@id": "#381cc113-2e23-45dc-85ca-52bf6fe6fce9" } ], "name": "nf-core/rnafusion" @@ -148,17 +148,17 @@ ], "contributor": [ { - "@id": "#9bc3bf47-ed5c-4c58-9f16-2b13aca19964" + "@id": "#fb14b5cd-3ed7-488b-9707-00a2ee8d2124" }, { "@id": "https://orcid.org/0009-0003-5619-1555" }, { - "@id": "#e7f5e3cc-2b4a-4166-889f-e22a23249b85" + "@id": "#9594f5b3-6275-4d07-a50a-252010cf55e3" } ], "dateCreated": "", - "dateModified": "2026-05-20T09:51:42Z", + "dateModified": "2026-05-28T09:25:34Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "image": { "@id": "docs/images/nf-core-rnafusion_metro_map.png" @@ -180,7 +180,7 @@ "@id": "https://orcid.org/0000-0001-7411-6063" }, { - "@id": "#9bc3bf47-ed5c-4c58-9f16-2b13aca19964" + "@id": "#fb14b5cd-3ed7-488b-9707-00a2ee8d2124" }, { "@id": "https://orcid.org/0009-0003-5619-1555" @@ -197,10 +197,10 @@ }, "url": [ "https://github.com/nf-core/rnafusion", - "https://nf-co.re/rnafusion/4.1.2/" + "https://nf-co.re/rnafusion/dev/" ], "version": [ - "4.1.2" + "4.1.3dev" ] }, { @@ -224,11 +224,11 @@ "name": "Workflow diagram" }, { - "@id": "#1429fcfc-1ec1-46c5-a62e-70e97cf33a65", + "@id": "#381cc113-2e23-45dc-85ca-52bf6fe6fce9", "@type": "TestSuite", "instance": [ { - "@id": "#fc1d8484-5bef-4030-9514-052ffc0d4df2" + "@id": "#6bda36dc-bb78-4650-8253-ed1fe6ccae09" } ], "mainEntity": { @@ -237,7 +237,7 @@ "name": "Test suite for nf-core/rnafusion" }, { - "@id": "#fc1d8484-5bef-4030-9514-052ffc0d4df2", + "@id": "#6bda36dc-bb78-4650-8253-ed1fe6ccae09", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/rnafusion", "resource": "repos/nf-core/rnafusion/actions/workflows/nf-test.yml", @@ -399,7 +399,7 @@ "url": "https://github.com/maxulysse" }, { - "@id": "#9bc3bf47-ed5c-4c58-9f16-2b13aca19964", + "@id": "#fb14b5cd-3ed7-488b-9707-00a2ee8d2124", "@type": "Person", "affiliation": "ZS Associates", "email": "18577080+atrigila@users.noreply.github.com", @@ -415,7 +415,7 @@ "url": "https://github.com/nvnieuwk" }, { - "@id": "#e7f5e3cc-2b4a-4166-889f-e22a23249b85", + "@id": "#9594f5b3-6275-4d07-a50a-252010cf55e3", "@type": "Person", "affiliation": "ZS Associates", "email": "155591053+delfiterradas@users.noreply.github.com", diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap index f0411b1a4..2e70dff01 100644 --- a/tests/test_build.nf.test.snap +++ b/tests/test_build.nf.test.snap @@ -47,7 +47,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap index 703e12206..9cde62ce3 100644 --- a/tests/test_stub.nf.test.snap +++ b/tests/test_stub.nf.test.snap @@ -71,7 +71,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -309,7 +309,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -470,7 +470,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -645,7 +645,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -876,7 +876,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1009,7 +1009,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1274,7 +1274,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1497,7 +1497,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1575,7 +1575,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1651,7 +1651,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1815,7 +1815,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ diff --git a/tests/test_stub_bam.nf.test.snap b/tests/test_stub_bam.nf.test.snap index 44b795ee1..949f175e8 100644 --- a/tests/test_stub_bam.nf.test.snap +++ b/tests/test_stub_bam.nf.test.snap @@ -51,7 +51,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -244,7 +244,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -363,7 +363,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -493,7 +493,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -712,7 +712,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -834,7 +834,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1057,7 +1057,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1265,7 +1265,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1362,7 +1362,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1509,7 +1509,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ @@ -1841,7 +1841,7 @@ "ucsc": 447 }, "Workflow": { - "nf-core/rnafusion": "v4.1.2" + "nf-core/rnafusion": "v4.1.3dev" } }, [ From 36abc6f05dfff3f6c90a0f659b85121125896354 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 09:41:36 +0000 Subject: [PATCH 13/19] Hopefully last fixes for snaps --- tests/test_build.nf.test.snap | 11 ++++---- tests/test_stub_bam.nf.test.snap | 43 +++++++++++++++++--------------- 2 files changed, 28 insertions(+), 26 deletions(-) diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap index 2e70dff01..8ddf6ed26 100644 --- a/tests/test_build.nf.test.snap +++ b/tests/test_build.nf.test.snap @@ -13,7 +13,7 @@ "ctatsplicing": "0.0.2" }, "FUSIONREPORT_DOWNLOAD": { - "fusion_report": "4.1.1" + "fusionreport": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" @@ -59,10 +59,10 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report", - "references/GRCh38/fusion_report/DB-timestamp.txt", - "references/GRCh38/fusion_report/fusiongdb2.db", - "references/GRCh38/fusion_report/mitelman.db", + "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/minigenome.dict", @@ -192,7 +192,6 @@ [ "minigenome.gtf.bed:md5,d41d8cd98f00b204e9800998ecf8427e", "minigenome.gtf_rrna.gtf.gz:md5,fb03ec66f68bc4becc71c299ed38b62d", - "DB-timestamp.txt:md5,4440427bdb435a0becd8ceb94dc8a42d", "fusiongdb2.db:md5,f249e3759b1556932f472919384d88be", "mitelman.db:md5,0de51547910cd60fde4d262924714706", "minigenome.dict:md5,f2dfb8df1d1f860050fc0dba1399fd9e", diff --git a/tests/test_stub_bam.nf.test.snap b/tests/test_stub_bam.nf.test.snap index 949f175e8..abf8b49d6 100644 --- a/tests/test_stub_bam.nf.test.snap +++ b/tests/test_stub_bam.nf.test.snap @@ -543,11 +543,12 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report", - "references/GRCh38/fusion_report/DB-timestamp.txt", - "references/GRCh38/fusion_report/cosmic.db", - "references/GRCh38/fusion_report/fusiongdb2.db", - "references/GRCh38/fusion_report/mitelman.db", + "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/cosmic.db", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1101,11 +1102,12 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report", - "references/GRCh38/fusion_report/DB-timestamp.txt", - "references/GRCh38/fusion_report/cosmic.db", - "references/GRCh38/fusion_report/fusiongdb2.db", - "references/GRCh38/fusion_report/mitelman.db", + "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/cosmic.db", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1584,11 +1586,12 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report", - "references/GRCh38/fusion_report/DB-timestamp.txt", - "references/GRCh38/fusion_report/cosmic.db", - "references/GRCh38/fusion_report/fusiongdb2.db", - "references/GRCh38/fusion_report/mitelman.db", + "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/cosmic.db", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1916,11 +1919,11 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report", - "references/GRCh38/fusion_report/DB-timestamp.txt", - "references/GRCh38/fusion_report/cosmic.db", - "references/GRCh38/fusion_report/fusiongdb2.db", - "references/GRCh38/fusion_report/mitelman.db", + "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/cosmic.db", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", From c6cd8c135ed21b8476d72de6e0a2c6d911556726 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 09:55:37 +0000 Subject: [PATCH 14/19] Adjust ignore patterns for timestamped files --- tests/.nftignore | 6 +++--- tests/test_build.nf.test.snap | 7 +------ tests/test_stub_bam.nf.test.snap | 16 ---------------- 3 files changed, 4 insertions(+), 25 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 6999cb967..929a691f2 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -12,9 +12,9 @@ fastqc/*_fastqc.{html,zip} pipeline_info/*.{html,json,txt,yml} references/GRCh38/hgnc/HGNC-DB-timestamp.txt references/GRCh38/hgnc/hgnc_complete_set.txt -references/GRCh38/fusion_report_db/DB-timestamp.txt -references/GRCh38/fusion_report_db/fusiongdb2.db -references/GRCh38/fusion_report_db/mitelman.db +references/GRCh38/fusion_report/DB-timestamp.txt +references/GRCh38/fusion_report/fusiongdb2.db +references/GRCh38/fusion_report/mitelman.db references/GRCh38/gencode_v*/salmon/ctable.bin references/GRCh38/gencode_v*/salmon/pos.bin references/GRCh38/gencode_v*/salmon/pre_indexing.log diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap index 8ddf6ed26..0cb7a68de 100644 --- a/tests/test_build.nf.test.snap +++ b/tests/test_build.nf.test.snap @@ -13,7 +13,7 @@ "ctatsplicing": "0.0.2" }, "FUSIONREPORT_DOWNLOAD": { - "fusionreport": "4.1.1" + "fusion_report": "4.1.1" }, "GATK4_BEDTOINTERVALLIST": { "gatk4": "4.6.1.0" @@ -60,9 +60,6 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", - "references/GRCh38/fusionreport/DB-timestamp.txt", - "references/GRCh38/fusionreport/fusiongdb2.db", - "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/minigenome.dict", @@ -192,8 +189,6 @@ [ "minigenome.gtf.bed:md5,d41d8cd98f00b204e9800998ecf8427e", "minigenome.gtf_rrna.gtf.gz:md5,fb03ec66f68bc4becc71c299ed38b62d", - "fusiongdb2.db:md5,f249e3759b1556932f472919384d88be", - "mitelman.db:md5,0de51547910cd60fde4d262924714706", "minigenome.dict:md5,f2dfb8df1d1f860050fc0dba1399fd9e", "minigenome.fa.fai:md5,e3f74a27219b33ae80fd5de5cbeaf32b", "minigenome.gtf.fasta:md5,349d42b5dbd73e163cdbad3453d8cd3a", diff --git a/tests/test_stub_bam.nf.test.snap b/tests/test_stub_bam.nf.test.snap index abf8b49d6..7077ca1bf 100644 --- a/tests/test_stub_bam.nf.test.snap +++ b/tests/test_stub_bam.nf.test.snap @@ -544,11 +544,7 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", - "references/GRCh38/fusionreport/DB-timestamp.txt", "references/GRCh38/fusionreport/fusion_report.log", - "references/GRCh38/fusionreport/cosmic.db", - "references/GRCh38/fusionreport/fusiongdb2.db", - "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1103,11 +1099,7 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", - "references/GRCh38/fusionreport/DB-timestamp.txt", "references/GRCh38/fusionreport/fusion_report.log", - "references/GRCh38/fusionreport/cosmic.db", - "references/GRCh38/fusionreport/fusiongdb2.db", - "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1587,11 +1579,7 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", - "references/GRCh38/fusionreport/DB-timestamp.txt", "references/GRCh38/fusionreport/fusion_report.log", - "references/GRCh38/fusionreport/cosmic.db", - "references/GRCh38/fusionreport/fusiongdb2.db", - "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1920,10 +1908,6 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", - "references/GRCh38/fusionreport/DB-timestamp.txt", - "references/GRCh38/fusionreport/cosmic.db", - "references/GRCh38/fusionreport/fusiongdb2.db", - "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", From 32a7475b121831dfd74e27a3cb86040f02a43517 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 09:56:31 +0000 Subject: [PATCH 15/19] Different pattern --- tests/.nftignore | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 929a691f2..d691c20a3 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -12,9 +12,9 @@ fastqc/*_fastqc.{html,zip} pipeline_info/*.{html,json,txt,yml} references/GRCh38/hgnc/HGNC-DB-timestamp.txt references/GRCh38/hgnc/hgnc_complete_set.txt -references/GRCh38/fusion_report/DB-timestamp.txt -references/GRCh38/fusion_report/fusiongdb2.db -references/GRCh38/fusion_report/mitelman.db +references/GRCh38/fusionreport/DB-timestamp.txt +references/GRCh38/fusionreport/fusiongdb2.db +references/GRCh38/fusionreport/mitelman.db references/GRCh38/gencode_v*/salmon/ctable.bin references/GRCh38/gencode_v*/salmon/pos.bin references/GRCh38/gencode_v*/salmon/pre_indexing.log From b4321aafc1cb91b4d38b1edc01d971d2fda16fe5 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 11:06:37 +0000 Subject: [PATCH 16/19] Lets see --- tests/.nftignore | 1 + tests/test_stub.nf.test.snap | 18 +++--------------- 2 files changed, 4 insertions(+), 15 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index d691c20a3..040a40748 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -14,6 +14,7 @@ references/GRCh38/hgnc/HGNC-DB-timestamp.txt references/GRCh38/hgnc/hgnc_complete_set.txt references/GRCh38/fusionreport/DB-timestamp.txt references/GRCh38/fusionreport/fusiongdb2.db +references/GRCh38/fusionreport/cosmic.db references/GRCh38/fusionreport/mitelman.db references/GRCh38/gencode_v*/salmon/ctable.bin references/GRCh38/gencode_v*/salmon/pos.bin diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap index 9cde62ce3..b103f3396 100644 --- a/tests/test_stub.nf.test.snap +++ b/tests/test_stub.nf.test.snap @@ -695,11 +695,7 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report", - "references/GRCh38/fusion_report/DB-timestamp.txt", - "references/GRCh38/fusion_report/cosmic.db", - "references/GRCh38/fusion_report/fusiongdb2.db", - "references/GRCh38/fusion_report/mitelman.db", + "references/GRCh38/fusionreport", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1318,11 +1314,7 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report", - "references/GRCh38/fusion_report/DB-timestamp.txt", - "references/GRCh38/fusion_report/cosmic.db", - "references/GRCh38/fusion_report/fusiongdb2.db", - "references/GRCh38/fusion_report/mitelman.db", + "references/GRCh38/fusionreport", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1890,11 +1882,7 @@ "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml", "references", "references/GRCh38", - "references/GRCh38/fusion_report", - "references/GRCh38/fusion_report/DB-timestamp.txt", - "references/GRCh38/fusion_report/cosmic.db", - "references/GRCh38/fusion_report/fusiongdb2.db", - "references/GRCh38/fusion_report/mitelman.db", + "references/GRCh38/fusionreport", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", From 769f4527b00e685f06ea0ca34728ceeea8254688 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 11:34:29 +0000 Subject: [PATCH 17/19] Fix tests --- tests/test_build.nf.test.snap | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap index 0cb7a68de..f0dbdf807 100644 --- a/tests/test_build.nf.test.snap +++ b/tests/test_build.nf.test.snap @@ -60,6 +60,9 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/minigenome.dict", @@ -277,10 +280,10 @@ "trans.blast.dat.gz:md5,85ba5ea96c566f751ad83a3e4b8ab128" ] ], - "timestamp": "2026-05-08T22:13:25.423950839", + "timestamp": "2026-05-28T11:31:31.557285215", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.2" } } -} +} \ No newline at end of file From c2dcd1ccb96c0c2ac8332dd62781c5da679c528f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 12:54:36 +0000 Subject: [PATCH 18/19] Fixed stub tests --- tests/test_stub.nf.test.snap | 29 ++++++++++++++++++++++------- 1 file changed, 22 insertions(+), 7 deletions(-) diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap index b103f3396..afb78fcc6 100644 --- a/tests/test_stub.nf.test.snap +++ b/tests/test_stub.nf.test.snap @@ -696,6 +696,11 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/cosmic.db", + "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -828,10 +833,10 @@ "star/testXd.out.bam" ] ], - "timestamp": "2026-05-08T16:45:16.799996263", + "timestamp": "2026-05-28T12:51:09.690773619", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.2" } }, "stub test salmon": { @@ -1315,6 +1320,11 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/cosmic.db", + "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1448,10 +1458,10 @@ "starfusion/test.starfusion.fusion_predictions.tsv" ] ], - "timestamp": "2026-05-08T16:41:58.814907158", + "timestamp": "2026-05-28T12:49:47.138995156", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.2" } }, "stub test fastp": { @@ -1883,6 +1893,11 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/cosmic.db", + "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -2051,10 +2066,10 @@ "stringtie/test.transcripts.gtf" ] ], - "timestamp": "2026-05-08T16:33:02.735330651", + "timestamp": "2026-05-28T12:46:12.232737413", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.2" } } -} +} \ No newline at end of file From f7b8cd981d7b990876be7bab2e7332e8219af739 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 28 May 2026 13:16:26 +0000 Subject: [PATCH 19/19] Fix last stub tests --- tests/test_stub_bam.nf.test.snap | 35 ++++++++++++++++++++++++-------- 1 file changed, 26 insertions(+), 9 deletions(-) diff --git a/tests/test_stub_bam.nf.test.snap b/tests/test_stub_bam.nf.test.snap index 7077ca1bf..03d30999c 100644 --- a/tests/test_stub_bam.nf.test.snap +++ b/tests/test_stub_bam.nf.test.snap @@ -544,7 +544,11 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/cosmic.db", "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -655,10 +659,10 @@ "star/test.Aligned.sortedByCoord.out.bam.bai" ] ], - "timestamp": "2026-05-08T16:28:13.66983016", + "timestamp": "2026-05-28T13:14:08.761052855", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.2" } }, "stub test salmon": { @@ -1099,7 +1103,11 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/cosmic.db", "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1208,10 +1216,10 @@ "starfusion/test.starfusion.fusion_predictions.tsv" ] ], - "timestamp": "2026-05-08T16:25:06.562473541", + "timestamp": "2026-05-28T13:12:37.307869713", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.2" } }, "stub test fastp": { @@ -1579,7 +1587,11 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/cosmic.db", "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -1726,10 +1738,10 @@ "stringtie/test.transcripts.gtf" ] ], - "timestamp": "2026-05-08T16:18:58.733461494", + "timestamp": "2026-05-28T13:08:58.515306208", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.2" } }, "default no fastqs provided": { @@ -1908,6 +1920,11 @@ "references", "references/GRCh38", "references/GRCh38/fusionreport", + "references/GRCh38/fusionreport/DB-timestamp.txt", + "references/GRCh38/fusionreport/cosmic.db", + "references/GRCh38/fusionreport/fusion_report.log", + "references/GRCh38/fusionreport/fusiongdb2.db", + "references/GRCh38/fusionreport/mitelman.db", "references/GRCh38/gencode_v46", "references/GRCh38/gencode_v46/gencode", "references/GRCh38/gencode_v46/gencode/Homo_sapiens.GRCh38.46.gtf", @@ -2059,10 +2076,10 @@ "stringtie/test.transcripts.gtf" ] ], - "timestamp": "2026-05-08T16:29:18.231193476", + "timestamp": "2026-05-28T13:14:52.675623227", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.2" } } -} +} \ No newline at end of file