diff --git a/modules/nf-core/modkit/pileup/environment.yml b/modules/nf-core/modkit/pileup/environment.yml index 7a87bce9d706..1e4d674d6c7c 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=0.3.0 + - ont-modkit=0.4.3 diff --git a/modules/nf-core/modkit/pileup/main.nf b/modules/nf-core/modkit/pileup/main.nf index f21a733f6677..7a3bb5e57799 100644 --- a/modules/nf-core/modkit/pileup/main.nf +++ b/modules/nf-core/modkit/pileup/main.nf @@ -4,12 +4,12 @@ process MODKIT_PILEUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ont-modkit:0.3.0--h5c23e0d_0': - 'biocontainers/ont-modkit:0.3.0--h5c23e0d_0' }" + 'https://depot.galaxyproject.org/singularity/ont-modkit:0.4.3--hcdda2d0_0': + 'biocontainers/ont-modkit:0.4.3--hcdda2d0_0' }" input: tuple val(meta), path(bam), path(bai) - tuple val(meta2), path(fasta) + tuple val(meta2), path(fasta), path(fai) tuple val(meta3), path(bed) output: diff --git a/modules/nf-core/modkit/pileup/meta.yml b/modules/nf-core/modkit/pileup/meta.yml index 2f274d0c8cdd..ad259e816389 100644 --- a/modules/nf-core/modkit/pileup/meta.yml +++ b/modules/nf-core/modkit/pileup/meta.yml @@ -37,6 +37,10 @@ input: description: Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering pattern: "*.fasta" + - fai: + type: file + description: Associated index file for FASTA + pattern: "*.fai" - - meta3: type: map description: | diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test b/modules/nf-core/modkit/pileup/tests/main.nf.test index 371cc3b94d49..6ce8dfe285b1 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { 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] = [[],[]] + input[1] = [[],[],[]] input[2] = [[],[]] """ } @@ -33,7 +33,7 @@ nextflow_process { } - test("[bam, bai], fasta, []") { + test("[bam, bai], [fasta, fai], []") { when { process { @@ -45,7 +45,8 @@ nextflow_process { ] 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', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [[],[]] """ @@ -61,7 +62,7 @@ nextflow_process { } - test("[bam, bai], fasta, bed") { + test("[bam, bai], [fasta, fai], bed") { when { process { @@ -73,7 +74,8 @@ nextflow_process { ] 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', 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) @@ -91,7 +93,7 @@ nextflow_process { } - test("[bam, bai], fasta, bed - traditional") { + test("[bam, bai], [fasta, fai], bed - traditional") { config "./nextflow.traditional.config" @@ -105,7 +107,8 @@ nextflow_process { ] 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', 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) @@ -123,7 +126,7 @@ nextflow_process { } - test("[bam, bai], fasta, bed - traditional, HP") { + test("[bam, bai], [fasta, fai], bed - traditional, HP") { config "./nextflow.traditional_hp.config" @@ -137,7 +140,8 @@ nextflow_process { ] 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', 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) @@ -155,7 +159,7 @@ nextflow_process { } - test("[bam, bai], fasta, bed - traditional, HP, bedgraph") { + test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph") { config "./nextflow.traditional_hp_bedgraph.config" @@ -169,7 +173,8 @@ nextflow_process { ] 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', 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) @@ -199,7 +204,7 @@ nextflow_process { 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] = [[],[]] + input[1] = [[],[],[]] input[2] = [[],[]] """ } @@ -214,7 +219,7 @@ nextflow_process { } - test("[bam, bai], fasta, [] - stub") { + test("[bam, bai], [fasta, fai], [] - stub") { options "-stub" @@ -228,7 +233,8 @@ nextflow_process { ] 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', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [[],[]] """ @@ -244,7 +250,7 @@ nextflow_process { } - test("[bam, bai], fasta, bed - stub") { + test("[bam, bai], [fasta, fai], bed - stub") { options "-stub" @@ -258,7 +264,8 @@ nextflow_process { ] 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', 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) @@ -276,7 +283,7 @@ nextflow_process { } - test("[bam, bai], fasta, bed - traditional - stub") { + test("[bam, bai], [fasta, fai], bed - traditional - stub") { config "./nextflow.traditional.config" options "-stub" @@ -291,7 +298,8 @@ nextflow_process { ] 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', 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) @@ -309,7 +317,7 @@ nextflow_process { } - test("[bam, bai], fasta, bed - traditional, HP - stub") { + test("[bam, bai], [fasta, fai], bed - traditional, HP - stub") { config "./nextflow.traditional_hp.config" options "-stub" @@ -324,7 +332,8 @@ nextflow_process { ] 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', 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) @@ -342,7 +351,7 @@ nextflow_process { } - test("[bam, bai], fasta, bed - traditional, HP, bedgraph - stub") { + test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub") { config "./nextflow.traditional_hp_bedgraph.config" options "-stub" @@ -357,7 +366,8 @@ nextflow_process { ] 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', 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) 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 b960409d2577..eefa7e6d667a 100644 --- a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap +++ b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap @@ -1,56 +1,5 @@ { - "[bam, bai], fasta, bed - traditional, HP": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - [ - "test_1.bed:md5,464a9870774c340753e79639aeaf76c2", - "test_2.bed:md5,118de4b653dd082d76faa8802df493eb" - ] - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" - ], - "bed": [ - [ - { - "id": "test" - }, - [ - "test_1.bed:md5,464a9870774c340753e79639aeaf76c2", - "test_2.bed:md5,118de4b653dd082d76faa8802df493eb" - ] - ] - ], - "bedgraph": [ - - ], - "log": [ - - ], - "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-10T09:09:40.272533628" - }, - "[bam, bai], fasta, bed - traditional, HP, bedgraph - stub": { + "[bam, bai], [fasta, fai], [] - stub": { "content": [ { "0": [ @@ -78,7 +27,7 @@ ] ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ @@ -105,17 +54,17 @@ ] ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:11:33.234594142" + "timestamp": "2025-04-04T17:33:00.452010671" }, - "[bam, bai], fasta, []": { + "[bam, bai], [fasta, fai], bed - traditional, HP": { "content": [ { "0": [ @@ -123,7 +72,10 @@ { "id": "test" }, - "test.bed:md5,f973de342df883efc1656c82a3a3978d" + [ + "test_1.bed:md5,464a9870774c340753e79639aeaf76c2", + "test_2.bed:md5,118de4b653dd082d76faa8802df493eb" + ] ] ], "1": [ @@ -133,14 +85,17 @@ ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ { "id": "test" }, - "test.bed:md5,f973de342df883efc1656c82a3a3978d" + [ + "test_1.bed:md5,464a9870774c340753e79639aeaf76c2", + "test_2.bed:md5,118de4b653dd082d76faa8802df493eb" + ] ] ], "bedgraph": [ @@ -150,17 +105,17 @@ ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:09:03.537667806" + "timestamp": "2025-04-04T17:32:39.967304077" }, - "[bam, bai], fasta, bed - traditional - stub": { + "[bam, bai], [], []": { "content": [ { "0": [ @@ -168,64 +123,44 @@ { "id": "test" }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed:md5,f973de342df883efc1656c82a3a3978d" ] ], "1": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "2": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ { "id": "test" }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed:md5,f973de342df883efc1656c82a3a3978d" ] ], "bedgraph": [ - [ - { - "id": "test" - }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "log": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:10:45.47904997" + "timestamp": "2025-04-04T18:20:59.925917273" }, - "[bam, bai], fasta, bed - traditional, HP - stub": { + "[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub": { "content": [ { "0": [ @@ -253,7 +188,7 @@ ] ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ @@ -280,17 +215,17 @@ ] ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:11:06.023194848" + "timestamp": "2025-04-04T17:33:30.43271761" }, - "[bam, bai], fasta, [] - stub": { + "[bam, bai], [fasta, fai], bed - stub": { "content": [ { "0": [ @@ -318,7 +253,7 @@ ] ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ @@ -345,17 +280,17 @@ ] ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:10:17.995261822" + "timestamp": "2025-04-04T17:33:07.843477848" }, - "[bam, bai], fasta, bed - stub": { + "[bam, bai], [fasta, fai], bed - traditional": { "content": [ { "0": [ @@ -363,64 +298,140 @@ { "id": "test" }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed:md5,db6333f714a8ea4aa33902404a8d4812" ] ], "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" + ], + "bed": [ [ { "id": "test" }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed:md5,db6333f714a8ea4aa33902404a8d4812" ] ], - "2": [ + "bedgraph": [ + + ], + "log": [ + + ], + "versions": [ + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-04-04T17:32:32.191090081" + }, + "[bam, bai], [fasta, fai], bed": { + "content": [ + { + "0": [ [ { "id": "test" }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170" ] + ], + "1": [ + + ], + "2": [ + ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ { "id": "test" }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170" ] ], "bedgraph": [ + + ], + "log": [ + + ], + "versions": [ + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-04-04T17:32:24.40436977" + }, + "[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph": { + "content": [ + { + "0": [ + + ], + "1": [ [ { "id": "test" }, - "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0", + "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9" + ] ] ], - "log": [ + "2": [ + + ], + "3": [ + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" + ], + "bed": [ + + ], + "bedgraph": [ [ { "id": "test" }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0", + "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9" + ] ] + ], + "log": [ + ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:10:30.574897879" + "timestamp": "2025-04-04T17:32:47.765198075" }, - "[bam, bai], [], []": { + "[bam, bai], [fasta, fai], []": { "content": [ { "0": [ @@ -438,7 +449,7 @@ ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ @@ -455,17 +466,17 @@ ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:08:51.291346508" + "timestamp": "2025-04-04T17:51:55.548559619" }, - "[bam, bai], [], [] - stub": { + "[bam, bai], [fasta, fai], bed - traditional, HP - stub": { "content": [ { "0": [ @@ -493,7 +504,7 @@ ] ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ @@ -520,17 +531,17 @@ ] ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:10:05.670301111" + "timestamp": "2025-04-04T17:33:22.629911029" }, - "[bam, bai], fasta, bed": { + "[bam, bai], [], [] - stub": { "content": [ { "0": [ @@ -538,95 +549,64 @@ { "id": "test" }, - "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170" + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" - ], - "bed": [ [ { "id": "test" }, - "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170" + "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "bedgraph": [ - - ], - "log": [ - - ], - "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-10T09:09:15.042805699" - }, - "[bam, bai], fasta, bed - traditional, HP, bedgraph": { - "content": [ - { - "0": [ - - ], - "1": [ + "2": [ [ { "id": "test" }, - [ - "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0", - "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9" - ] + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "2": [ - ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ - + [ + { + "id": "test" + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "bedgraph": [ [ { "id": "test" }, - [ - "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0", - "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9" - ] + "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "log": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:09:52.968133216" + "timestamp": "2025-04-04T17:35:16.289350959" }, - "[bam, bai], fasta, bed - traditional": { + "[bam, bai], [fasta, fai], bed - traditional - stub": { "content": [ { "0": [ @@ -634,41 +614,61 @@ { "id": "test" }, - "test.bed:md5,db6333f714a8ea4aa33902404a8d4812" + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ - + [ + { + "id": "test" + }, + "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "3": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ], "bed": [ [ { "id": "test" }, - "test.bed:md5,db6333f714a8ea4aa33902404a8d4812" + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bedgraph": [ - + [ + { + "id": "test" + }, + "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "log": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - "versions.yml:md5,aa9f1fd8a0c9ab9709f381f864f6cdbe" + "versions.yml:md5,8ecd5929497f9f807e1fbb44f1034dc3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-06-10T09:09:27.735400826" + "timestamp": "2025-04-04T17:33:15.218082198" } } \ No newline at end of file diff --git a/modules/nf-core/porechop/porechop/environment.yml b/modules/nf-core/porechop/porechop/environment.yml index b2696aeddff2..109cf8bd68fa 100644 --- a/modules/nf-core/porechop/porechop/environment.yml +++ b/modules/nf-core/porechop/porechop/environment.yml @@ -5,3 +5,4 @@ channels: - bioconda dependencies: - bioconda::porechop=0.2.4 + - conda-forge::pigz=2.8 diff --git a/modules/nf-core/porechop/porechop/main.nf b/modules/nf-core/porechop/porechop/main.nf index 1ff02a12a520..34daf3e8951f 100644 --- a/modules/nf-core/porechop/porechop/main.nf +++ b/modules/nf-core/porechop/porechop/main.nf @@ -3,9 +3,10 @@ process PORECHOP_PORECHOP { label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' : - 'biocontainers/porechop:0.2.4--py39h7cff6ad_2' }" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2bce1f10c51906a66c4c4d3a7485394f67e304177192ad1cce6cf586a3a18bae/data' : + 'community.wave.seqera.io/library/porechop_pigz:d1655e5b5bad786c' }" + input: tuple val(meta), path(reads)