From d838e25146034dfd0b2ebd6586ac833299f2c677 Mon Sep 17 00:00:00 2001 From: ra25wog Date: Thu, 11 Dec 2025 11:36:04 +0100 Subject: [PATCH 01/13] update yaml --- modules/nf-core/modkit/pileup/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/modkit/pileup/environment.yml b/modules/nf-core/modkit/pileup/environment.yml index c7c61cdfe973..67c67438a94d 100644 --- a/modules/nf-core/modkit/pileup/environment.yml +++ b/modules/nf-core/modkit/pileup/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - ont-modkit=0.5.0 + - ont-modkit=0.6.0 From 350ff3da1b0cb185701a0f6633ac043fcbbe79bc Mon Sep 17 00:00:00 2001 From: ra25wog Date: Thu, 11 Dec 2025 11:36:32 +0100 Subject: [PATCH 02/13] update main.nf --- modules/nf-core/modkit/pileup/main.nf | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/modkit/pileup/main.nf b/modules/nf-core/modkit/pileup/main.nf index a3ef3bf14607..279aed622de6 100644 --- a/modules/nf-core/modkit/pileup/main.nf +++ b/modules/nf-core/modkit/pileup/main.nf @@ -4,8 +4,8 @@ process MODKIT_PILEUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ont-modkit:0.5.0--hcdda2d0_2': - 'biocontainers/ont-modkit:0.5.0--hcdda2d0_2' }" + 'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.0--hcdda2d0_0': + 'biocontainers/ont-modkit:0.6.0--hcdda2d0_0' }" input: tuple val(meta), path(bam), path(bai) @@ -13,8 +13,7 @@ process MODKIT_PILEUP { tuple val(meta3), path(bed) output: - tuple val(meta), path("*.bed") , emit: bed , optional: true - tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true + tuple val(meta), path("*.bed.gz") , emit: bedgz , optional: true tuple val(meta), path("*.log") , emit: log , optional: true path "versions.yml" , emit: versions @@ -31,6 +30,8 @@ process MODKIT_PILEUP { modkit \\ pileup \\ $args \\ + --bgzf \\ + --bgzf-threads ${task.cpus} \\ --threads ${task.cpus} \\ --prefix ${prefix} \\ $reference \\ From 3240588ab4f1eaaf52004d886e73dfa38002f3a9 Mon Sep 17 00:00:00 2001 From: ra25wog Date: Thu, 11 Dec 2025 11:37:03 +0100 Subject: [PATCH 03/13] modified test runs --- .../nf-core/modkit/pileup/tests/main.nf.test | 92 +--- .../modkit/pileup/tests/main.nf.test.snap | 480 ++++-------------- ...tional.config => nextflow.5mC_5hmC.config} | 2 +- .../tests/nextflow.phased_5mC_5hmC.config | 5 + .../tests/nextflow.traditional_hp.config | 5 - .../nextflow.traditional_hp_bedgraph.config | 5 - 6 files changed, 110 insertions(+), 479 deletions(-) rename modules/nf-core/modkit/pileup/tests/{nextflow.traditional.config => nextflow.5mC_5hmC.config} (51%) create mode 100644 modules/nf-core/modkit/pileup/tests/nextflow.phased_5mC_5hmC.config delete mode 100644 modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp.config delete mode 100644 modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp_bedgraph.config diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test b/modules/nf-core/modkit/pileup/tests/main.nf.test index 030d28ba1d1f..f49f7cbe9df1 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test @@ -64,38 +64,7 @@ nextflow_process { test("[bam, bai], [fasta, fai], bed") { - when { - process { - """ - input[0] = [ - [ id: 'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true) - ] - input[1] = [ - [ id: 'test_ref' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - input[2] = Channel.of('chr22\t0\t1000') - .collectFile(name: 'chr22.bed', newLine: true) - .map { file -> [ [ id:'chr22' ], file ] } - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - test("[bam, bai], [fasta, fai], bed - traditional") { - - config "./nextflow.traditional.config" + config "./nextflow.5mC_5hmC.config" when { process { @@ -126,9 +95,9 @@ nextflow_process { } - test("[bam, bai], [fasta, fai], bed - traditional, HP") { + test("[bam, bai], [fasta, fai], [], phased") { - config "./nextflow.traditional_hp.config" + config "./nextflow.phased_5mC_5hmC.config" when { process { @@ -143,9 +112,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = Channel.of('chr22\t0\t1000') - .collectFile(name: 'chr22.bed', newLine: true) - .map { file -> [ [ id:'chr22' ], file ] } + input[2] = [[],[]] """ } } @@ -159,9 +126,9 @@ nextflow_process { } - test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph") { + test("[bam, bai], [fasta, fai], bed, phased") { - config "./nextflow.traditional_hp_bedgraph.config" + config "./nextflow.phased_5mC_5hmC.config" when { process { @@ -252,6 +219,7 @@ nextflow_process { test("[bam, bai], [fasta, fai], bed - stub") { + config "./nextflow.5mC_5hmC.config" options "-stub" when { @@ -283,43 +251,9 @@ nextflow_process { } - test("[bam, bai], [fasta, fai], bed - traditional - stub") { - - config "./nextflow.traditional.config" - options "-stub" - - when { - process { - """ - input[0] = [ - [ id: 'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true) - ] - input[1] = [ - [ id: 'test_ref' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - input[2] = Channel.of('chr22\t0\t1000') - .collectFile(name: 'chr22.bed', newLine: true) - .map { file -> [ [ id:'chr22' ], file ] } - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - test("[bam, bai], [fasta, fai], bed - traditional, HP - stub") { + test("[bam, bai], [fasta, fai], [], phased - stub") { - config "./nextflow.traditional_hp.config" + config "./nextflow.phased_5mC_5hmC.config" options "-stub" when { @@ -335,9 +269,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = Channel.of('chr22\t0\t1000') - .collectFile(name: 'chr22.bed', newLine: true) - .map { file -> [ [ id:'chr22' ], file ] } + input[2] = [[],[]] """ } } @@ -351,9 +283,9 @@ nextflow_process { } - test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub") { + test("[bam, bai], [fasta, fai], bed, phased - stub") { - config "./nextflow.traditional_hp_bedgraph.config" + config "./nextflow.phased_5mC_5hmC.config" options "-stub" when { diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap index 3ed08d3655dd..4b79ccfa811e 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap @@ -1,69 +1,11 @@ { - "[bam, bai], [fasta, fai], bed": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170" - ] - ], - "bedgraph": [ - - ], - "log": [ - - ], - "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.2" - }, - "timestamp": "2025-10-29T13:33:40.323944879" - }, "[bam, bai], [fasta, fai], [] - stub": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ [ { "id": "test" @@ -71,24 +13,11 @@ "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "2": [ + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "bedgraph": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "bedgz": [ + ], "log": [ [ @@ -99,7 +28,7 @@ ] ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -107,50 +36,28 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:34:25.818328219" + "timestamp": "2025-12-11T11:11:31.657080381" }, - "[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph": { + "[bam, bai], [], []": { "content": [ { "0": [ ], "1": [ - [ - { - "id": "test" - }, - [ - "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0", - "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9" - ] - ] - ], - "2": [ ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "2": [ + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "bed": [ + "bedgz": [ - ], - "bedgraph": [ - [ - { - "id": "test" - }, - [ - "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0", - "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9" - ] - ] ], "log": [ ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -158,9 +65,9 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:34:09.480034362" + "timestamp": "2025-12-11T11:10:42.18976559" }, - "[bam, bai], [fasta, fai], bed - traditional, HP": { + "[bam, bai], [fasta, fai], bed, phased": { "content": [ { "0": [ @@ -169,8 +76,9 @@ "id": "test" }, [ - "test_1.bed:md5,464a9870774c340753e79639aeaf76c2", - "test_2.bed:md5,118de4b653dd082d76faa8802df493eb" + "test_combined.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472", + "test_hp1.bed.gz:md5,8125fff82b626811d73c6a09c292ed31", + "test_hp2.bed.gz:md5,6438ea42b16a21db197ddf73ec665685" ] ] ], @@ -178,30 +86,25 @@ ], "2": [ - - ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "bed": [ + "bedgz": [ [ { "id": "test" }, [ - "test_1.bed:md5,464a9870774c340753e79639aeaf76c2", - "test_2.bed:md5,118de4b653dd082d76faa8802df493eb" + "test_combined.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472", + "test_hp1.bed.gz:md5,8125fff82b626811d73c6a09c292ed31", + "test_hp2.bed.gz:md5,6438ea42b16a21db197ddf73ec665685" ] ] - ], - "bedgraph": [ - ], "log": [ ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -209,44 +112,38 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:34:01.652042889" + "timestamp": "2025-12-11T11:11:16.350826558" }, - "[bam, bai], [fasta, fai], []": { + "[bam, bai], [fasta, fai], bed, phased - stub": { "content": [ { "0": [ + + ], + "1": [ [ { "id": "test" }, - "test.bed:md5,f973de342df883efc1656c82a3a3978d" + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - ], "2": [ - + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "bedgz": [ + ], - "bed": [ + "log": [ [ { "id": "test" }, - "test.bed:md5,f973de342df883efc1656c82a3a3978d" + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "bedgraph": [ - - ], - "log": [ - ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -254,28 +151,15 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:33:30.820830386" + "timestamp": "2025-12-11T11:21:42.424626168" }, - "[bam, bai], [fasta, fai], bed - traditional, HP - stub": { + "[bam, bai], [fasta, fai], bed - stub": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ [ { "id": "test" @@ -283,24 +167,11 @@ "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "2": [ + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "bedgraph": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "bedgz": [ + ], "log": [ [ @@ -311,7 +182,7 @@ ] ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -319,44 +190,28 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:34:51.355845894" + "timestamp": "2025-12-11T11:11:39.656988428" }, - "[bam, bai], [], []": { + "[bam, bai], [fasta, fai], bed": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed:md5,f973de342df883efc1656c82a3a3978d" - ] + ], "1": [ ], "2": [ - + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,f973de342df883efc1656c82a3a3978d" - ] - ], - "bedgraph": [ + "bedgz": [ ], "log": [ ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -364,9 +219,9 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:33:22.654774712" + "timestamp": "2025-12-11T11:10:59.900592089" }, - "[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub": { + "[bam, bai], [fasta, fai], [], phased": { "content": [ { "0": [ @@ -374,54 +229,36 @@ { "id": "test" }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test_combined.bed.gz:md5,2ade8f1d8c163ff61698d828d0ef3fb0", + "test_hp1.bed.gz:md5,e8e8c00005127492fd5610a9fa0cd098", + "test_hp2.bed.gz:md5,b211935a2e88b0ebeee987abc3a622e2" + ] ] ], "1": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "2": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "bedgraph": [ + "bedgz": [ [ { "id": "test" }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test_combined.bed.gz:md5,2ade8f1d8c163ff61698d828d0ef3fb0", + "test_hp1.bed.gz:md5,e8e8c00005127492fd5610a9fa0cd098", + "test_hp2.bed.gz:md5,b211935a2e88b0ebeee987abc3a622e2" + ] ] ], "log": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -429,28 +266,15 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:35:00.477494397" + "timestamp": "2025-12-11T11:11:07.981955957" }, - "[bam, bai], [], [] - stub": { + "[bam, bai], [fasta, fai], [], phased - stub": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ [ { "id": "test" @@ -458,24 +282,11 @@ "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "2": [ + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "bedgraph": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "bedgz": [ + ], "log": [ [ @@ -486,7 +297,7 @@ ] ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -494,64 +305,28 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:34:17.906798987" + "timestamp": "2025-12-11T11:11:47.292468928" }, - "[bam, bai], [fasta, fai], bed - traditional - stub": { + "[bam, bai], [fasta, fai], []": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "2": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bedgraph": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "bedgz": [ + ], "log": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -559,28 +334,15 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:34:42.242953279" + "timestamp": "2025-12-11T11:10:51.19816951" }, - "[bam, bai], [fasta, fai], bed - stub": { + "[bam, bai], [], [] - stub": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ [ { "id": "test" @@ -588,24 +350,11 @@ "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "2": [ + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], - "bedgraph": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "bedgz": [ + ], "log": [ [ @@ -616,52 +365,7 @@ ] ], "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.2" - }, - "timestamp": "2025-10-29T13:34:34.378006702" - }, - "[bam, bai], [fasta, fai], bed - traditional": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.bed:md5,db6333f714a8ea4aa33902404a8d4812" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" - ], - "bed": [ - [ - { - "id": "test" - }, - "test.bed:md5,db6333f714a8ea4aa33902404a8d4812" - ] - ], - "bedgraph": [ - - ], - "log": [ - - ], - "versions": [ - "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a" + "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ] } ], @@ -669,6 +373,6 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-10-29T13:33:48.061931781" + "timestamp": "2025-12-11T11:11:24.158494151" } } \ No newline at end of file diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.traditional.config b/modules/nf-core/modkit/pileup/tests/nextflow.5mC_5hmC.config similarity index 51% rename from modules/nf-core/modkit/pileup/tests/nextflow.traditional.config rename to modules/nf-core/modkit/pileup/tests/nextflow.5mC_5hmC.config index 672598d51332..e61fa05f76b1 100644 --- a/modules/nf-core/modkit/pileup/tests/nextflow.traditional.config +++ b/modules/nf-core/modkit/pileup/tests/nextflow.5mC_5hmC.config @@ -1,5 +1,5 @@ process { withName: 'MODKIT_PILEUP' { - ext.args = '--preset traditional' + ext.args = '--modified-bases 5mC 5hmC' } } diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.phased_5mC_5hmC.config b/modules/nf-core/modkit/pileup/tests/nextflow.phased_5mC_5hmC.config new file mode 100644 index 000000000000..4ec7db3131c4 --- /dev/null +++ b/modules/nf-core/modkit/pileup/tests/nextflow.phased_5mC_5hmC.config @@ -0,0 +1,5 @@ +process { + withName: 'MODKIT_PILEUP' { + ext.args = '--phased --modified-bases 5mC 5hmC' + } +} diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp.config b/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp.config deleted file mode 100644 index c0e0d79a5264..000000000000 --- a/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'MODKIT_PILEUP' { - ext.args = '--preset traditional --partition-tag HP' - } -} diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp_bedgraph.config b/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp_bedgraph.config deleted file mode 100644 index 4f456dcd9fb2..000000000000 --- a/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp_bedgraph.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'MODKIT_PILEUP' { - ext.args = '--preset traditional --partition-tag HP --bedgraph' - } -} From fc76ab7356b239ab5488cfe3cb2a6a1e7efffd32 Mon Sep 17 00:00:00 2001 From: ra25wog Date: Thu, 11 Dec 2025 11:37:59 +0100 Subject: [PATCH 04/13] update bedmethyltobigwig tests --- .../bedmethyltobigwig/tests/main.nf.test | 6 +- .../bedmethyltobigwig/tests/main.nf.test.snap | 66 +++++-------------- 2 files changed, 21 insertions(+), 51 deletions(-) diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test index afdd1cec2429..723d2c93fb6c 100644 --- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test +++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test @@ -32,7 +32,7 @@ nextflow_process { when { process { """ - input[0] = MODKIT_PILEUP.out.bed + input[0] = MODKIT_PILEUP.out.bedgz input[1] = [ [ id : 'hg38' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -55,7 +55,7 @@ nextflow_process { when { process { """ - input[0] = MODKIT_PILEUP.out.bed + input[0] = MODKIT_PILEUP.out.bedgz input[1] = [ [ id : 'hg38' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -78,7 +78,7 @@ nextflow_process { when { process { """ - input[0] = MODKIT_PILEUP.out.bed + input[0] = MODKIT_PILEUP.out.bedgz input[1] = [ [ id : 'hg38' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap index d3ebb75cfbcd..d0e9d2211494 100644 --- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap @@ -3,99 +3,69 @@ "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" - ] + ], "1": [ - "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" + ], "bw": [ - [ - { - "id": "test" - }, - "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" - ] + ], "versions": [ - "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" + ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T09:38:52.912687858" + "timestamp": "2025-12-11T11:10:33.219227007" }, "homo sapiens - bedmethyl, fai, list": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" - ] + ], "1": [ - "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" + ], "bw": [ - [ - { - "id": "test" - }, - "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" - ] + ], "versions": [ - "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" + ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T09:38:35.894897541" + "timestamp": "2025-12-11T11:10:20.056318171" }, "homo sapiens - bedmethyl, fai, string": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" - ] + ], "1": [ - "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" + ], "bw": [ - [ - { - "id": "test" - }, - "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" - ] + ], "versions": [ - "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" + ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T09:38:44.647742811" + "timestamp": "2025-12-11T11:10:26.664679432" } } \ No newline at end of file From cef040baf3424776269bb0802dbef680ba81da2a Mon Sep 17 00:00:00 2001 From: ra25wog Date: Thu, 11 Dec 2025 13:47:04 +0100 Subject: [PATCH 05/13] update main --- modules/nf-core/modkit/pileup/main.nf | 2 +- .../modkit/pileup/tests/main.nf.test.snap | 138 +++++++++++------- 2 files changed, 85 insertions(+), 55 deletions(-) diff --git a/modules/nf-core/modkit/pileup/main.nf b/modules/nf-core/modkit/pileup/main.nf index 279aed622de6..fc4068cc125d 100644 --- a/modules/nf-core/modkit/pileup/main.nf +++ b/modules/nf-core/modkit/pileup/main.nf @@ -46,7 +46,7 @@ process MODKIT_PILEUP { fi done else - mv ${prefix}.tmp ${prefix}.bed + mv ${prefix}.tmp ${prefix}.bed.gz fi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap index 4b79ccfa811e..50c288326b76 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap @@ -1,31 +1,31 @@ { - "[bam, bai], [fasta, fai], [] - stub": { + "[bam, bai], [fasta, fai], bed": { "content": [ { "0": [ - - ], - "1": [ [ { "id": "test" }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472" ] + ], + "1": [ + ], "2": [ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], "bedgz": [ - - ], - "log": [ [ { "id": "test" }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472" ] + ], + "log": [ + ], "versions": [ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" @@ -36,16 +36,21 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:11:31.657080381" + "timestamp": "2025-12-11T11:55:19.440161459" }, - "[bam, bai], [], []": { + "[bam, bai], [fasta, fai], [] - stub": { "content": [ { "0": [ ], "1": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" @@ -54,7 +59,12 @@ ], "log": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" @@ -65,9 +75,9 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:10:42.18976559" + "timestamp": "2025-12-11T11:11:31.657080381" }, - "[bam, bai], [fasta, fai], bed, phased": { + "[bam, bai], [fasta, fai], [], phased": { "content": [ { "0": [ @@ -76,9 +86,9 @@ "id": "test" }, [ - "test_combined.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472", - "test_hp1.bed.gz:md5,8125fff82b626811d73c6a09c292ed31", - "test_hp2.bed.gz:md5,6438ea42b16a21db197ddf73ec665685" + "test_combined.bed.gz:md5,2ade8f1d8c163ff61698d828d0ef3fb0", + "test_hp1.bed.gz:md5,e8e8c00005127492fd5610a9fa0cd098", + "test_hp2.bed.gz:md5,b211935a2e88b0ebeee987abc3a622e2" ] ] ], @@ -94,9 +104,9 @@ "id": "test" }, [ - "test_combined.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472", - "test_hp1.bed.gz:md5,8125fff82b626811d73c6a09c292ed31", - "test_hp2.bed.gz:md5,6438ea42b16a21db197ddf73ec665685" + "test_combined.bed.gz:md5,2ade8f1d8c163ff61698d828d0ef3fb0", + "test_hp1.bed.gz:md5,e8e8c00005127492fd5610a9fa0cd098", + "test_hp2.bed.gz:md5,b211935a2e88b0ebeee987abc3a622e2" ] ] ], @@ -112,9 +122,9 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:11:16.350826558" + "timestamp": "2025-12-11T11:11:07.981955957" }, - "[bam, bai], [fasta, fai], bed, phased - stub": { + "[bam, bai], [fasta, fai], [], phased - stub": { "content": [ { "0": [ @@ -151,35 +161,35 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:21:42.424626168" + "timestamp": "2025-12-11T11:11:47.292468928" }, - "[bam, bai], [fasta, fai], bed - stub": { + "[bam, bai], [fasta, fai], []": { "content": [ { "0": [ - - ], - "1": [ [ { "id": "test" }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed.gz:md5,f973de342df883efc1656c82a3a3978d" ] + ], + "1": [ + ], "2": [ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], "bedgz": [ - - ], - "log": [ [ { "id": "test" }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed.gz:md5,f973de342df883efc1656c82a3a3978d" ] + ], + "log": [ + ], "versions": [ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" @@ -190,13 +200,18 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:11:39.656988428" + "timestamp": "2025-12-11T11:55:10.542809235" }, - "[bam, bai], [fasta, fai], bed": { + "[bam, bai], [], []": { "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test.bed.gz:md5,f973de342df883efc1656c82a3a3978d" + ] ], "1": [ @@ -205,7 +220,12 @@ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" ], "bedgz": [ - + [ + { + "id": "test" + }, + "test.bed.gz:md5,f973de342df883efc1656c82a3a3978d" + ] ], "log": [ @@ -219,9 +239,9 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:10:59.900592089" + "timestamp": "2025-12-11T11:54:55.481500164" }, - "[bam, bai], [fasta, fai], [], phased": { + "[bam, bai], [fasta, fai], bed, phased": { "content": [ { "0": [ @@ -230,9 +250,9 @@ "id": "test" }, [ - "test_combined.bed.gz:md5,2ade8f1d8c163ff61698d828d0ef3fb0", - "test_hp1.bed.gz:md5,e8e8c00005127492fd5610a9fa0cd098", - "test_hp2.bed.gz:md5,b211935a2e88b0ebeee987abc3a622e2" + "test_combined.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472", + "test_hp1.bed.gz:md5,8125fff82b626811d73c6a09c292ed31", + "test_hp2.bed.gz:md5,6438ea42b16a21db197ddf73ec665685" ] ] ], @@ -248,9 +268,9 @@ "id": "test" }, [ - "test_combined.bed.gz:md5,2ade8f1d8c163ff61698d828d0ef3fb0", - "test_hp1.bed.gz:md5,e8e8c00005127492fd5610a9fa0cd098", - "test_hp2.bed.gz:md5,b211935a2e88b0ebeee987abc3a622e2" + "test_combined.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472", + "test_hp1.bed.gz:md5,8125fff82b626811d73c6a09c292ed31", + "test_hp2.bed.gz:md5,6438ea42b16a21db197ddf73ec665685" ] ] ], @@ -266,9 +286,9 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:11:07.981955957" + "timestamp": "2025-12-11T11:11:16.350826558" }, - "[bam, bai], [fasta, fai], [], phased - stub": { + "[bam, bai], [fasta, fai], bed, phased - stub": { "content": [ { "0": [ @@ -305,16 +325,21 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:11:47.292468928" + "timestamp": "2025-12-11T11:21:42.424626168" }, - "[bam, bai], [fasta, fai], []": { + "[bam, bai], [], [] - stub": { "content": [ { "0": [ ], "1": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" @@ -323,7 +348,12 @@ ], "log": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3" @@ -334,9 +364,9 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:10:51.19816951" + "timestamp": "2025-12-11T11:11:24.158494151" }, - "[bam, bai], [], [] - stub": { + "[bam, bai], [fasta, fai], bed - stub": { "content": [ { "0": [ @@ -373,6 +403,6 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:11:24.158494151" + "timestamp": "2025-12-11T11:11:39.656988428" } } \ No newline at end of file From 94163095816bb9594578629e44cbbfe7061f1ee4 Mon Sep 17 00:00:00 2001 From: ra25wog Date: Thu, 11 Dec 2025 13:47:24 +0100 Subject: [PATCH 06/13] update snapshot --- .../tests/decompressed.config | 5 ++ .../bedmethyltobigwig/tests/main.nf.test | 17 +++++- .../bedmethyltobigwig/tests/main.nf.test.snap | 60 ++++++++++++++----- 3 files changed, 64 insertions(+), 18 deletions(-) create mode 100644 modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config b/modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config new file mode 100644 index 000000000000..3b1c30f5ed20 --- /dev/null +++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = '-d' + } +} diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test index 723d2c93fb6c..9e286fe321da 100644 --- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test +++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test @@ -9,6 +9,7 @@ nextflow_process { tag "modkit" tag "modkit/bedmethyltobigwig" tag "modkit/pileup" + tag "tabix/bgzip" setup { run("MODKIT_PILEUP"){ @@ -25,6 +26,16 @@ nextflow_process { """ } } + + run("TABIX_BGZIP"){ + script "../../../tabix/bgzip/main.nf" + process { + """ + input[0] = MODKIT_PILEUP.out.bedgz + params.args = '-d' + """ + } + } } test("homo sapiens - bedmethyl, fai, list") { @@ -32,7 +43,7 @@ nextflow_process { when { process { """ - input[0] = MODKIT_PILEUP.out.bedgz + input[0] = TABIX_BGZIP.out.output input[1] = [ [ id : 'hg38' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -55,7 +66,7 @@ nextflow_process { when { process { """ - input[0] = MODKIT_PILEUP.out.bedgz + input[0] = TABIX_BGZIP.out.output input[1] = [ [ id : 'hg38' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -78,7 +89,7 @@ nextflow_process { when { process { """ - input[0] = MODKIT_PILEUP.out.bedgz + input[0] = TABIX_BGZIP.out.output input[1] = [ [ id : 'hg38' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap index d0e9d2211494..a1eb686ed5f4 100644 --- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap @@ -3,16 +3,26 @@ "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + ] ], "1": [ - + "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" ], "bw": [ - + [ + { + "id": "test" + }, + "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + ] ], "versions": [ - + "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" ] } ], @@ -20,22 +30,32 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:10:33.219227007" + "timestamp": "2025-12-11T13:41:13.127222805" }, "homo sapiens - bedmethyl, fai, list": { "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + ] ], "1": [ - + "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" ], "bw": [ - + [ + { + "id": "test" + }, + "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + ] ], "versions": [ - + "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" ] } ], @@ -43,22 +63,32 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:10:20.056318171" + "timestamp": "2025-12-11T13:40:48.68442879" }, "homo sapiens - bedmethyl, fai, string": { "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + ] ], "1": [ - + "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" ], "bw": [ - + [ + { + "id": "test" + }, + "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + ] ], "versions": [ - + "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b" ] } ], @@ -66,6 +96,6 @@ "nf-test": "0.9.3", "nextflow": "25.04.2" }, - "timestamp": "2025-12-11T11:10:26.664679432" + "timestamp": "2025-12-11T13:41:01.248184796" } } \ No newline at end of file From e7005fccdbf0c28cb939204d310c18af40037faf Mon Sep 17 00:00:00 2001 From: ra25wog Date: Thu, 11 Dec 2025 14:10:03 +0100 Subject: [PATCH 07/13] fix linting --- modules/nf-core/modkit/pileup/meta.yml | 30 +++++++++----------------- 1 file changed, 10 insertions(+), 20 deletions(-) diff --git a/modules/nf-core/modkit/pileup/meta.yml b/modules/nf-core/modkit/pileup/meta.yml index 32aba6add7fc..3d7d9fd5b8ee 100644 --- a/modules/nf-core/modkit/pileup/meta.yml +++ b/modules/nf-core/modkit/pileup/meta.yml @@ -6,8 +6,8 @@ keywords: - long-read tools: - "modkit": - description: A bioinformatics tool for working with modified bases in Oxford Nanopore - sequencing data + description: A bioinformatics tool for working with modified bases in Oxford + Nanopore sequencing data homepage: https://github.com/nanoporetech/modkit documentation: https://github.com/nanoporetech/modkit tool_dev_url: https://github.com/nanoporetech/modkit @@ -36,8 +36,8 @@ input: e.g. `[ id:'hg38' ]` - fasta: type: file - description: Reference sequence in FASTA format. Required for motif (e.g. CpG) - filtering + description: Reference sequence in FASTA format. Required for motif (e.g. + CpG) filtering pattern: "*.fasta" ontologies: [] - fai: @@ -52,33 +52,22 @@ input: e.g. `[ id:'regions' ]` - bed: type: file - description: BED file that will restrict threshold estimation and pileup results - to positions overlapping intervals in the file + description: BED file that will restrict threshold estimation and pileup + results to positions overlapping intervals in the file pattern: "*.bed" ontologies: [] output: - bed: + bedgz: - - meta: type: map description: | Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]` - - "*.bed": + - "*.bed.gz": type: file - description: bedMethyl output file(s) + description: bgzf-compressed bedMethyl output file(s) pattern: "*.bed" ontologies: [] - bedgraph: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - "*.bedgraph": - type: file - description: bedgraph output files - pattern: "*.bedgraph" - ontologies: [] log: - - meta: type: map @@ -102,3 +91,4 @@ authors: - "@fellen31" maintainers: - "@fellen31" + - "@jkh00" From b95940c64b88625635f5dff0d925c0e28cc4d5a2 Mon Sep 17 00:00:00 2001 From: Jinn <155078830+jkh00@users.noreply.github.com> Date: Thu, 11 Dec 2025 14:22:31 +0000 Subject: [PATCH 08/13] update snapshots --- .../bedmethyltobigwig/tests/main.nf.test.snap | 24 +++++------ .../modkit/pileup/tests/main.nf.test.snap | 40 +++++++++---------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap index a1eb686ed5f4..48c989060696 100644 --- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" ] ], "1": [ @@ -18,7 +18,7 @@ { "id": "test" }, - "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" ] ], "versions": [ @@ -28,9 +28,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T13:41:13.127222805" + "timestamp": "2025-12-11T14:18:11.382889943" }, "homo sapiens - bedmethyl, fai, list": { "content": [ @@ -40,7 +40,7 @@ { "id": "test" }, - "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" ] ], "1": [ @@ -51,7 +51,7 @@ { "id": "test" }, - "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" ] ], "versions": [ @@ -61,9 +61,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T13:40:48.68442879" + "timestamp": "2025-12-11T14:17:52.811754475" }, "homo sapiens - bedmethyl, fai, string": { "content": [ @@ -73,7 +73,7 @@ { "id": "test" }, - "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" ] ], "1": [ @@ -84,7 +84,7 @@ { "id": "test" }, - "test.bw:md5,73506398d8e4b3351a92edfcc886a667" + "test.bw:md5,944ae7cef280c04afeef5eae4beb4b43" ] ], "versions": [ @@ -94,8 +94,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T13:41:01.248184796" + "timestamp": "2025-12-11T14:18:02.079953932" } } \ No newline at end of file diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap index 50c288326b76..2011be7c9e03 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap @@ -34,9 +34,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:55:19.440161459" + "timestamp": "2025-12-11T14:18:34.613472799" }, "[bam, bai], [fasta, fai], [] - stub": { "content": [ @@ -73,9 +73,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:11:31.657080381" + "timestamp": "2025-12-11T14:19:04.629490834" }, "[bam, bai], [fasta, fai], [], phased": { "content": [ @@ -120,9 +120,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:11:07.981955957" + "timestamp": "2025-12-11T14:18:42.290304403" }, "[bam, bai], [fasta, fai], [], phased - stub": { "content": [ @@ -159,9 +159,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:11:47.292468928" + "timestamp": "2025-12-11T14:19:19.17467827" }, "[bam, bai], [fasta, fai], []": { "content": [ @@ -198,9 +198,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:55:10.542809235" + "timestamp": "2025-12-11T14:18:26.964056871" }, "[bam, bai], [], []": { "content": [ @@ -237,9 +237,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:54:55.481500164" + "timestamp": "2025-12-11T14:18:19.273553787" }, "[bam, bai], [fasta, fai], bed, phased": { "content": [ @@ -284,9 +284,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:11:16.350826558" + "timestamp": "2025-12-11T14:18:50.043853179" }, "[bam, bai], [fasta, fai], bed, phased - stub": { "content": [ @@ -323,9 +323,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:21:42.424626168" + "timestamp": "2025-12-11T14:19:26.675056899" }, "[bam, bai], [], [] - stub": { "content": [ @@ -362,9 +362,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:11:24.158494151" + "timestamp": "2025-12-11T14:18:56.962234621" }, "[bam, bai], [fasta, fai], bed - stub": { "content": [ @@ -401,8 +401,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-11T11:11:39.656988428" + "timestamp": "2025-12-11T14:19:11.953321139" } } \ No newline at end of file From ee95270b2deef8c201b35d1b774b277c417f6eaa Mon Sep 17 00:00:00 2001 From: ra25wog Date: Fri, 12 Dec 2025 11:34:39 +0100 Subject: [PATCH 09/13] remove config --- .../modkit/bedmethyltobigwig/tests/decompressed.config | 5 ----- modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test | 1 - 2 files changed, 6 deletions(-) delete mode 100644 modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config b/modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config deleted file mode 100644 index 3b1c30f5ed20..000000000000 --- a/modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: TABIX_BGZIP { - ext.args = '-d' - } -} diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test index 9e286fe321da..5f3499da00ef 100644 --- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test +++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test @@ -32,7 +32,6 @@ nextflow_process { process { """ input[0] = MODKIT_PILEUP.out.bedgz - params.args = '-d' """ } } From 1e647ca8b15b83f1967636f2f64072f2819f1038 Mon Sep 17 00:00:00 2001 From: ra25wog Date: Fri, 12 Dec 2025 11:47:48 +0100 Subject: [PATCH 10/13] update module_args --- .../nf-core/modkit/pileup/tests/main.nf.test | 29 ++++++++++++------- .../pileup/tests/nextflow.5mC_5hmC.config | 5 ---- .../modkit/pileup/tests/nextflow.config | 5 ++++ .../tests/nextflow.phased_5mC_5hmC.config | 5 ---- 4 files changed, 24 insertions(+), 20 deletions(-) delete mode 100644 modules/nf-core/modkit/pileup/tests/nextflow.5mC_5hmC.config create mode 100644 modules/nf-core/modkit/pileup/tests/nextflow.config delete mode 100644 modules/nf-core/modkit/pileup/tests/nextflow.phased_5mC_5hmC.config diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test b/modules/nf-core/modkit/pileup/tests/main.nf.test index f49f7cbe9df1..0c3035e0b2df 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test @@ -7,6 +7,7 @@ nextflow_process { tag "modkit" tag "modkit/pileup" process "MODKIT_PILEUP" + config "./nextflow.config" test("[bam, bai], [], []") { @@ -64,9 +65,10 @@ nextflow_process { test("[bam, bai], [fasta, fai], bed") { - config "./nextflow.5mC_5hmC.config" - when { + params { + module_args = '--modified-bases 5mC 5hmC' + } process { """ input[0] = [ @@ -97,9 +99,10 @@ nextflow_process { test("[bam, bai], [fasta, fai], [], phased") { - config "./nextflow.phased_5mC_5hmC.config" - when { + params { + module_args = '--phased --modified-bases 5mC 5hmC' + } process { """ input[0] = [ @@ -128,9 +131,10 @@ nextflow_process { test("[bam, bai], [fasta, fai], bed, phased") { - config "./nextflow.phased_5mC_5hmC.config" - when { + params { + module_args = '--phased --modified-bases 5mC 5hmC' + } process { """ input[0] = [ @@ -218,11 +222,12 @@ nextflow_process { } test("[bam, bai], [fasta, fai], bed - stub") { - - config "./nextflow.5mC_5hmC.config" options "-stub" when { + params { + module_args = '--modified-bases 5mC 5hmC' + } process { """ input[0] = [ @@ -253,10 +258,12 @@ nextflow_process { test("[bam, bai], [fasta, fai], [], phased - stub") { - config "./nextflow.phased_5mC_5hmC.config" options "-stub" when { + params { + module_args = '--phased --modified-bases 5mC 5hmC' + } process { """ input[0] = [ @@ -285,10 +292,12 @@ nextflow_process { test("[bam, bai], [fasta, fai], bed, phased - stub") { - config "./nextflow.phased_5mC_5hmC.config" options "-stub" when { + params { + module_args = '--phased --modified-bases 5mC 5hmC' + } process { """ input[0] = [ diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.5mC_5hmC.config b/modules/nf-core/modkit/pileup/tests/nextflow.5mC_5hmC.config deleted file mode 100644 index e61fa05f76b1..000000000000 --- a/modules/nf-core/modkit/pileup/tests/nextflow.5mC_5hmC.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'MODKIT_PILEUP' { - ext.args = '--modified-bases 5mC 5hmC' - } -} diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.config b/modules/nf-core/modkit/pileup/tests/nextflow.config new file mode 100644 index 000000000000..f74d947cf776 --- /dev/null +++ b/modules/nf-core/modkit/pileup/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MODULE' { + ext.args = params.module_args + } +} \ No newline at end of file diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.phased_5mC_5hmC.config b/modules/nf-core/modkit/pileup/tests/nextflow.phased_5mC_5hmC.config deleted file mode 100644 index 4ec7db3131c4..000000000000 --- a/modules/nf-core/modkit/pileup/tests/nextflow.phased_5mC_5hmC.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'MODKIT_PILEUP' { - ext.args = '--phased --modified-bases 5mC 5hmC' - } -} From d50ec1801a0b053cbb6c87fbe1fe34d4bb9722d9 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 12 Dec 2025 10:50:26 +0000 Subject: [PATCH 11/13] [automated] Fix linting with Prettier --- modules/nf-core/modkit/pileup/tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.config b/modules/nf-core/modkit/pileup/tests/nextflow.config index f74d947cf776..9dcaca63e09a 100644 --- a/modules/nf-core/modkit/pileup/tests/nextflow.config +++ b/modules/nf-core/modkit/pileup/tests/nextflow.config @@ -2,4 +2,4 @@ process { withName: 'MODULE' { ext.args = params.module_args } -} \ No newline at end of file +} From 7ef89553ca6b09d9fac2592b357e0be12617f178 Mon Sep 17 00:00:00 2001 From: Jinn <155078830+jkh00@users.noreply.github.com> Date: Fri, 12 Dec 2025 10:57:07 +0000 Subject: [PATCH 12/13] changed name --- modules/nf-core/modkit/pileup/tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.config b/modules/nf-core/modkit/pileup/tests/nextflow.config index 9dcaca63e09a..62521d0b5fe2 100644 --- a/modules/nf-core/modkit/pileup/tests/nextflow.config +++ b/modules/nf-core/modkit/pileup/tests/nextflow.config @@ -1,5 +1,5 @@ process { - withName: 'MODULE' { + withName: 'MODKIT_PILEUP' { ext.args = params.module_args } } From 79d459e4fb1e683cde0e4cbae8e0a5f757c5cf93 Mon Sep 17 00:00:00 2001 From: Jinn <155078830+jkh00@users.noreply.github.com> Date: Fri, 12 Dec 2025 11:17:24 +0000 Subject: [PATCH 13/13] update main --- modules/nf-core/modkit/pileup/tests/main.nf.test | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test b/modules/nf-core/modkit/pileup/tests/main.nf.test index 0c3035e0b2df..652b725ae556 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test @@ -12,6 +12,9 @@ nextflow_process { test("[bam, bai], [], []") { when { + params { + module_args = '' + } process { """ input[0] = [ @@ -37,6 +40,9 @@ nextflow_process { test("[bam, bai], [fasta, fai], []") { when { + params { + module_args = '' + } process { """ input[0] = [ @@ -168,6 +174,9 @@ nextflow_process { options "-stub" when { + params { + module_args = '' + } process { """ input[0] = [ @@ -195,6 +204,9 @@ nextflow_process { options "-stub" when { + params { + module_args = '' + } process { """ input[0] = [