From 48304c0b444de153494e85b0d46fcaa6fb45c8c7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 31 Oct 2023 12:01:23 +0100 Subject: [PATCH 1/3] update bclconvert to 4.2.4 --- modules.json | 10 +- modules/nf-core/bcl2fastq/environment.yml | 4 + modules/nf-core/bcl2fastq/meta.yml | 3 +- modules/nf-core/bcl2fastq/tests/main.nf.test | 32 +++ .../nf-core/bcl2fastq/tests/main.nf.test.snap | 215 ++++++++++++++++++ .../nf-core/bcl2fastq/tests/nextflow.config | 6 + modules/nf-core/bcl2fastq/tests/tags.yml | 2 + modules/nf-core/bclconvert/environment.yml | 4 + modules/nf-core/bclconvert/main.nf | 2 +- modules/nf-core/bclconvert/meta.yml | 4 +- modules/nf-core/bclconvert/tests/main.nf.test | 41 ++++ .../bclconvert/tests/main.nf.test.snap | 64 ++++++ .../nf-core/bclconvert/tests/nextflow.config | 10 + modules/nf-core/bclconvert/tests/tags.yml | 2 + modules/nf-core/untar/environment.yml | 8 + modules/nf-core/untar/main.nf | 2 +- modules/nf-core/untar/meta.yml | 5 + subworkflows/nf-core/bcl_demultiplex/meta.yml | 2 + 18 files changed, 407 insertions(+), 9 deletions(-) create mode 100644 modules/nf-core/bcl2fastq/environment.yml create mode 100644 modules/nf-core/bcl2fastq/tests/main.nf.test create mode 100644 modules/nf-core/bcl2fastq/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcl2fastq/tests/nextflow.config create mode 100644 modules/nf-core/bcl2fastq/tests/tags.yml create mode 100644 modules/nf-core/bclconvert/environment.yml create mode 100644 modules/nf-core/bclconvert/tests/main.nf.test create mode 100644 modules/nf-core/bclconvert/tests/main.nf.test.snap create mode 100644 modules/nf-core/bclconvert/tests/nextflow.config create mode 100644 modules/nf-core/bclconvert/tests/tags.yml create mode 100644 modules/nf-core/untar/environment.yml diff --git a/modules.json b/modules.json index fd66ecb0..d0ec3d5a 100644 --- a/modules.json +++ b/modules.json @@ -12,12 +12,12 @@ }, "bcl2fastq": { "branch": "master", - "git_sha": "23ca653e098ef2869598f355a6d15cd7e4807b95", + "git_sha": "bb0fc446bbf417c1fc48e5663e06cbb4e5e42b34", "installed_by": ["bcl_demultiplex"] }, "bclconvert": { "branch": "master", - "git_sha": "23ca653e098ef2869598f355a6d15cd7e4807b95", + "git_sha": "01d7c442ac81bf0445650496806a14345b5e93aa", "installed_by": ["bcl_demultiplex"] }, "custom/dumpsoftwareversions": { @@ -57,8 +57,8 @@ }, "untar": { "branch": "master", - "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", - "installed_by": ["modules", "bcl_demultiplex"] + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", + "installed_by": ["modules"] } } }, @@ -66,7 +66,7 @@ "nf-core": { "bcl_demultiplex": { "branch": "master", - "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/bcl2fastq/environment.yml b/modules/nf-core/bcl2fastq/environment.yml new file mode 100644 index 00000000..bcd3a8b1 --- /dev/null +++ b/modules/nf-core/bcl2fastq/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/bcl2fastq/meta.yml b/modules/nf-core/bcl2fastq/meta.yml index 22248d3b..34d7762f 100644 --- a/modules/nf-core/bcl2fastq/meta.yml +++ b/modules/nf-core/bcl2fastq/meta.yml @@ -10,7 +10,6 @@ tools: homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software" documentation: "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf" licence: "ILLUMINA" - input: - meta: type: map @@ -61,3 +60,5 @@ output: pattern: "*.{bin}" authors: - "@matthdsm" +maintainers: + - "@matthdsm" diff --git a/modules/nf-core/bcl2fastq/tests/main.nf.test b/modules/nf-core/bcl2fastq/tests/main.nf.test new file mode 100644 index 00000000..ca03b972 --- /dev/null +++ b/modules/nf-core/bcl2fastq/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test Process BCL2FASTQ" + script "modules/nf-core/bcl2fastq/main.nf" + process "BCL2FASTQ" + config "./nextflow.config" + tag "bcl2fastq" + tag "modules" + tag "modules_nfcore" + + test("homo sapiens illumina [bcl]") { + when { + process { + //TODO use new test dataset when available, see https://github.com/nf-core/test-datasets/issues/996 + """ + input[0] = [ + [ id: 'test', lane:1 ], + file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/bcl2fastq/tests/main.nf.test.snap b/modules/nf-core/bcl2fastq/tests/main.nf.test.snap new file mode 100644 index 00000000..7f3e217e --- /dev/null +++ b/modules/nf-core/bcl2fastq/tests/main.nf.test.snap @@ -0,0 +1,215 @@ +{ + "homo sapiens illumina [bcl]": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "lane": 1 + }, + "Sample1_S1_L001_R1_001.fastq.gz:md5,e92fce7b86c6447b053d72c5cb4be89c" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + [ + { + "id": "test", + "lane": 1 + }, + [ + [ + [ + [ + [ + [ + "lane.html:md5,794e48287f47a9f22dcb6b6d0c22c3eb", + "laneBarcode.html:md5,2bbdae3ee57151eab520c966597d7438" + ], + [ + + ] + ] + ], + [ + [ + [ + "lane.html:md5,f741870307050dcea79a838f5971770f", + "laneBarcode.html:md5,ffe2e863811c76cb9da27d5d124e0611" + ], + [ + "lane.html:md5,cca97e771d3491dbc8cd3fe389595b09", + "laneBarcode.html:md5,cca97e771d3491dbc8cd3fe389595b09" + ] + ], + [ + [ + "lane.html:md5,c383b0768d9978733d3f5d3b91c15af0", + "laneBarcode.html:md5,48842c23b9a2816aec540177df870968" + ], + [ + + ] + ] + ] + ], + "Report.css:md5,eb7d3eb68fc1539f411404987246b59b", + "index.html:md5,5747c407854ae2c358d0ec201ce622d8", + "tree.html:md5,a1b9bf592973ca829ec69ddf888b7e34" + ] + ] + ] + ], + "5": [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "AdapterTrimming.txt:md5,48ed2b914b1246c0b5d8667525550946", + "ConversionStats.xml:md5,8fe0f57f3f5d256a0762dba75ac62d05", + "DemultiplexingStats.xml:md5,2047ff18f5b9107c084de06e9ff943ad", + "DemuxSummaryF1L1.txt:md5,03e5fd0c1e3079c5f8c7b4d0501b37ff", + "FastqSummaryF1L1.txt:md5,0c6f2d87ee183b84d1051cde9a5643d1", + "Stats.json:md5,8e5f038b8aa9e465599d3575f930e604" + ] + ] + ], + "6": [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "ControlMetricsOut.bin:md5,6d77b38d0793a6e1ce1e85706e488953", + "CorrectedIntMetricsOut.bin:md5,2bbf84d3be72734addaa2fe794711434", + "ErrorMetricsOut.bin:md5,38c88def138e9bb832539911affdb286", + "ExtractionMetricsOut.bin:md5,7497c3178837eea8f09350b5cd252e99", + "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf", + "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c", + "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c" + ] + ] + ], + "7": [ + "versions.yml:md5,12f3dca40b6a65cec6ba51c0fd872152" + ], + "fastq": [ + [ + { + "id": "test", + "lane": 1 + }, + "Sample1_S1_L001_R1_001.fastq.gz:md5,e92fce7b86c6447b053d72c5cb4be89c" + ] + ], + "fastq_idx": [ + + ], + "interop": [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "ControlMetricsOut.bin:md5,6d77b38d0793a6e1ce1e85706e488953", + "CorrectedIntMetricsOut.bin:md5,2bbf84d3be72734addaa2fe794711434", + "ErrorMetricsOut.bin:md5,38c88def138e9bb832539911affdb286", + "ExtractionMetricsOut.bin:md5,7497c3178837eea8f09350b5cd252e99", + "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf", + "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c", + "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c" + ] + ] + ], + "reports": [ + [ + { + "id": "test", + "lane": 1 + }, + [ + [ + [ + [ + [ + [ + "lane.html:md5,794e48287f47a9f22dcb6b6d0c22c3eb", + "laneBarcode.html:md5,2bbdae3ee57151eab520c966597d7438" + ], + [ + + ] + ] + ], + [ + [ + [ + "lane.html:md5,f741870307050dcea79a838f5971770f", + "laneBarcode.html:md5,ffe2e863811c76cb9da27d5d124e0611" + ], + [ + "lane.html:md5,cca97e771d3491dbc8cd3fe389595b09", + "laneBarcode.html:md5,cca97e771d3491dbc8cd3fe389595b09" + ] + ], + [ + [ + "lane.html:md5,c383b0768d9978733d3f5d3b91c15af0", + "laneBarcode.html:md5,48842c23b9a2816aec540177df870968" + ], + [ + + ] + ] + ] + ], + "Report.css:md5,eb7d3eb68fc1539f411404987246b59b", + "index.html:md5,5747c407854ae2c358d0ec201ce622d8", + "tree.html:md5,a1b9bf592973ca829ec69ddf888b7e34" + ] + ] + ] + ], + "stats": [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "AdapterTrimming.txt:md5,48ed2b914b1246c0b5d8667525550946", + "ConversionStats.xml:md5,8fe0f57f3f5d256a0762dba75ac62d05", + "DemultiplexingStats.xml:md5,2047ff18f5b9107c084de06e9ff943ad", + "DemuxSummaryF1L1.txt:md5,03e5fd0c1e3079c5f8c7b4d0501b37ff", + "FastqSummaryF1L1.txt:md5,0c6f2d87ee183b84d1051cde9a5643d1", + "Stats.json:md5,8e5f038b8aa9e465599d3575f930e604" + ] + ] + ], + "undetermined": [ + + ], + "undetermined_idx": [ + + ], + "versions": [ + "versions.yml:md5,12f3dca40b6a65cec6ba51c0fd872152" + ] + } + ], + "timestamp": "2023-10-25T11:06:04.763448" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcl2fastq/tests/nextflow.config b/modules/nf-core/bcl2fastq/tests/nextflow.config new file mode 100644 index 00000000..d1985111 --- /dev/null +++ b/modules/nf-core/bcl2fastq/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + ext.args = "--tiles s_1_1101" +} diff --git a/modules/nf-core/bcl2fastq/tests/tags.yml b/modules/nf-core/bcl2fastq/tests/tags.yml new file mode 100644 index 00000000..991d1761 --- /dev/null +++ b/modules/nf-core/bcl2fastq/tests/tags.yml @@ -0,0 +1,2 @@ +bcl2fastq: + - modules/nf-core/bcl2fastq/** diff --git a/modules/nf-core/bclconvert/environment.yml b/modules/nf-core/bclconvert/environment.yml new file mode 100644 index 00000000..bcd3a8b1 --- /dev/null +++ b/modules/nf-core/bclconvert/environment.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf index 95460dc9..3530e5c5 100644 --- a/modules/nf-core/bclconvert/main.nf +++ b/modules/nf-core/bclconvert/main.nf @@ -2,7 +2,7 @@ process BCLCONVERT { tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" } label 'process_high' - container "nf-core/bclconvert:4.0.3" + container "nf-core/bclconvert:4.2.4" input: tuple val(meta), path(samplesheet), path(run_dir) diff --git a/modules/nf-core/bclconvert/meta.yml b/modules/nf-core/bclconvert/meta.yml index c7f9bbd3..c62b2057 100644 --- a/modules/nf-core/bclconvert/meta.yml +++ b/modules/nf-core/bclconvert/meta.yml @@ -10,7 +10,6 @@ tools: homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html" documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm" licence: "ILLUMINA" - input: - meta: type: map @@ -61,3 +60,6 @@ output: pattern: "*.{bin}" authors: - "@matthdsm" +maintainers: + - "@matthdsm" + - "@maxulysse" diff --git a/modules/nf-core/bclconvert/tests/main.nf.test b/modules/nf-core/bclconvert/tests/main.nf.test new file mode 100644 index 00000000..ec0623af --- /dev/null +++ b/modules/nf-core/bclconvert/tests/main.nf.test @@ -0,0 +1,41 @@ +nextflow_process { + + name "Test Process BCLCONVERT" + script "../main.nf" + process "BCLCONVERT" + config "./nextflow.config" + tag "bclconvert" + tag "modules" + tag "modules_nfcore" + + test("homo sapiens illumina [bcl]") { + when { + process { + //TODO use new test dataset when available, see https://github.com/nf-core/test-datasets/issues/996 + """ + input[0] = [ + [ id: 'test', lane:1 ], + file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.reports, + process.out.versions, + process.out.fastq, + process.out.undetermined, + file(process.out.logs.get(0).get(1)).list().sort(), + process.out.interop.get(0).get(1).findAll { file(it).name != "IndexMetricsOut.bin" }, + ).match() + }, + { assert file(process.out.interop.get(0).get(1).find { file(it).name == "IndexMetricsOut.bin" }).exists() } + ) + } + } +} diff --git a/modules/nf-core/bclconvert/tests/main.nf.test.snap b/modules/nf-core/bclconvert/tests/main.nf.test.snap new file mode 100644 index 00000000..46e6cc66 --- /dev/null +++ b/modules/nf-core/bclconvert/tests/main.nf.test.snap @@ -0,0 +1,64 @@ +{ + "homo sapiens illumina [bcl]": { + "content": [ + [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", + "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", + "Demultiplex_Stats.csv:md5,93949a8cd96f907d83e0808c1ec2a04b", + "Demultiplex_Tile_Stats.csv:md5,83120160b0f22a1303fa1db31c19f6e9", + "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf", + "Index_Hopping_Counts.csv:md5,1059369e375fd8f8423c0f6c934be978", + "Quality_Metrics.csv:md5,6614accb1bb414fe312b17b81f5521f7", + "Quality_Tile_Metrics.csv:md5,cdc89fd2962bdd4a24f71e186112118a", + "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a", + "SampleSheet.csv:md5,dc0dffd39541dd6cc5b4801d768a8d2b", + "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc", + "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0" + ] + ] + ], + [ + "versions.yml:md5,71376e3913c75d766bb13d26f9f26e89" + ], + [ + [ + { + "id": "test", + "lane": 1 + }, + "Sample1_S1_L001_R1_001.fastq.gz:md5,a0c1359a2c922967660524a6e77db494" + ] + ], + [ + [ + { + "id": "test", + "lane": 1 + }, + "Undetermined_S0_L001_R1_001.fastq.gz:md5,163be0a88c70ca629fd516dbaadad96a" + ] + ], + [ + "Errors.log", + "FastqComplete.txt", + "Info.log", + "Warnings.log" + ], + [ + "ControlMetricsOut.bin:md5,6d77b38d0793a6e1ce1e85706e488953", + "CorrectedIntMetricsOut.bin:md5,2bbf84d3be72734addaa2fe794711434", + "ErrorMetricsOut.bin:md5,38c88def138e9bb832539911affdb286", + "ExtractionMetricsOut.bin:md5,7497c3178837eea8f09350b5cd252e99", + "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c", + "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c" + ] + ], + "timestamp": "2023-10-31T11:16:15.787477" + } +} \ No newline at end of file diff --git a/modules/nf-core/bclconvert/tests/nextflow.config b/modules/nf-core/bclconvert/tests/nextflow.config new file mode 100644 index 00000000..344f4720 --- /dev/null +++ b/modules/nf-core/bclconvert/tests/nextflow.config @@ -0,0 +1,10 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + ext.args = {[ + meta.lane ? "--bcl-only-lane ${meta.lane}" : "", + "--force", + "--first-tile-only true" + ].join(" ").trim()} +} diff --git a/modules/nf-core/bclconvert/tests/tags.yml b/modules/nf-core/bclconvert/tests/tags.yml new file mode 100644 index 00000000..da3e03d5 --- /dev/null +++ b/modules/nf-core/bclconvert/tests/tags.yml @@ -0,0 +1,2 @@ +bclconvert: + - modules/nf-core/bclconvert/** diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml new file mode 100644 index 00000000..2d52ce64 --- /dev/null +++ b/modules/nf-core/untar/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 + - conda-forge::grep=3.11 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 61461c39..04f5f1b2 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ process UNTAR { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" + conda 'modules/nf-core/untar/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index db241a6e..a9a2110f 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -39,3 +39,8 @@ authors: - "@drpatelh" - "@matthdsm" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@matthdsm" + - "@jfy133" diff --git a/subworkflows/nf-core/bcl_demultiplex/meta.yml b/subworkflows/nf-core/bcl_demultiplex/meta.yml index 12a0619d..2fc8f7aa 100644 --- a/subworkflows/nf-core/bcl_demultiplex/meta.yml +++ b/subworkflows/nf-core/bcl_demultiplex/meta.yml @@ -54,3 +54,5 @@ output: pattern: "versions.yml" authors: - "@matthdsm" +maintainers: + - "@matthdsm" From 2b8df8a021c1467a8fbea92d53782c58dd5ad2b3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 31 Oct 2023 16:03:52 +0100 Subject: [PATCH 2/3] update snapshot --- tests/pipeline/bclconvert.nf.test.snap | 10 ++--- tests/pipeline/skip_tools.nf.test.snap | 56 +++++++++++++------------- 2 files changed, 33 insertions(+), 33 deletions(-) diff --git a/tests/pipeline/bclconvert.nf.test.snap b/tests/pipeline/bclconvert.nf.test.snap index 45c309af..1ac47bc9 100644 --- a/tests/pipeline/bclconvert.nf.test.snap +++ b/tests/pipeline/bclconvert.nf.test.snap @@ -2,9 +2,9 @@ "bclconvert": { "content": [ "Sample1_S1_L001.fastp.fastq.gz:md5,8a723787b4a0c0fbf5b81d3a0b989c69", - "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1", + "Sample1_S1_L001_R1_001.fastq.gz:md5,a0c1359a2c922967660524a6e77db494", "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", - "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,163be0a88c70ca629fd516dbaadad96a", [ "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", @@ -20,13 +20,13 @@ "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0" ] ], - "timestamp": "2023-10-17T07:59:12+0000" + "timestamp": "2023-10-31T12:33:16.768754" }, "software_versions": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T07:59:12+0000" + "timestamp": "2023-10-31T12:33:16.074351" }, "multiqc": { "content": [ diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap index 24669f58..a8de4104 100644 --- a/tests/pipeline/skip_tools.nf.test.snap +++ b/tests/pipeline/skip_tools.nf.test.snap @@ -1,15 +1,15 @@ { "software_versions_skip_trimming": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:40:12.308416" }, "skip_fastqc": { "content": [ - "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1", + "Sample1_S1_L001_R1_001.fastq.gz:md5,a0c1359a2c922967660524a6e77db494", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,163be0a88c70ca629fd516dbaadad96a", [ "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", @@ -25,13 +25,13 @@ "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0" ] ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:41:59.969786" }, "skip_fastp": { "content": [ - "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1", - "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,c547a3c03e7c60c871d78018ec5d933f", - "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0", + "Sample1_S1_L001_R1_001.fastq.gz:md5,a0c1359a2c922967660524a6e77db494", + "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,10295d4e5ca66dae7788bbf24886cded", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,163be0a88c70ca629fd516dbaadad96a", [ "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", @@ -47,13 +47,13 @@ "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0" ] ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:40:44.801689" }, "skip_multiqc": { "content": [ - "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1", + "Sample1_S1_L001_R1_001.fastq.gz:md5,a0c1359a2c922967660524a6e77db494", "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,163be0a88c70ca629fd516dbaadad96a", [ "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", @@ -69,13 +69,13 @@ "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0" ] ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:43:37.155748" }, "skip_fastp_fastqc": { "content": [ - "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1", - "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,c547a3c03e7c60c871d78018ec5d933f", - "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0", + "Sample1_S1_L001_R1_001.fastq.gz:md5,a0c1359a2c922967660524a6e77db494", + "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,10295d4e5ca66dae7788bbf24886cded", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,163be0a88c70ca629fd516dbaadad96a", [ "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", @@ -91,37 +91,37 @@ "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0" ] ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:42:35.089011" }, "software_versions_skip_fastqc": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:41:58.993732" }, "software_versions_skip_fastp_fastqc": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:42:33.138684" }, "software_versions_skip_multiqc": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:43:35.278888" }, "software_versions_skip_fastp": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:40:44.187338" }, "skip_trimming": { "content": [ - "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1", - "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,c547a3c03e7c60c871d78018ec5d933f", - "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0", + "Sample1_S1_L001_R1_001.fastq.gz:md5,a0c1359a2c922967660524a6e77db494", + "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,10295d4e5ca66dae7788bbf24886cded", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,163be0a88c70ca629fd516dbaadad96a", [ "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", @@ -137,6 +137,6 @@ "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0" ] ], - "timestamp": "2023-10-17T08:05:28+0000" + "timestamp": "2023-10-31T12:40:12.565447" } } \ No newline at end of file From 4290c024817b9f408e39fe003aa7b1aef0a3e122 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 31 Oct 2023 16:10:36 +0100 Subject: [PATCH 3/3] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2c664482..75894667 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,12 +8,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - [#141](https://github.com/nf-core/demultiplex/pull/141) Updated template to nf-core/tools v2.10 +- [#152](https://github.com/nf-core/demultiplex/pull/152) Updated bclconvert module to 4.2.4 ### `Fixed` - [#127](https://github.com/nf-core/demultiplex/pull/127) Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0 - [#140](https://github.com/nf-core/demultiplex/pull/140) Make it possible to skip MultiQC, fix error raising - [#145](https://github.com/nf-core/demultiplex/pull/145) Fix MultiQC report generation +- [#152](https://github.com/nf-core/demultiplex/pull/152) Close [#150](https://github.com/nf-core/demultiplex/issues/150) ## `Removed`