diff --git a/CHANGELOG.md b/CHANGELOG.md index fa165f22..a004f55c 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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) - [#157](https://github.com/nf-core/demultiplex/pull/157) Fix bcl2fastq and bclconvert publishDir +- [#158](https://github.com/nf-core/demultiplex/pull/158) Update all modules ## `Removed` diff --git a/modules.json b/modules.json index d0ec3d5a..a50fc12b 100644 --- a/modules.json +++ b/modules.json @@ -7,57 +7,57 @@ "nf-core": { "bases2fastq": { "branch": "master", - "git_sha": "716ef3019b66772a817b417078edce2f7b337858", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "bcl2fastq": { "branch": "master", - "git_sha": "bb0fc446bbf417c1fc48e5663e06cbb4e5e42b34", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["bcl_demultiplex"] }, "bclconvert": { "branch": "master", - "git_sha": "01d7c442ac81bf0445650496806a14345b5e93aa", + "git_sha": "e140d75607c5abcd6bbfedf290276323194aca79", "installed_by": ["bcl_demultiplex"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", + "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", "installed_by": ["modules"] }, "falco": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd", + "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", "installed_by": ["modules"] }, "fqtk": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "md5sum": { "branch": "master", - "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", + "git_sha": "4ab13872435962dadc239979554d13709e20bf29", "installed_by": ["modules"] }, "sgdemux": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bclconvert/environment.yml b/modules/nf-core/bases2fastq/environment.yml similarity index 74% rename from modules/nf-core/bclconvert/environment.yml rename to modules/nf-core/bases2fastq/environment.yml index bcd3a8b1..80d04671 100644 --- a/modules/nf-core/bclconvert/environment.yml +++ b/modules/nf-core/bases2fastq/environment.yml @@ -1,3 +1,4 @@ +name: bases2fastq channels: - conda-forge - bioconda diff --git a/modules/nf-core/bases2fastq/meta.yml b/modules/nf-core/bases2fastq/meta.yml index 97afce2f..9b6f44dd 100644 --- a/modules/nf-core/bases2fastq/meta.yml +++ b/modules/nf-core/bases2fastq/meta.yml @@ -10,7 +10,6 @@ tools: homepage: "https://go.elementbiosciences.com/bases2fastq-download" documentation: "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq" licence: "http://go.elembio.link/eula" - input: - meta: type: map @@ -24,7 +23,6 @@ input: - run_dir: type: directory description: "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied" - output: - meta: type: map @@ -63,6 +61,7 @@ output: type: file description: Unassigned Sequences pattern: "output/UnassignedSequences.csv" - authors: - "@Emiller88" +maintainers: + - "@Emiller88" diff --git a/modules/nf-core/bcl2fastq/environment.yml b/modules/nf-core/bcl2fastq/environment.yml index bcd3a8b1..17e01d94 100644 --- a/modules/nf-core/bcl2fastq/environment.yml +++ b/modules/nf-core/bcl2fastq/environment.yml @@ -1,3 +1,4 @@ +name: bcl2fastq channels: - conda-forge - bioconda diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf index 3530e5c5..2fa682b0 100644 --- a/modules/nf-core/bclconvert/main.nf +++ b/modules/nf-core/bclconvert/main.nf @@ -60,8 +60,7 @@ process BCLCONVERT { $args \\ --output-directory . \\ --bcl-input-directory ${input_dir} \\ - --sample-sheet ${samplesheet} \\ - --bcl-num-parallel-tiles ${task.cpus} + --sample-sheet ${samplesheet} cp -r ${input_dir}/InterOp . diff --git a/modules/nf-core/bclconvert/meta.yml b/modules/nf-core/bclconvert/meta.yml index c62b2057..c4acdb51 100644 --- a/modules/nf-core/bclconvert/meta.yml +++ b/modules/nf-core/bclconvert/meta.yml @@ -9,7 +9,7 @@ tools: description: "Demultiplex Illumina BCL files" homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html" documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm" - licence: "ILLUMINA" + licence: ["ILLUMINA"] input: - meta: type: map diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..f0c63f69 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c9d014b1..7685b33c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap index 8713b921..4274ed57 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -3,25 +3,25 @@ "content": [ { "0": [ - "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" ], "1": [ - "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" ], "2": [ - "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + "versions.yml:md5,3843ac526e762117eedf8825b40683df" ], "mqc_yml": [ - "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" ], "versions": [ - "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + "versions.yml:md5,3843ac526e762117eedf8825b40683df" ], "yml": [ - "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" ] } ], - "timestamp": "2023-10-11T17:10:02.930699" + "timestamp": "2023-11-03T14:43:22.157011" } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/falco/environment.yml b/modules/nf-core/falco/environment.yml new file mode 100644 index 00000000..eeedb5b7 --- /dev/null +++ b/modules/nf-core/falco/environment.yml @@ -0,0 +1,7 @@ +name: falco +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::falco=1.2.1 diff --git a/modules/nf-core/falco/main.nf b/modules/nf-core/falco/main.nf index 73e79609..ab060542 100644 --- a/modules/nf-core/falco/main.nf +++ b/modules/nf-core/falco/main.nf @@ -3,7 +3,7 @@ process FALCO { label 'process_single' - conda "bioconda::falco=1.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3': 'biocontainers/falco:1.2.1--h867801b_3' }" diff --git a/modules/nf-core/falco/meta.yml b/modules/nf-core/falco/meta.yml index 63846491..71f69e91 100644 --- a/modules/nf-core/falco/meta.yml +++ b/modules/nf-core/falco/meta.yml @@ -8,12 +8,9 @@ keywords: tools: - fastqc: description: "falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads." - homepage: "https://falco.readthedocs.io/" documentation: "https://falco.readthedocs.io/" - licence: "['GPL v3']" - input: - meta: type: map @@ -49,3 +46,5 @@ output: pattern: "versions.yml" authors: - "@lucacozzuto" +maintainers: + - "@lucacozzuto" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml new file mode 100644 index 00000000..70389e66 --- /dev/null +++ b/modules/nf-core/fastp/environment.yml @@ -0,0 +1,7 @@ +name: fastp +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 831b7f12..5fac3c1a 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -2,7 +2,7 @@ process FASTP { tag "$meta.id" label 'process_medium' - conda "bioconda::fastp=0.23.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' : 'biocontainers/fastp:0.23.4--h5f740d0_0' }" @@ -45,7 +45,7 @@ process FASTP { $adapter_list \\ $fail_fastq \\ $args \\ - 2> ${prefix}.fastp.log \\ + 2> >(tee ${prefix}.fastp.log >&2) \\ | gzip -c > ${prefix}.fastp.fastq.gz cat <<-END_VERSIONS > versions.yml @@ -66,7 +66,7 @@ process FASTP { $adapter_list \\ $fail_fastq \\ $args \\ - 2> ${prefix}.fastp.log + 2> >(tee ${prefix}.fastp.log >&2) cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -91,7 +91,7 @@ process FASTP { --thread $task.cpus \\ --detect_adapter_for_pe \\ $args \\ - 2> ${prefix}.fastp.log + 2> >(tee ${prefix}.fastp.log >&2) cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 197ea7ca..c22a16ab 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -33,7 +33,6 @@ input: - save_merged: type: boolean description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz` - output: - meta: type: map @@ -71,3 +70,6 @@ output: authors: - "@drpatelh" - "@kevinmenden" +maintainers: + - "@drpatelh" + - "@kevinmenden" diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test new file mode 100644 index 00000000..f610b735 --- /dev/null +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -0,0 +1,485 @@ +nextflow_process { + + name "Test Process FASTP" + script "../main.nf" + process "FASTP" + tag "modules" + tag "modules_nfcore" + tag "fastp" + + test("test_fastp_single_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ + [ id:'test', single_end:true ], + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:12.922000 K (92.984097%)", + "single end (151 cycles)" ] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 99" ] + def read_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("test_fastp_single_end_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "The input has little adapter percentage (~0.000000%), probably it's trimmed before."] + def log_text = [ "No adapter detected for read1", + "Q30 bases: 12281(88.3716%)"] + def json_text = ['"passed_filter_reads": 198'] + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("fastp test_fastp_interleaved") { + config './nextflow.config' + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "paired end (151 cycles + 151 cycles)"] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 198"] + def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("fastp test_fastp_interleaved_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_single_end_trim_fail") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:12.922000 K (92.984097%)", + "single end (151 cycles)"] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 99" ] + def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { failed_read_lines.each { failed_read_line -> + { assert path(process.out.reads_fail.get(0).get(1)).linesGzip.contains(failed_read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("test_fastp_single_end_trim_fail_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_trim_fail") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "The input has little adapter percentage (~0.000000%), probably it's trimmed before."] + def log_text = [ "No adapter detected for read1", + "Q30 bases: 12281(88.3716%)"] + def json_text = ['"passed_filter_reads": 198'] + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { failed_read2_lines.each { failed_read2_line -> + { assert path(process.out.reads_fail.get(0).get(1).get(1)).linesGzip.contains(failed_read2_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_merged") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = true + + input[0] = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "
"] + def log_text = [ "Merged and filtered:", + "total reads: 75", + "total bases: 13683"] + def json_text = ['"merged_and_filtered": {', '"total_reads": 75', '"total_bases": 13683'] + def read1_lines = [ "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1", + "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC", + "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { read_merged_lines.each { read_merged_line -> + { assert path(process.out.reads_merged.get(0).get(1)).linesGzip.contains(read_merged_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_merged_adapterlist") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta", checkIfExists: true) + save_trimmed_fail = false + save_merged = true + + input[0] = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "
"] + def log_text = [ "Merged and filtered:", + "total reads: 75", + "total bases: 13683"] + def json_text = ['"merged_and_filtered": {', '"total_reads": 75', '"total_bases": 13683',"--adapter_fasta"] + def read1_lines = ["@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1", + "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC", + "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { read_merged_lines.each { read_merged_line -> + { assert path(process.out.reads_merged.get(0).get(1)).linesGzip.contains(read_merged_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } +} diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap new file mode 100644 index 00000000..0fa68c7d --- /dev/null +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -0,0 +1,52 @@ +{ + "fastp test_fastp_interleaved_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,168f516f7bd4b7b6c32da7cba87299a4" + ] + ] + ], + "timestamp": "2023-10-17T11:04:45.794175881" + }, + "test_fastp_single_end_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc" + ] + ] + ], + "timestamp": "2023-10-17T11:04:10.566343705" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "timestamp": "2023-10-17T11:04:10.582076024" + }, + "test_fastp_single_end_trim_fail_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5" + ] + ] + ], + "timestamp": "2023-10-17T11:05:00.379878948" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastp/tests/nextflow.config b/modules/nf-core/fastp/tests/nextflow.config new file mode 100644 index 00000000..0f7849ad --- /dev/null +++ b/modules/nf-core/fastp/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + + withName: FASTP { + ext.args = "--interleaved_in" + } +} diff --git a/modules/nf-core/fastp/tests/tags.yml b/modules/nf-core/fastp/tests/tags.yml new file mode 100644 index 00000000..c1afcce7 --- /dev/null +++ b/modules/nf-core/fastp/tests/tags.yml @@ -0,0 +1,2 @@ +fastp: + - modules/nf-core/fastp/** diff --git a/modules/nf-core/fqtk/environment.yml b/modules/nf-core/fqtk/environment.yml new file mode 100644 index 00000000..1ea15744 --- /dev/null +++ b/modules/nf-core/fqtk/environment.yml @@ -0,0 +1,7 @@ +name: fqtk +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fqtk=0.2.1 diff --git a/modules/nf-core/fqtk/main.nf b/modules/nf-core/fqtk/main.nf index 2b5896b3..5bd11e12 100644 --- a/modules/nf-core/fqtk/main.nf +++ b/modules/nf-core/fqtk/main.nf @@ -2,7 +2,7 @@ process FQTK { tag "$meta.id" label 'process_high' - conda "bioconda::fqtk=0.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fqtk:0.2.1--h9f5acd7_0' : 'biocontainers/fqtk:0.2.1--h9f5acd7_0' }" diff --git a/modules/nf-core/fqtk/meta.yml b/modules/nf-core/fqtk/meta.yml index 1568bdf8..5788b1ba 100644 --- a/modules/nf-core/fqtk/meta.yml +++ b/modules/nf-core/fqtk/meta.yml @@ -10,7 +10,6 @@ tools: homepage: "https://github.com/fulcrumgenomics/fqtk" documentation: "https://github.com/fulcrumgenomics/fqtk" licence: "['MIT']" - input: - meta: type: map @@ -24,7 +23,6 @@ input: - fastq_readstructure_pairs: type: map description: List of lists i.e. [[, , ],...] - output: - meta: type: map @@ -49,6 +47,9 @@ output: description: | File containing unmatched fastq records pattern: "output/unmatched*.fq.gz" - authors: - - "Samantha White @sam-white04" + - "@nh13" + - "@sam-white04" +maintainers: + - "@nh13" + - "@sam-white04" diff --git a/modules/nf-core/md5sum/environment.yml b/modules/nf-core/md5sum/environment.yml new file mode 100644 index 00000000..a7220f8c --- /dev/null +++ b/modules/nf-core/md5sum/environment.yml @@ -0,0 +1,7 @@ +name: md5sum +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::coreutils=9.1 diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf index 189f7e9b..6f718dd7 100644 --- a/modules/nf-core/md5sum/main.nf +++ b/modules/nf-core/md5sum/main.nf @@ -2,7 +2,7 @@ process MD5SUM { tag "$meta.id" label 'process_single' - conda "conda-forge::coreutils=9.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/md5sum/meta.yml b/modules/nf-core/md5sum/meta.yml index 0c9d196f..eb6e5bc9 100644 --- a/modules/nf-core/md5sum/meta.yml +++ b/modules/nf-core/md5sum/meta.yml @@ -10,7 +10,6 @@ tools: homepage: "https://www.gnu.org" documentation: "https://man7.org/linux/man-pages/man1/md5sum.1.html" licence: GPLv3+ - input: - meta: type: map @@ -21,7 +20,6 @@ input: type: file description: Any file pattern: "*.*" - output: - meta: type: map @@ -36,6 +34,7 @@ output: type: file description: File containing checksum pattern: "*.md5" - authors: - "@matthdsm" +maintainers: + - "@matthdsm" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..bc0bdb5b --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.18 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 65d7dd0d..00cc48d2 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : + 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..f1aa660e 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 00000000..c2dad217 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("MULTIQC: FASTQC") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } + + test("MULTIQC: FASTQC and a config file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 00000000..bea6c0d3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/modules/nf-core/sgdemux/environment.yml b/modules/nf-core/sgdemux/environment.yml new file mode 100644 index 00000000..57eccdd2 --- /dev/null +++ b/modules/nf-core/sgdemux/environment.yml @@ -0,0 +1,7 @@ +name: sgdemux +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::sgdemux=1.1.1 diff --git a/modules/nf-core/sgdemux/main.nf b/modules/nf-core/sgdemux/main.nf index 21829623..e817e7bd 100644 --- a/modules/nf-core/sgdemux/main.nf +++ b/modules/nf-core/sgdemux/main.nf @@ -2,7 +2,7 @@ process SGDEMUX { tag "$meta.id" label 'process_high' - conda "bioconda::sgdemux=1.1.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sgdemux:1.1.1--ha982bd6_0' : 'biocontainers/sgdemux:1.1.1--ha982bd6_0' }" diff --git a/modules/nf-core/sgdemux/meta.yml b/modules/nf-core/sgdemux/meta.yml index 977091c7..4c683aff 100644 --- a/modules/nf-core/sgdemux/meta.yml +++ b/modules/nf-core/sgdemux/meta.yml @@ -10,7 +10,6 @@ tools: homepage: "https://github.com/Singular-Genomics/singular-demux" documentation: "https://github.com/Singular-Genomics/singular-demux#sgdemux" licence: "['For Singular G4™ Sequencing Platform only']" - input: - meta: type: map @@ -24,7 +23,6 @@ input: - fastqs_dir: type: directory description: "Input directory containing bgzipped (not gzip) FASTQ files" - output: - meta: type: map @@ -63,6 +61,9 @@ output: File output for dual-indexed runs with barcodes which are unexpected combinations of expected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT pattern: "output/sample_barcode_hop_metrics/tsv" - authors: - - "Samantha White: @samfulcrum" + - "@nh13" + - "@sam-white04" +maintainers: + - "@nh13" + - "@sam-white04" diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 2d52ce64..d6917da3 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,3 +1,4 @@ +name: untar channels: - conda-forge - bioconda diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 04f5f1b2..8a75bb95 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ process UNTAR { tag "$archive" label 'process_single' - conda 'modules/nf-core/untar/environment.yml' + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test new file mode 100644 index 00000000..d40db13d --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test @@ -0,0 +1,77 @@ +nextflow_process { + + name "Test Process UNTAR" + script "../main.nf" + process "UNTAR" + + tag "modules" + tag "modules_nfcore" + tag "untar" + + test("test_untar") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar") }, + ) + } + + } + + test("test_untar_different_output_path") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar_different_output_path") }, + ) + } + + } + + test("test_untar_onlyfiles") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + ) + } + + } + +} diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap new file mode 100644 index 00000000..146c8678 --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -0,0 +1,513 @@ +{ + "test_untar_different_output_path": { + "content": [ + [ + [ + [ + + ], + [ + [ + [ + [ + [ + [ + "s_1_1101.bcl:md5,ad01889e2ff43e2f194224e20bdb600c", + "s_1_1101.stats:md5,4bbbf103454b37fbc3138fadf1b4446b" + ], 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a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml new file mode 100644 index 00000000..feb6f15c --- /dev/null +++ b/modules/nf-core/untar/tests/tags.yml @@ -0,0 +1,2 @@ +untar: + - modules/nf-core/untar/** diff --git a/tests/pipeline/bases2fastq.nf.test.snap b/tests/pipeline/bases2fastq.nf.test.snap index 99f0953c..08f262a8 100644 --- a/tests/pipeline/bases2fastq.nf.test.snap +++ b/tests/pipeline/bases2fastq.nf.test.snap @@ -1,9 +1,9 @@ { "software_versions": { "content": [ - "{BASES2FASTQ={bases2fastq=1.1.0.593880262, use subject to license available at elementbiosciences.com}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BASES2FASTQ={bases2fastq=1.1.0.593880262, use subject to license available at elementbiosciences.com}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T07:59:51+0000" + "timestamp": "2023-12-11T16:57:34.674489" }, "bases2fastq": { "content": [ diff --git a/tests/pipeline/bcl2fastq.nf.test.snap b/tests/pipeline/bcl2fastq.nf.test.snap index 78247b89..e6d68979 100644 --- a/tests/pipeline/bcl2fastq.nf.test.snap +++ b/tests/pipeline/bcl2fastq.nf.test.snap @@ -1,9 +1,9 @@ { "software_versions": { "content": [ - "{BCL2FASTQ={bcl2fastq=2.20.0.422}, 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}}" + "{BCL2FASTQ={bcl2fastq=2.20.0.422}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T07:58:06+0000" + "timestamp": "2023-12-11T16:55:21.645426" }, "bcl2fastq": { "content": [ @@ -64,10 +64,10 @@ }, "multiqc": { "content": [ - "multiqc_bcl2fastq_bylane.txt:md5,3c90d50fec9eb01e32c0f9d7e8295d85", - "multiqc_fastp.txt:md5,76b067a76f4f58759526ca2aa4d6679d", + "multiqc_bcl2fastq_bylane.txt:md5,1425b49f727306a50a8792e7c779a52d", + "multiqc_fastp.txt:md5,d65cc0ccd033e949132c2e46b1f81717", "multiqc_bcl2fastq_bysample.txt:md5,1865f27f430d153085b26c86320718fe" ], - "timestamp": "2023-12-11T16:24:41.682929" + "timestamp": "2023-12-11T16:55:21.680453" } } \ No newline at end of file diff --git a/tests/pipeline/bclconvert.nf.test.snap b/tests/pipeline/bclconvert.nf.test.snap index 8a1ae8b4..5fdda8b7 100644 --- a/tests/pipeline/bclconvert.nf.test.snap +++ b/tests/pipeline/bclconvert.nf.test.snap @@ -24,16 +24,16 @@ }, "software_versions": { "content": [ - "{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}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-31T12:33:16.074351" + "timestamp": "2023-12-11T16:56:35.649441" }, "multiqc": { "content": [ - "multiqc_bclconvert_bylane.txt:md5,8ef9efabf1d2f9de8221e651d0b10e2f", - "multiqc_fastp.txt:md5,76b067a76f4f58759526ca2aa4d6679d", - "multiqc_bclconvert_bysample.txt:md5,b68dcbf3fdb26e6eb483995eb114cdd8" + "multiqc_bclconvert_bylane.txt:md5,9d7173439fd77fdec5936bddd686749f", + "multiqc_fastp.txt:md5,d65cc0ccd033e949132c2e46b1f81717", + "multiqc_bclconvert_bysample.txt:md5,37bf84cfc38af8e044ce92ce47211ebe" ], - "timestamp": "2023-10-17T07:59:12+0000" + "timestamp": "2023-12-11T16:56:35.661017" } } \ No newline at end of file diff --git a/tests/pipeline/fqtk.nf.test.snap b/tests/pipeline/fqtk.nf.test.snap index 868fae29..a483e0c8 100644 --- a/tests/pipeline/fqtk.nf.test.snap +++ b/tests/pipeline/fqtk.nf.test.snap @@ -7,8 +7,8 @@ }, "software_versions": { "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, FQTK={fqtk=0.2.1}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, FQTK={fqtk=0.2.1}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T08:06:53+0000" + "timestamp": "2023-12-11T17:05:36.315291" } } \ No newline at end of file diff --git a/tests/pipeline/sgdemux.nf.test.snap b/tests/pipeline/sgdemux.nf.test.snap index ea3b3b4c..0a68ffc5 100644 --- a/tests/pipeline/sgdemux.nf.test.snap +++ b/tests/pipeline/sgdemux.nf.test.snap @@ -1,9 +1,9 @@ { "software_versions": { "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, SGDEMUX={sgdemux=1.1.1}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, SGDEMUX={sgdemux=1.1.1}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-17T08:01:14+0000" + "timestamp": "2023-12-11T16:59:13.85618" }, "sgdemux": { "content": [ diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap index feab5952..00b82028 100644 --- a/tests/pipeline/skip_tools.nf.test.snap +++ b/tests/pipeline/skip_tools.nf.test.snap @@ -1,9 +1,9 @@ { "software_versions_skip_trimming": { "content": [ - "{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}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-31T12:40:12.308416" + "timestamp": "2023-12-11T17:00:30.102965" }, "skip_fastqc": { "content": [ @@ -95,27 +95,27 @@ }, "software_versions_skip_fastqc": { "content": [ - "{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}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" ], - "timestamp": "2023-10-31T12:41:58.993732" + "timestamp": "2023-12-11T17:02:16.631766" }, "software_versions_skip_fastp_fastqc": { "content": [ - "{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}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, 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