From 506a74416e0c48ab2a2689d034f2dea244ccd742 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 14 Oct 2024 18:33:27 +0000 Subject: [PATCH 01/12] fix samplesheet generation --- CHANGELOG.md | 10 +++++ modules/local/fastq_to_samplesheet/main.nf | 7 +++- nextflow.config | 1 + workflows/demultiplex.nf | 46 ++++++++++++++++------ 4 files changed, 49 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 537a33f5..a11f144c 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 1.5.2dev - (UNRELEASED) + +### `Added` + +### `Changed` + +### `Fixed` + +- [#277](https://github.com/nf-core/demultiplex/pull/277) Improved samplesheet generation to always produce all types of samplesheets, added the ability to explicitly set strandedness, and fixed output paths to correctly reflect the `publishDir` subdirectory structure. + ## 1.5.2 - 2024-10-07 ### `Changed` diff --git a/modules/local/fastq_to_samplesheet/main.nf b/modules/local/fastq_to_samplesheet/main.nf index f79cabcf..92429d51 100644 --- a/modules/local/fastq_to_samplesheet/main.nf +++ b/modules/local/fastq_to_samplesheet/main.nf @@ -14,15 +14,18 @@ process FASTQ_TO_SAMPLESHEET { exec: + // Calculate the dynamic output directory based on meta.lane + def outputDir = meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}" : "${params.outdir}/${meta.id}" + // Add relevant fields to the map def pipeline_map = [ sample : meta.samplename, - fastq_1 : meta.fastq_1 + fastq_1 : outputDir + '/' + file(meta.fastq_1).fileName ] // Add fastq_2 if it's a paired-end sample if (!meta.single_end) { - pipeline_map.fastq_2 = meta.fastq_2 + pipeline_map.fastq_2 = outputDir + '/' + file(meta.fastq_2).fileName } // Add pipeline-specific entries diff --git a/nextflow.config b/nextflow.config index 7d764432..f1b79d3b 100755 --- a/nextflow.config +++ b/nextflow.config @@ -28,6 +28,7 @@ params { // Downstream Nextflow pipeline downstream_pipeline = "default" // enum string [rnaseq, atacseq, taxprofiler, default] + strandedness = "auto" // enum string [auto, reverse, forward, unstranded] // Options: CheckQC checkqc_config = [] // file .yaml diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf index eae296d4..b6335e7a 100644 --- a/workflows/demultiplex.nf +++ b/workflows/demultiplex.nf @@ -8,14 +8,16 @@ // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { BCL_DEMULTIPLEX } from '../subworkflows/nf-core/bcl_demultiplex/main' -include { FASTQ_CONTAM_SEQTK_KRAKEN } from '../subworkflows/nf-core/fastq_contam_seqtk_kraken/main' -include { BASES_DEMULTIPLEX } from '../subworkflows/local/bases_demultiplex/main' -include { FQTK_DEMULTIPLEX } from '../subworkflows/local/fqtk_demultiplex/main' -include { MKFASTQ_DEMULTIPLEX } from '../subworkflows/local/mkfastq_demultiplex/main' -include { SINGULAR_DEMULTIPLEX } from '../subworkflows/local/singular_demultiplex/main' -include { RUNDIR_CHECKQC } from '../subworkflows/local/rundir_checkqc/main' -include { FASTQ_TO_SAMPLESHEET } from '../modules/local/fastq_to_samplesheet/main' +include { BCL_DEMULTIPLEX } from '../subworkflows/nf-core/bcl_demultiplex/main' +include { FASTQ_CONTAM_SEQTK_KRAKEN } from '../subworkflows/nf-core/fastq_contam_seqtk_kraken/main' +include { BASES_DEMULTIPLEX } from '../subworkflows/local/bases_demultiplex/main' +include { FQTK_DEMULTIPLEX } from '../subworkflows/local/fqtk_demultiplex/main' +include { MKFASTQ_DEMULTIPLEX } from '../subworkflows/local/mkfastq_demultiplex/main' +include { SINGULAR_DEMULTIPLEX } from '../subworkflows/local/singular_demultiplex/main' +include { RUNDIR_CHECKQC } from '../subworkflows/local/rundir_checkqc/main' +include { FASTQ_TO_SAMPLESHEET as FASTQ_TO_SAMPLESHEET_RNASEQ } from '../modules/local/fastq_to_samplesheet/main' +include { FASTQ_TO_SAMPLESHEET as FASTQ_TO_SAMPLESHEET_ATACSEQ } from '../modules/local/fastq_to_samplesheet/main' +include { FASTQ_TO_SAMPLESHEET as FASTQ_TO_SAMPLESHEET_TAXPROFILER } from '../modules/local/fastq_to_samplesheet/main' // @@ -59,7 +61,7 @@ workflow DEMULTIPLEX { skip_tools = params.skip_tools ? params.skip_tools.split(',') : [] // list: [falco, fastp, multiqc] sample_size = params.sample_size // int kraken_db = params.kraken_db // path - downstream_pipeline = params.downstream_pipeline // string: rnaseq, atacseq, taxprofiler + strandedness = params.strandedness // string: auto, reverse, forward, unstranded // Channel inputs @@ -282,13 +284,31 @@ workflow DEMULTIPLEX { } // Module: FASTQ to samplesheet - FASTQ_TO_SAMPLESHEET(ch_meta_fastq, downstream_pipeline, 'auto') + ch_meta_fastq_rnaseq = ch_meta_fastq + FASTQ_TO_SAMPLESHEET_RNASEQ(ch_meta_fastq_rnaseq, "rnaseq", strandedness) + FASTQ_TO_SAMPLESHEET_RNASEQ.out.samplesheet + .map { it[1] } + .collectFile(name:'tmp_rnaseq_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName }) + .map { it.text.tokenize('\n').join('\n') } + .collectFile(name:'rnaseq_samplesheet.csv', storeDir: "${params.outdir}/samplesheet") + .set { ch_samplesheet } + + ch_meta_fastq_atacseq = ch_meta_fastq + FASTQ_TO_SAMPLESHEET_ATACSEQ(ch_meta_fastq_atacseq, "atacseq", strandedness) + FASTQ_TO_SAMPLESHEET_ATACSEQ.out.samplesheet + .map { it[1] } + .collectFile(name:'tmp_atac_seq_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName }) + .map { it.text.tokenize('\n').join('\n') } + .collectFile(name:'atacseq_samplesheet.csv', storeDir: "${params.outdir}/samplesheet") + .set { ch_samplesheet } - FASTQ_TO_SAMPLESHEET.out.samplesheet + ch_meta_fastq_taxprofiler = ch_meta_fastq + FASTQ_TO_SAMPLESHEET_TAXPROFILER(ch_meta_fastq_taxprofiler, "taxprofiler", strandedness) + FASTQ_TO_SAMPLESHEET_TAXPROFILER.out.samplesheet .map { it[1] } - .collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName }) + .collectFile(name:'tmp_taxprofiler_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName }) .map { it.text.tokenize('\n').join('\n') } - .collectFile(name:'samplesheet.csv', storeDir: "${params.outdir}/samplesheet") + .collectFile(name:'taxprofiler_samplesheet.csv', storeDir: "${params.outdir}/samplesheet") .set { ch_samplesheet } // From 92521448104fa86e31ca407ef583643dcebd912d Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 17 Oct 2024 18:19:25 +0000 Subject: [PATCH 02/12] update tests and config --- nextflow.config | 1 - tests/pipeline/bases2fastq.nf.test | 2 +- tests/pipeline/bcl2fastq.nf.test | 2 +- tests/pipeline/bclconvert.nf.test | 2 +- tests/pipeline/bclconvert_mini.nf.test | 2 +- tests/pipeline/fqtk.nf.test | 2 +- tests/pipeline/kraken.nf.test | 2 +- tests/pipeline/mkfastq.nf.test | 2 +- tests/pipeline/sgdemux.nf.test | 2 +- tests/pipeline/skip_tools.nf.test | 2 +- tests/pipeline/test_pe.nf.test | 2 +- 11 files changed, 10 insertions(+), 11 deletions(-) diff --git a/nextflow.config b/nextflow.config index f1b79d3b..5ab16b1b 100755 --- a/nextflow.config +++ b/nextflow.config @@ -27,7 +27,6 @@ params { kraken_db = null // file .tar.gz // Downstream Nextflow pipeline - downstream_pipeline = "default" // enum string [rnaseq, atacseq, taxprofiler, default] strandedness = "auto" // enum string [auto, reverse, forward, unstranded] // Options: CheckQC diff --git a/tests/pipeline/bases2fastq.nf.test b/tests/pipeline/bases2fastq.nf.test index 7a92b9d3..e9f5a488 100644 --- a/tests/pipeline/bases2fastq.nf.test +++ b/tests/pipeline/bases2fastq.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 8 }, + { assert workflow.trace.succeeded().size() == 10 }, { assert snapshot( // FIXME // path("$outputDir/sim-data/DefaultSample_R1.fastq.gz.md5"), diff --git a/tests/pipeline/bcl2fastq.nf.test b/tests/pipeline/bcl2fastq.nf.test index 312ff522..27abd5fe 100644 --- a/tests/pipeline/bcl2fastq.nf.test +++ b/tests/pipeline/bcl2fastq.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 6 }, + { assert workflow.trace.succeeded().size() == 8 }, { assert snapshot( path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), diff --git a/tests/pipeline/bclconvert.nf.test b/tests/pipeline/bclconvert.nf.test index ab3d93d0..d6766e1e 100644 --- a/tests/pipeline/bclconvert.nf.test +++ b/tests/pipeline/bclconvert.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 6 }, + { assert workflow.trace.succeeded().size() == 8 }, { assert snapshot( path("$outputDir/multiqc/multiqc_data/bclconvert_lane_counts.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), diff --git a/tests/pipeline/bclconvert_mini.nf.test b/tests/pipeline/bclconvert_mini.nf.test index 6f947349..4e0f2b61 100644 --- a/tests/pipeline/bclconvert_mini.nf.test +++ b/tests/pipeline/bclconvert_mini.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 26 }, + { assert workflow.trace.succeeded().size() == 38 }, { assert snapshot( path("$outputDir/multiqc/multiqc_data/bclconvert_lane_counts.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), diff --git a/tests/pipeline/fqtk.nf.test b/tests/pipeline/fqtk.nf.test index 97dbd755..8a2029f3 100644 --- a/tests/pipeline/fqtk.nf.test +++ b/tests/pipeline/fqtk.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 129 }, + { assert workflow.trace.succeeded().size() == 131 }, { assert snapshot(path("$outputDir/test/demux-metrics.txt")).match("fqtk") }, { assert new File("$outputDir/test/unmatched_1.fastp.fastq.gz").exists() }, { assert new File("$outputDir/test/unmatched_2.fastp.fastq.gz").exists() }, diff --git a/tests/pipeline/kraken.nf.test b/tests/pipeline/kraken.nf.test index 0ee43998..22519c2e 100644 --- a/tests/pipeline/kraken.nf.test +++ b/tests/pipeline/kraken.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 9 }, + { assert workflow.trace.succeeded().size() == 11 }, { assert snapshot( path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test index 584656b7..618af15f 100644 --- a/tests/pipeline/mkfastq.nf.test +++ b/tests/pipeline/mkfastq.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 10 }, + { assert workflow.trace.succeeded().size() == 12 }, // How many directories were produced? {assert path("${outputDir}").list().size() == 6}, // How many files were produced? diff --git a/tests/pipeline/sgdemux.nf.test b/tests/pipeline/sgdemux.nf.test index 6539dec2..cd88baad 100644 --- a/tests/pipeline/sgdemux.nf.test +++ b/tests/pipeline/sgdemux.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 128 }, + { assert workflow.trace.succeeded().size() == 130 }, { assert snapshot( path("$outputDir/sim-data/metrics.tsv"), path("$outputDir/sim-data/per_project_metrics.tsv"), diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test index 4b9521ea..15ff01e0 100644 --- a/tests/pipeline/skip_tools.nf.test +++ b/tests/pipeline/skip_tools.nf.test @@ -22,7 +22,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_trimming") }, - { assert workflow.trace.succeeded().size() == 6 }, + { assert workflow.trace.succeeded().size() == 8 }, { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, { assert snapshot( path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), diff --git a/tests/pipeline/test_pe.nf.test b/tests/pipeline/test_pe.nf.test index 94a61db6..45c78044 100644 --- a/tests/pipeline/test_pe.nf.test +++ b/tests/pipeline/test_pe.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 7 }, + { assert workflow.trace.succeeded().size() == 9 }, { assert snapshot( path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), From 4af1b9ea0cd4b9aa19bf0084c6bafa13a079ec89 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 17 Oct 2024 18:22:03 +0000 Subject: [PATCH 03/12] add and remove params in schema --- nextflow_schema.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 9857da5d..bddff01c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -35,12 +35,6 @@ "type": "string", "format": "file-path", "description": "Path to Illumina v2 samplesheet validator .json file" - }, - "downstream_pipeline": { - "type": "string", - "description": "Name of downstream nf-core pipeline (one of: rnaseq, atacseq, taxprofiler or default). Used to produce the input samplesheet for that pipeline.", - "default": "default", - "enum": ["rnaseq", "atacseq", "taxprofiler", "default"] } } }, @@ -276,5 +270,11 @@ { "$ref": "#/$defs/generic_options" } - ] + ], + "properties": { + "strandedness": { + "type": "string", + "default": "auto" + } + } } From ed4dd9ac9c03012f3f6acb21a1e7f757344e1518 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 17 Oct 2024 19:20:04 +0000 Subject: [PATCH 04/12] update snapshots --- tests/bases2fastq.nf.test.snap | 17 ++- tests/bcl2fastq.nf.test.snap | 17 ++- tests/bclconvert.nf.test.snap | 17 ++- tests/bclconvert_mini.nf.test.snap | 17 ++- tests/fqtk.nf.test.snap | 15 ++- tests/kraken.nf.test.snap | 17 ++- tests/mkfastq.nf.test.snap | 17 ++- tests/sgdemux.nf.test.snap | 195 ++--------------------------- 8 files changed, 85 insertions(+), 227 deletions(-) diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap index 317657ae..8fddd6bf 100644 --- a/tests/bases2fastq.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -1,7 +1,7 @@ { "Bases2Fastq": { "content": [ - 8, + 10, { "BASES2FASTQ": { "bases2fastq": "1.8.0.1260801529, use subject to license available at elementbiosciences.com" @@ -23,7 +23,7 @@ } }, [ - "fastq", + "fastq", "fastq/DefaultSample.samplesheet.csv", "multiqc", "multiqc/multiqc_data", @@ -148,7 +148,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv", + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv", "sim-data", "sim-data.csv", "sim-data/20230404-Bases2Fastq-Sim_QC.html", @@ -199,6 +201,9 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,4b372fcce4dbb8b0dbe685c6380f4a97", "fastqc_sequence_length_distribution_plot.txt:md5,5b002b51364b518093ad98ebe0a0ca39", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "atacseq_samplesheet.csv:md5,cbcd0c351176a3af8220e4d7ea0aa5fc", + "rnaseq_samplesheet.csv:md5,b801f052db66f58dde575504fb506a71", + "taxprofiler_samplesheet.csv:md5,e408437751e7d42d5dc54d634f0340c7", "sim-data.csv:md5,1d1dab697bd88c411fff89c102024295", "DefaultSample.fastp.json:md5,9c10bbfbc4beb9523ca3a114f95709db", "Metrics.csv:md5,ad7af77573845924062e2554cc641b16", @@ -210,8 +215,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T16:37:55.855747" + "timestamp": "2024-10-17T18:30:22.925323602" } -} +} \ No newline at end of file diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap index 7fb8ea17..a827cc47 100644 --- a/tests/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -1,7 +1,7 @@ { "Bcl2Fastq": { "content": [ - 6, + 8, { "BCL2FASTQ": { "bcl2fastq": "2.20.0.422" @@ -191,7 +191,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", @@ -232,13 +234,16 @@ "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "atacseq_samplesheet.csv:md5,9bcb1c0013047759567b318030d2f683", + "rnaseq_samplesheet.csv:md5,10ef4bf601cf15f399466f486657103d", + "taxprofiler_samplesheet.csv:md5,0967d7e933f4d186923f2317ffd5dad3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T16:39:25.304794" + "timestamp": "2024-10-17T18:31:41.999930695" } -} +} \ No newline at end of file diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap index f064c458..0fea050e 100644 --- a/tests/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -1,7 +1,7 @@ { "BCL-CONVERT": { "content": [ - 6, + 8, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -177,7 +177,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", @@ -228,13 +230,16 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "atacseq_samplesheet.csv:md5,e1392ffbaf78a5f37d54cacc4f49eab6", + "rnaseq_samplesheet.csv:md5,c4def806947a14a032e69d8309fbd807", + "taxprofiler_samplesheet.csv:md5,3c27f6f279e3c1c7c995756c8500b014" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T16:41:01.01928" + "timestamp": "2024-10-17T18:33:04.837079854" } -} +} \ No newline at end of file diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 77ba8a65..0d464242 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -1,7 +1,7 @@ { "BCL-CONVERT-mini": { "content": [ - 26, + 38, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -248,7 +248,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "HBRR1_S1_L001.fastp.fastq.gz:md5,451657490d4816dd5ff904e34ecc7fdf", @@ -341,13 +343,16 @@ "fastqc_sequence_length_distribution_plot.txt:md5,70de269b5d06021f286c44d3ac91b54b", "multiqc_bclconvert_bylane.txt:md5,5067dc968fcca1f47db0663f4d407807", "multiqc_bclconvert_bysample.txt:md5,29634775947e43972c864bdb08ceb61e", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "atacseq_samplesheet.csv:md5,8aa449c77bc73e004747485f7879f0fa", + "rnaseq_samplesheet.csv:md5,e3fecf57a1e946c380c1da1d6f32d67a", + "taxprofiler_samplesheet.csv:md5,39d06ae1eae4a6398ee41e990c22d0f1" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-16T10:59:08.175426" + "timestamp": "2024-10-17T18:35:59.027921384" } -} +} \ No newline at end of file diff --git a/tests/fqtk.nf.test.snap b/tests/fqtk.nf.test.snap index c5cbb5ec..fb95568f 100644 --- a/tests/fqtk.nf.test.snap +++ b/tests/fqtk.nf.test.snap @@ -1,7 +1,7 @@ { "FQTK": { "content": [ - 129, + 179, { "CSV2TSV": { "sed": 4.8 @@ -169,7 +169,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv", + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv", "test", "test.csv", "test/demux-metrics.txt", @@ -497,6 +499,9 @@ "fastqc_sequence_counts_plot.txt:md5,5168b647c4bbd6b3be17373e134fb296", "fastqc_sequence_duplication_levels_plot.txt:md5,d6db81670f1240dda7a91e14a29557c0", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "atacseq_samplesheet.csv:md5,449aad4e862548aa012f86e08af24400", + "rnaseq_samplesheet.csv:md5,80dab2378e072b91e5fb989160cf537c", + "taxprofiler_samplesheet.csv:md5,50dff691a23d86a2d3a8052feba9d388", "test.csv:md5,c01a880241575a67e3eb5dc461a4972c", "demux-metrics.txt:md5,1d587fa959f9129155314cf531103347", "s1.fastp.json:md5,be9a4b1838890e0ef5c586a3dc83b728", @@ -728,8 +733,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T16:56:01.494868" + "timestamp": "2024-10-17T18:38:44.767695631" } -} +} \ No newline at end of file diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap index 36a6b165..94d639a7 100644 --- a/tests/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -1,7 +1,7 @@ { "kraken2": { "content": [ - 9, + 11, { "BCL2FASTQ": { "bcl2fastq": "2.20.0.422" @@ -205,7 +205,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", @@ -250,13 +252,16 @@ "kraken-top-n-plot.txt:md5,add0b89a8b3d1729dac311870959b1e7", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,97f1dcb4348072ce2865c29c5c306a3d", - "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654" + "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654", + "atacseq_samplesheet.csv:md5,4ec94f762cdd68490c6efd7b4f1b476a", + "rnaseq_samplesheet.csv:md5,7ba7608a843bc9887af098bc6f4d8a08", + "taxprofiler_samplesheet.csv:md5,5fe3bde653a4a2d748f4fbbb8f043652" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T16:57:22.70902" + "timestamp": "2024-10-17T18:40:14.136394606" } -} +} \ No newline at end of file diff --git a/tests/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap index c95a793e..cffe3569 100644 --- a/tests/mkfastq.nf.test.snap +++ b/tests/mkfastq.nf.test.snap @@ -1,7 +1,7 @@ { "MKFASTQ": { "content": [ - 10, + 14, { "CELLRANGER_MKFASTQ": { "cellranger": "8.0.0" @@ -161,7 +161,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "cellranger-tiny-bcl-simple.lane1_no_adapters.csv:md5,86a945ab9d579c7bc98d43f76a07118b", @@ -195,13 +197,16 @@ "fastp-seq-quality-plot_Read_2_After_filtering.txt:md5,d6fc359d4e2be31d802b8553bcf5af93", "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,e80f62d45ca21cacbd19f899f768c308", "fastp_filtered_reads_plot.txt:md5,39d2e637c3e1482821c62c00482c8421", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "atacseq_samplesheet.csv:md5,ffde237bdd8a473b76cfec227fd3de29", + "rnaseq_samplesheet.csv:md5,ad629e23c7e89d50559363faeaae585e", + "taxprofiler_samplesheet.csv:md5,c6fbf9b56975f504f1243f1bc93143a7" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T14:34:23.682439" + "timestamp": "2024-10-17T18:42:31.446555384" } -} +} \ No newline at end of file diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap index e11ba9ee..74a6dc8d 100644 --- a/tests/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -1,7 +1,7 @@ { "SGDEMUX": { "content": [ - 128, + 178, { "FALCO": { "falco": "1.2.1" @@ -49,162 +49,12 @@ "fastq/s7_S7_L001.samplesheet.csv", "fastq/s8_S8_L001.samplesheet.csv", "fastq/s9_S9_L001.samplesheet.csv", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_2_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_2_Before_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_2_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_2_Before_filtering.txt", - "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt", - "multiqc/multiqc_data/fastp-seq-quality-plot_Read_2_After_filtering.txt", - "multiqc/multiqc_data/fastp-seq-quality-plot_Read_2_Before_filtering.txt", - "multiqc/multiqc_data/fastp_filtered_reads_plot.txt", - "multiqc/multiqc_data/fastqc-1-status-check-heatmap.txt", - "multiqc/multiqc_data/fastqc-1_per_base_n_content_plot.txt", - "multiqc/multiqc_data/fastqc-1_per_base_sequence_quality_plot.txt", - "multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt", - "multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.txt", - "multiqc/multiqc_data/fastqc-1_sequence_counts_plot.txt", - "multiqc/multiqc_data/fastqc-1_sequence_duplication_levels_plot.txt", - "multiqc/multiqc_data/fastqc-1_top_overrepresented_sequences_table.txt", - "multiqc/multiqc_data/fastqc-2-status-check-heatmap.txt", - "multiqc/multiqc_data/fastqc-2_per_base_n_content_plot.txt", - "multiqc/multiqc_data/fastqc-2_per_base_sequence_quality_plot.txt", - "multiqc/multiqc_data/fastqc-2_per_sequence_gc_content_plot_Counts.txt", - "multiqc/multiqc_data/fastqc-2_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/multiqc_data/fastqc-2_per_sequence_quality_scores_plot.txt", - "multiqc/multiqc_data/fastqc-2_sequence_counts_plot.txt", - "multiqc/multiqc_data/fastqc-2_sequence_duplication_levels_plot.txt", - "multiqc/multiqc_data/fastqc-2_top_overrepresented_sequences_table.txt", - "multiqc/multiqc_data/multiqc.log", - "multiqc/multiqc_data/multiqc_citations.txt", - "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_fastp.txt", - "multiqc/multiqc_data/multiqc_fastqc.txt", - "multiqc/multiqc_data/multiqc_fastqc_1.txt", - "multiqc/multiqc_data/multiqc_general_stats.txt", - "multiqc/multiqc_data/multiqc_software_versions.txt", - "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_2_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_2_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_2_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_2_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_2_After_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_2_Before_filtering.pdf", - "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc-1_top_overrepresented_sequences_table.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc-2_top_overrepresented_sequences_table.pdf", - "multiqc/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_1_After_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_1_Before_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_2_After_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-gc-plot_Read_2_Before_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_1_After_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_1_Before_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_2_After_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-content-n-plot_Read_2_Before_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_1_After_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_1_Before_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_2_After_filtering.png", - "multiqc/multiqc_plots/png/fastp-seq-quality-plot_Read_2_Before_filtering.png", - "multiqc/multiqc_plots/png/fastp_filtered_reads_plot-cnt.png", - "multiqc/multiqc_plots/png/fastp_filtered_reads_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc-1-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc-1_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc-1_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc-1_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc-1_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc-1_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc-1_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc-1_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc-1_top_overrepresented_sequences_table.png", - "multiqc/multiqc_plots/png/fastqc-2-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc-2_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc-2_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc-2_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc-2_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc-2_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc-2_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc-2_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc-2_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc-2_top_overrepresented_sequences_table.png", - "multiqc/multiqc_plots/png/general_stats_table.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastp-seq-content-gc-plot_Read_1_After_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-content-gc-plot_Read_1_Before_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-content-gc-plot_Read_2_After_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-content-gc-plot_Read_2_Before_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_1_After_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_1_Before_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_2_After_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-content-n-plot_Read_2_Before_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_1_After_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_1_Before_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_2_After_filtering.svg", - "multiqc/multiqc_plots/svg/fastp-seq-quality-plot_Read_2_Before_filtering.svg", - "multiqc/multiqc_plots/svg/fastp_filtered_reads_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastp_filtered_reads_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc-1_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc-1_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc-1_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc-1_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc-1_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc-1_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc-1_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc-1_top_overrepresented_sequences_table.svg", - "multiqc/multiqc_plots/svg/fastqc-2-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc-2_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc-2_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc-2_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc-2_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc-2_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc-2_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc-2_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc-2_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc-2_top_overrepresented_sequences_table.svg", - "multiqc/multiqc_plots/svg/general_stats_table.svg", - "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv", + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv", "sim-data", "sim-data.csv", "sim-data/Undetermined_S25_L001.fastp.html", @@ -514,36 +364,9 @@ "sim-data/sample_barcode_hop_metrics.tsv" ], [ - "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,f574676225613f374b561ef8d4779f33", - "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,f574676225613f374b561ef8d4779f33", - "fastp-seq-content-gc-plot_Read_2_After_filtering.txt:md5,c5c2bfa3d096ebeef6823d147fa652fb", - "fastp-seq-content-gc-plot_Read_2_Before_filtering.txt:md5,c5c2bfa3d096ebeef6823d147fa652fb", - "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,d2c7fc0c344909e4823099492d72e209", - "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,d2c7fc0c344909e4823099492d72e209", - "fastp-seq-content-n-plot_Read_2_After_filtering.txt:md5,d2c7fc0c344909e4823099492d72e209", - "fastp-seq-content-n-plot_Read_2_Before_filtering.txt:md5,d2c7fc0c344909e4823099492d72e209", - "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", - "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", - "fastp-seq-quality-plot_Read_2_After_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", - "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", - "fastp_filtered_reads_plot.txt:md5,0e60fe7db5d84497e03d814a9818e4c4", - "fastqc-1_per_base_n_content_plot.txt:md5,c0d889e3447bb580a91c26d58367ea3d", - "fastqc-1_per_base_sequence_quality_plot.txt:md5,fc98fee907d0942dc1e0a2c046e697fc", - "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,d76e3dbdcdcbb0c5dc60912c275be5e1", - "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,727231c2c86c657e506296c2fda2025d", - "fastqc-1_per_sequence_quality_scores_plot.txt:md5,89cb687875c238d4920f01401635edd4", - "fastqc-1_sequence_counts_plot.txt:md5,020f9eacc4ddf1eef1f4187a3cf0122e", - "fastqc-1_sequence_duplication_levels_plot.txt:md5,3c42607c5bda6eb3d39f45982f1c8e53", - "fastqc-1_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "fastqc-2_per_base_n_content_plot.txt:md5,dee7d9c094c60dc3a67c4da1954303f2", - "fastqc-2_per_base_sequence_quality_plot.txt:md5,5d63f6647b7589d04bf2f2f9db88f584", - "fastqc-2_per_sequence_gc_content_plot_Counts.txt:md5,ae1a7e984622d704f03cb658d5f160f5", - "fastqc-2_per_sequence_gc_content_plot_Percentages.txt:md5,7ade5018e5188777fddc82e35b06ef3f", - "fastqc-2_per_sequence_quality_scores_plot.txt:md5,5d1d91faa379b3551b27a9b5c39ce5b0", - "fastqc-2_sequence_counts_plot.txt:md5,1d5fa5876e4261235b9fa8650ee3ff7f", - "fastqc-2_sequence_duplication_levels_plot.txt:md5,a524a5e16ed509a3615ea05aa6d36bd0", - "fastqc-2_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", + "atacseq_samplesheet.csv:md5,06f0b7297e6dbf8c36ff5c1bdee557bb", + "rnaseq_samplesheet.csv:md5,135d17fff6382bea7b5ec71e7252df1e", + "taxprofiler_samplesheet.csv:md5,54f51c0d30b0245e3f7b45445ac70c44", "sim-data.csv:md5,a5ea0ad63c5df73b5fc2436dd8d9dbfe", "Undetermined_S25_L001.fastp.json:md5,577922aa75bb6ab549ed7699ae45becc", "metrics.tsv:md5,7627e4bd2a56ea551fd74b4a2b5cb4b2", @@ -580,6 +403,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T16:07:45.042862" + "timestamp": "2024-10-17T19:04:04.078111423" } -} +} \ No newline at end of file From 27301ab2730f15e67f8647524165c657726990b7 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 17 Oct 2024 23:20:21 +0000 Subject: [PATCH 05/12] ignore all samplesheets from nf-tests (full paths will change depending on platform) --- tests/.nftignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/.nftignore b/tests/.nftignore index 2c7e41e2..5b668254 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -22,7 +22,7 @@ multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html pipeline_info/*.{html,json,txt,yml} -samplesheet/samplesheet.csv +samplesheet/*.csv sim-data/*-Bases2Fastq-Sim_QC.html sim-data/*.fastp.fastq.gz sim-data/*.fastp.fastq.gz.md5 From 1ef66805c56f32b56ce9989568f167f6b0a0c94e Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 18 Oct 2024 00:01:26 +0000 Subject: [PATCH 06/12] update snapshots --- tests/bases2fastq.nf.test.snap | 5 +---- tests/bcl2fastq.nf.test.snap | 7 ++----- tests/bclconvert.nf.test.snap | 7 ++----- tests/bclconvert_mini.nf.test.snap | 7 ++----- tests/fqtk.nf.test.snap | 5 +---- tests/kraken.nf.test.snap | 7 ++----- tests/mkfastq.nf.test.snap | 7 ++----- 7 files changed, 12 insertions(+), 33 deletions(-) diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap index 8fddd6bf..7a8c9b96 100644 --- a/tests/bases2fastq.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -201,9 +201,6 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,4b372fcce4dbb8b0dbe685c6380f4a97", "fastqc_sequence_length_distribution_plot.txt:md5,5b002b51364b518093ad98ebe0a0ca39", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "atacseq_samplesheet.csv:md5,cbcd0c351176a3af8220e4d7ea0aa5fc", - "rnaseq_samplesheet.csv:md5,b801f052db66f58dde575504fb506a71", - "taxprofiler_samplesheet.csv:md5,e408437751e7d42d5dc54d634f0340c7", "sim-data.csv:md5,1d1dab697bd88c411fff89c102024295", "DefaultSample.fastp.json:md5,9c10bbfbc4beb9523ca3a114f95709db", "Metrics.csv:md5,ad7af77573845924062e2554cc641b16", @@ -217,6 +214,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T18:30:22.925323602" + "timestamp": "2024-10-17T23:29:10.785062467" } } \ No newline at end of file diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap index a827cc47..cdda06ef 100644 --- a/tests/bcl2fastq.nf.test.snap +++ b/tests/bcl2fastq.nf.test.snap @@ -234,16 +234,13 @@ "fastqc_sequence_counts_plot.txt:md5,662c69090978601ca7d39504b1ac736b", "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "atacseq_samplesheet.csv:md5,9bcb1c0013047759567b318030d2f683", - "rnaseq_samplesheet.csv:md5,10ef4bf601cf15f399466f486657103d", - "taxprofiler_samplesheet.csv:md5,0967d7e933f4d186923f2317ffd5dad3" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T18:31:41.999930695" + "timestamp": "2024-10-17T23:30:33.296858681" } } \ No newline at end of file diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap index 0fea050e..1339d5e3 100644 --- a/tests/bclconvert.nf.test.snap +++ b/tests/bclconvert.nf.test.snap @@ -230,16 +230,13 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,cc02a5151984c0a9fdf8316bfb05088b", "multiqc_bclconvert_bylane.txt:md5,2f779a97f3a5429454f62059a19856e6", "multiqc_bclconvert_bysample.txt:md5,6a1ababe7d8242995ba5c5f78699cd63", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "atacseq_samplesheet.csv:md5,e1392ffbaf78a5f37d54cacc4f49eab6", - "rnaseq_samplesheet.csv:md5,c4def806947a14a032e69d8309fbd807", - "taxprofiler_samplesheet.csv:md5,3c27f6f279e3c1c7c995756c8500b014" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T18:33:04.837079854" + "timestamp": "2024-10-17T23:31:58.719385372" } } \ No newline at end of file diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap index 0d464242..8bdd4e5c 100644 --- a/tests/bclconvert_mini.nf.test.snap +++ b/tests/bclconvert_mini.nf.test.snap @@ -343,16 +343,13 @@ "fastqc_sequence_length_distribution_plot.txt:md5,70de269b5d06021f286c44d3ac91b54b", "multiqc_bclconvert_bylane.txt:md5,5067dc968fcca1f47db0663f4d407807", "multiqc_bclconvert_bysample.txt:md5,29634775947e43972c864bdb08ceb61e", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "atacseq_samplesheet.csv:md5,8aa449c77bc73e004747485f7879f0fa", - "rnaseq_samplesheet.csv:md5,e3fecf57a1e946c380c1da1d6f32d67a", - "taxprofiler_samplesheet.csv:md5,39d06ae1eae4a6398ee41e990c22d0f1" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T18:35:59.027921384" + "timestamp": "2024-10-17T23:34:50.670465424" } } \ No newline at end of file diff --git a/tests/fqtk.nf.test.snap b/tests/fqtk.nf.test.snap index fb95568f..24a3644f 100644 --- a/tests/fqtk.nf.test.snap +++ b/tests/fqtk.nf.test.snap @@ -499,9 +499,6 @@ "fastqc_sequence_counts_plot.txt:md5,5168b647c4bbd6b3be17373e134fb296", "fastqc_sequence_duplication_levels_plot.txt:md5,d6db81670f1240dda7a91e14a29557c0", "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "atacseq_samplesheet.csv:md5,449aad4e862548aa012f86e08af24400", - "rnaseq_samplesheet.csv:md5,80dab2378e072b91e5fb989160cf537c", - "taxprofiler_samplesheet.csv:md5,50dff691a23d86a2d3a8052feba9d388", "test.csv:md5,c01a880241575a67e3eb5dc461a4972c", "demux-metrics.txt:md5,1d587fa959f9129155314cf531103347", "s1.fastp.json:md5,be9a4b1838890e0ef5c586a3dc83b728", @@ -735,6 +732,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T18:38:44.767695631" + "timestamp": "2024-10-17T23:37:31.252912431" } } \ No newline at end of file diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap index 94d639a7..7cdd3b53 100644 --- a/tests/kraken.nf.test.snap +++ b/tests/kraken.nf.test.snap @@ -252,16 +252,13 @@ "kraken-top-n-plot.txt:md5,add0b89a8b3d1729dac311870959b1e7", "multiqc_bcl2fastq_bysample.txt:md5,baaa56d8315c18633f6ce6568d6f0657", "multiqc_citations.txt:md5,97f1dcb4348072ce2865c29c5c306a3d", - "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654", - "atacseq_samplesheet.csv:md5,4ec94f762cdd68490c6efd7b4f1b476a", - "rnaseq_samplesheet.csv:md5,7ba7608a843bc9887af098bc6f4d8a08", - "taxprofiler_samplesheet.csv:md5,5fe3bde653a4a2d748f4fbbb8f043652" + "multiqc_kraken.txt:md5,a90fd69786a0df1e43b948e423545654" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T18:40:14.136394606" + "timestamp": "2024-10-17T23:39:05.363547947" } } \ No newline at end of file diff --git a/tests/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap index cffe3569..155a792f 100644 --- a/tests/mkfastq.nf.test.snap +++ b/tests/mkfastq.nf.test.snap @@ -197,16 +197,13 @@ "fastp-seq-quality-plot_Read_2_After_filtering.txt:md5,d6fc359d4e2be31d802b8553bcf5af93", "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,e80f62d45ca21cacbd19f899f768c308", "fastp_filtered_reads_plot.txt:md5,39d2e637c3e1482821c62c00482c8421", - "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", - "atacseq_samplesheet.csv:md5,ffde237bdd8a473b76cfec227fd3de29", - "rnaseq_samplesheet.csv:md5,ad629e23c7e89d50559363faeaae585e", - "taxprofiler_samplesheet.csv:md5,c6fbf9b56975f504f1243f1bc93143a7" + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T18:42:31.446555384" + "timestamp": "2024-10-17T23:40:20.21203835" } } \ No newline at end of file From 193fd04519e04ea4305098787b7bbe285639df5b Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 18 Oct 2024 00:25:56 +0000 Subject: [PATCH 07/12] update tests again --- tests/pipeline/fqtk.nf.test | 2 +- tests/pipeline/sgdemux.nf.test | 2 +- tests/pipeline/skip_tools.nf.test | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/pipeline/fqtk.nf.test b/tests/pipeline/fqtk.nf.test index 8a2029f3..23fea228 100644 --- a/tests/pipeline/fqtk.nf.test +++ b/tests/pipeline/fqtk.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 131 }, + { assert workflow.trace.succeeded().size() == 179 }, { assert snapshot(path("$outputDir/test/demux-metrics.txt")).match("fqtk") }, { assert new File("$outputDir/test/unmatched_1.fastp.fastq.gz").exists() }, { assert new File("$outputDir/test/unmatched_2.fastp.fastq.gz").exists() }, diff --git a/tests/pipeline/sgdemux.nf.test b/tests/pipeline/sgdemux.nf.test index cd88baad..2aff767b 100644 --- a/tests/pipeline/sgdemux.nf.test +++ b/tests/pipeline/sgdemux.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 130 }, + { assert workflow.trace.succeeded().size() == 178 }, { assert snapshot( path("$outputDir/sim-data/metrics.tsv"), path("$outputDir/sim-data/per_project_metrics.tsv"), diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test index 15ff01e0..af903f3e 100644 --- a/tests/pipeline/skip_tools.nf.test +++ b/tests/pipeline/skip_tools.nf.test @@ -50,7 +50,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastp") }, - { assert workflow.trace.succeeded().size() == 5 }, + { assert workflow.trace.succeeded().size() == 7 }, { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, { assert snapshot( path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), @@ -78,7 +78,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastqc") }, - { assert workflow.trace.succeeded().size() == 6 }, + { assert workflow.trace.succeeded().size() == 8 }, { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, { assert snapshot( path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), @@ -106,7 +106,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastp_fastqc") }, - { assert workflow.trace.succeeded().size() == 5 }, + { assert workflow.trace.succeeded().size() == 7 }, { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, { assert snapshot( path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), @@ -134,7 +134,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_multiqc") }, - { assert workflow.trace.succeeded().size() == 5 }, + { assert workflow.trace.succeeded().size() == 7 }, { assert !path("$outputDir/multiqc/multiqc_report.html").exists() }, { assert snapshot( path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), From f9b68c7b33805df03e554e80a5bb27a71de8893f Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 18 Oct 2024 00:42:33 +0000 Subject: [PATCH 08/12] delete old tests --- tests/pipeline/bases2fastq.nf.test | 40 ------- tests/pipeline/bcl2fastq.nf.test | 39 ------- tests/pipeline/bclconvert.nf.test | 39 ------- tests/pipeline/bclconvert_mini.nf.test | 55 --------- tests/pipeline/fqtk.nf.test | 75 ------------- tests/pipeline/kraken.nf.test | 47 -------- tests/pipeline/mkfastq.nf.test | 51 --------- tests/pipeline/sgdemux.nf.test | 83 -------------- tests/pipeline/skip_tools.nf.test | 150 ------------------------- tests/pipeline/test_pe.nf.test | 44 -------- tests/skip_tools.nf.test.snap | 52 +++++---- tests/test_pe.nf.test.snap | 12 +- 12 files changed, 38 insertions(+), 649 deletions(-) delete mode 100644 tests/pipeline/bases2fastq.nf.test delete mode 100644 tests/pipeline/bcl2fastq.nf.test delete mode 100644 tests/pipeline/bclconvert.nf.test delete mode 100644 tests/pipeline/bclconvert_mini.nf.test delete mode 100644 tests/pipeline/fqtk.nf.test delete mode 100644 tests/pipeline/kraken.nf.test delete mode 100644 tests/pipeline/mkfastq.nf.test delete mode 100644 tests/pipeline/sgdemux.nf.test delete mode 100644 tests/pipeline/skip_tools.nf.test delete mode 100644 tests/pipeline/test_pe.nf.test diff --git a/tests/pipeline/bases2fastq.nf.test b/tests/pipeline/bases2fastq.nf.test deleted file mode 100644 index e9f5a488..00000000 --- a/tests/pipeline/bases2fastq.nf.test +++ /dev/null @@ -1,40 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - BASES2FASTQ" - script "main.nf" - profile "test_bases2fastq" - tag "bases2fastq" - tag "pipeline" - - test("Bases2Fastq") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 10 }, - { assert snapshot( - // FIXME - // path("$outputDir/sim-data/DefaultSample_R1.fastq.gz.md5"), - // path("$outputDir/sim-data/DefaultSample_R2.fastq.gz.md5"), - path("$outputDir/sim-data/Metrics.csv"), - path("$outputDir/sim-data/UnassignedSequences.csv"), - path("$outputDir/sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_R1.fastq.gz"), - path("$outputDir/sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_R2.fastq.gz") - ).match("bases2fastq") }, - { assert new File("$outputDir/sim-data/20230404-Bases2Fastq-Sim_QC.html").exists() }, - { assert new File("$outputDir/sim-data/RunStats.json").exists() }, - { assert new File("$outputDir/sim-data/Samples/DefaultProject/DefaultSample/DefaultSample_stats.json").exists() }, - { assert new File("$outputDir/sim-data/RunManifest.json").exists() } - ) - } - - } - -} diff --git a/tests/pipeline/bcl2fastq.nf.test b/tests/pipeline/bcl2fastq.nf.test deleted file mode 100644 index 27abd5fe..00000000 --- a/tests/pipeline/bcl2fastq.nf.test +++ /dev/null @@ -1,39 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - BCL2FASTQ" - script "main.nf" - profile "test_bcl2fastq" - tag "bcl2fastq" - tag "pipeline" - - test("Bcl2Fastq") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 8 }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bcl2fastq_sample_counts.txt") - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Stats/").list() - ).match("bcl2fastq") } - ) - } - - } - -} diff --git a/tests/pipeline/bclconvert.nf.test b/tests/pipeline/bclconvert.nf.test deleted file mode 100644 index d6766e1e..00000000 --- a/tests/pipeline/bclconvert.nf.test +++ /dev/null @@ -1,39 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - BCLCONVERT" - script "main.nf" - profile "test" - tag "bclconvert" - tag "pipeline" - - test("BCL-CONVERT") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 8 }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bclconvert_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt") - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("bclconvert") } - ) - } - - } - -} diff --git a/tests/pipeline/bclconvert_mini.nf.test b/tests/pipeline/bclconvert_mini.nf.test deleted file mode 100644 index 4e0f2b61..00000000 --- a/tests/pipeline/bclconvert_mini.nf.test +++ /dev/null @@ -1,55 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - BCLCONVERT-mini" - script "main.nf" - profile "test_bclconvert" - tag "bclconvert" - tag "pipeline" - - test("BCL-CONVERT-mini") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 38 }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bclconvert_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt") - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001.fastp.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001_summary.txt"), - path("$outputDir/miniseq_truseq_smrna/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/miniseq_truseq_smrna/Reports/").list(), - path("$outputDir/miniseq_truseq_smrna/InterOp/").list() - ).match("bclconvert") } - ) - } - - } - -} diff --git a/tests/pipeline/fqtk.nf.test b/tests/pipeline/fqtk.nf.test deleted file mode 100644 index 23fea228..00000000 --- a/tests/pipeline/fqtk.nf.test +++ /dev/null @@ -1,75 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - FQTK" - script "main.nf" - profile "test_fqtk" - tag "fqtk" - - test("FQTK") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 179 }, - { assert snapshot(path("$outputDir/test/demux-metrics.txt")).match("fqtk") }, - { assert new File("$outputDir/test/unmatched_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/unmatched_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s10_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s10_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s11_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s11_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s12_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s12_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s13_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s13_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s14_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s14_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s15_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s15_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s16_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s16_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s17_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s17_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s18_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s18_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s19_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s19_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s1_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s1_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s20_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s20_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s21_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s21_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s22_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s22_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s23_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s23_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s24_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s24_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s2_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s2_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s3_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s3_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s4_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s4_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s5_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s5_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s6_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s6_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s7_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s7_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s8_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s8_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s9_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/test/s9_2.fastp.fastq.gz").exists() } - ) - } - } -} diff --git a/tests/pipeline/kraken.nf.test b/tests/pipeline/kraken.nf.test deleted file mode 100644 index 22519c2e..00000000 --- a/tests/pipeline/kraken.nf.test +++ /dev/null @@ -1,47 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - Kraken" - script "main.nf" - config "../../conf/test_kraken.config" - profile "test" - tag "kraken" - tag "pipeline" - - test("kraken2") { - - when { - params { - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' - demultiplexer = 'bcl2fastq' - outdir = "$outputDir" - skip_tools = "checkqc,samshee" - kraken_db = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/db/kraken2.tar.gz' - - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 11 }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bcl2fastq_sample_counts.txt"), - path("$outputDir/multiqc/multiqc_data/kraken-top-n-plot.txt"), - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.kraken2.report.txt"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_summary.txt"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Stats/").list(), - ).match("kraken") } - ) - } - - } - -} diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test deleted file mode 100644 index 618af15f..00000000 --- a/tests/pipeline/mkfastq.nf.test +++ /dev/null @@ -1,51 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - mkfastq" - script "main.nf" - profile "test_mkfastq" - tag "mkfastq" - tag "pipeline" - - test("MKFASTQ") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 12 }, - // How many directories were produced? - {assert path("${outputDir}").list().size() == 6}, - // How many files were produced? - {assert path("$outputDir/cellranger-tiny-bcl-simple/").list().size() == 2}, - {assert path("$outputDir/multiqc/").list().size() == 3}, - {assert path("$outputDir/pipeline_info/").list().size() == 5}, - // File assertions: Files that should be exactly the same with every pipeline execution. - {assert snapshot( - //Check output files - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz.md5"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz.md5"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz.md5"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R1_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R2_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_I1_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R1_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R2_001.fastq.gz"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.html").exists(), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.json"), - path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.json"), - path("${outputDir}/cellranger-tiny-bcl-simple/InterOp/IndexMetricsOut.bin") - ).match("file_assertions_mkfastq")} - ) - } - } -} diff --git a/tests/pipeline/sgdemux.nf.test b/tests/pipeline/sgdemux.nf.test deleted file mode 100644 index 2aff767b..00000000 --- a/tests/pipeline/sgdemux.nf.test +++ /dev/null @@ -1,83 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - Sgdemux" - script "main.nf" - profile "test_sgdemux" - tag "sgdemux" - tag "pipeline" - - test("SGDEMUX") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 178 }, - { assert snapshot( - path("$outputDir/sim-data/metrics.tsv"), - path("$outputDir/sim-data/per_project_metrics.tsv"), - path("$outputDir/sim-data/per_sample_metrics.tsv"), - path("$outputDir/sim-data/sample_barcode_hop_metrics.tsv") - ).match("sgdemux") }, - { assert new File("$outputDir/sim-data/Undetermined_S25_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/Undetermined_S25_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s10_S10_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s10_S10_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s11_S11_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s11_S11_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s12_S12_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s12_S12_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s13_S13_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s13_S13_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s14_S14_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s14_S14_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s15_S15_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s15_S15_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s16_S16_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s16_S16_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s17_S17_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s17_S17_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s18_S18_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s18_S18_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s19_S19_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s19_S19_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s1_S1_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s1_S1_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s20_S20_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s20_S20_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s21_S21_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s21_S21_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s22_S22_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s22_S22_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s23_S23_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s23_S23_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s24_S24_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s24_S24_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s2_S2_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s2_S2_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s3_S3_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s3_S3_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s4_S4_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s4_S4_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s5_S5_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s5_S5_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s6_S6_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s6_S6_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s7_S7_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s7_S7_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s8_S8_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s8_S8_L001_2.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s9_S9_L001_1.fastp.fastq.gz").exists() }, - { assert new File("$outputDir/sim-data/s9_S9_L001_2.fastp.fastq.gz").exists() } - ) - } - - } - -} diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test deleted file mode 100644 index af903f3e..00000000 --- a/tests/pipeline/skip_tools.nf.test +++ /dev/null @@ -1,150 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - Skip Tools" - script "main.nf" - profile "test" - tag "skip_trimming" - tag "pipeline" - - - test("Skip Trimming") { - - when { - params { - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' - demultiplexer = 'bclconvert' - outdir = "$outputDir" - trim_fastq = false - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_trimming") }, - { assert workflow.trace.succeeded().size() == 8 }, - { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_trimming") } - ) - } - - } - - test("Skip Fastp") { - - when { - params { - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' - demultiplexer = 'bclconvert' - outdir = "$outputDir" - skip_tools = "fastp,samshee" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastp") }, - { assert workflow.trace.succeeded().size() == 7 }, - { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_fastp") } - ) - } - - } - - test("Skip Fastqc") { - - when { - params { - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' - demultiplexer = 'bclconvert' - outdir = "$outputDir" - skip_tools = "fastqc,samshee" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastqc") }, - { assert workflow.trace.succeeded().size() == 8 }, - { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_fastqc") } - ) - } - - } - - test("Skip Fastp & Fastqc") { - - when { - params { - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' - demultiplexer = 'bclconvert' - outdir = "$outputDir" - skip_tools = "fastp,fastqc,samshee" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastp_fastqc") }, - { assert workflow.trace.succeeded().size() == 7 }, - { assert path("$outputDir/multiqc/multiqc_report.html").exists() }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_fastp_fastqc") } - ) - } - - } - - test("Skip MultiQC") { - - when { - params { - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' - demultiplexer = 'bclconvert' - outdir = "$outputDir" - skip_tools = "multiqc,samshee" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_multiqc") }, - { assert workflow.trace.succeeded().size() == 7 }, - { assert !path("$outputDir/multiqc/multiqc_report.html").exists() }, - { assert snapshot( - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Sample1_S1_L001.fastp.fastq.gz.md5"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Undetermined_S0_L001_R1_001.fastq.gz"), - path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), - ).match("skip_multiqc") } - ) - } - - } - -} diff --git a/tests/pipeline/test_pe.nf.test b/tests/pipeline/test_pe.nf.test deleted file mode 100644 index 45c78044..00000000 --- a/tests/pipeline/test_pe.nf.test +++ /dev/null @@ -1,44 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf - Test PE" - script "main.nf" - profile "test_pe" - tag "bcl2fastq_pe" - tag "pipeline" - - test("Bcl2Fastq_pe") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 9 }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/bcl2fastq_lane_counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/bcl2fastq_sample_counts.txt") - - ).match("multiqc") }, - { assert snapshot( - path("$outputDir/PE_Sample.lane1_no_adapters.csv"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_1.fastp.fastq.gz"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_2.fastp.fastq.gz"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_R2_001.fastq.gz"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_1.fastp.fastq.gz_summary.txt"), - path("$outputDir/PE_Sample/L001/Sample1_S1_L001_2.fastp.fastq.gz_summary.txt"), - path("$outputDir/PE_Sample/L001/Reports/").list(), - path("$outputDir/PE_Sample/L001/Stats/").list() - ).match("bcl2fastq_pe") } - ) - } - - } - -} diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap index a7b0d626..4a414e55 100644 --- a/tests/skip_tools.nf.test.snap +++ b/tests/skip_tools.nf.test.snap @@ -1,7 +1,7 @@ { "Skip Fastp": { "content": [ - 5, + 7, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -139,7 +139,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", @@ -186,13 +188,13 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T11:16:29.215413" + "timestamp": "2024-10-18T00:25:42.942384924" }, "Skip Trimming": { "content": [ - 6, + 8, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -367,7 +369,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", @@ -422,13 +426,13 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T14:36:31.319794" + "timestamp": "2024-10-18T00:24:59.739085162" }, "Skip MultiQC": { "content": [ - 5, + 7, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -485,7 +489,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", @@ -519,13 +525,13 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T11:20:29.598072" + "timestamp": "2024-10-18T00:29:21.376431772" }, "Skip Fastp & Fastqc": { "content": [ - 5, + 7, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -663,7 +669,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", @@ -710,13 +718,13 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T11:19:11.741332" + "timestamp": "2024-10-18T00:28:05.245862992" }, "Skip Fastqc": { "content": [ - 6, + 8, { "BCLCONVERT": { "bclconvert": "4.3.6" @@ -892,7 +900,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c", @@ -948,8 +958,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T14:38:35.728344" + "timestamp": "2024-10-18T00:27:11.29098668" } -} +} \ No newline at end of file diff --git a/tests/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap index 4e4248e6..eaebb98b 100644 --- a/tests/test_pe.nf.test.snap +++ b/tests/test_pe.nf.test.snap @@ -1,7 +1,7 @@ { "Bcl2Fastq_pe": { "content": [ - 7, + 9, { "BCL2FASTQ": { "bcl2fastq": "2.20.0.422" @@ -259,7 +259,9 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", - "samplesheet/samplesheet.csv" + "samplesheet/atacseq_samplesheet.csv", + "samplesheet/rnaseq_samplesheet.csv", + "samplesheet/taxprofiler_samplesheet.csv" ], [ "PE_Sample.lane1_no_adapters.csv:md5,c31cca10b3a1aed8ec68daf779217d91", @@ -320,8 +322,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.2" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-15T14:42:45.369275" + "timestamp": "2024-10-18T00:32:00.49132579" } -} +} \ No newline at end of file From d0597e7132d1facd0ad0abee7f1ca75ddc40fad2 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 18 Oct 2024 04:34:12 +0000 Subject: [PATCH 09/12] update sgdemux --- tests/sgdemux.nf.test.snap | 187 ++++++++++++++++++++++++++++++++++++- 1 file changed, 183 insertions(+), 4 deletions(-) diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap index 74a6dc8d..285d4c9c 100644 --- a/tests/sgdemux.nf.test.snap +++ b/tests/sgdemux.nf.test.snap @@ -49,6 +49,158 @@ "fastq/s7_S7_L001.samplesheet.csv", "fastq/s8_S8_L001.samplesheet.csv", "fastq/s9_S9_L001.samplesheet.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-content-n-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_2_After_filtering.txt", + "multiqc/multiqc_data/fastp-seq-quality-plot_Read_2_Before_filtering.txt", + "multiqc/multiqc_data/fastp_filtered_reads_plot.txt", + "multiqc/multiqc_data/fastqc-1-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc-1_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc-1_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc-1_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc-1_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc-1_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/fastqc-2-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc-2_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc-2_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc-2_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc-2_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc-2_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc-2_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc-2_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc-2_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastp.txt", + "multiqc/multiqc_data/multiqc_fastqc.txt", + "multiqc/multiqc_data/multiqc_fastqc_1.txt", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_2_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-gc-plot_Read_2_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_2_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-content-n-plot_Read_2_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_1_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_2_After_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp-seq-quality-plot_Read_2_Before_filtering.pdf", + "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastp_filtered_reads_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", + 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"multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "samplesheet", @@ -364,9 +516,36 @@ "sim-data/sample_barcode_hop_metrics.tsv" ], [ - "atacseq_samplesheet.csv:md5,06f0b7297e6dbf8c36ff5c1bdee557bb", - "rnaseq_samplesheet.csv:md5,135d17fff6382bea7b5ec71e7252df1e", - "taxprofiler_samplesheet.csv:md5,54f51c0d30b0245e3f7b45445ac70c44", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,f574676225613f374b561ef8d4779f33", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,f574676225613f374b561ef8d4779f33", + "fastp-seq-content-gc-plot_Read_2_After_filtering.txt:md5,c5c2bfa3d096ebeef6823d147fa652fb", + "fastp-seq-content-gc-plot_Read_2_Before_filtering.txt:md5,c5c2bfa3d096ebeef6823d147fa652fb", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,d2c7fc0c344909e4823099492d72e209", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,d2c7fc0c344909e4823099492d72e209", + "fastp-seq-content-n-plot_Read_2_After_filtering.txt:md5,d2c7fc0c344909e4823099492d72e209", + "fastp-seq-content-n-plot_Read_2_Before_filtering.txt:md5,d2c7fc0c344909e4823099492d72e209", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", + "fastp-seq-quality-plot_Read_2_After_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", + "fastp-seq-quality-plot_Read_2_Before_filtering.txt:md5,b5e3d7a8aca6895859654a4115b38708", + "fastp_filtered_reads_plot.txt:md5,0e60fe7db5d84497e03d814a9818e4c4", + "fastqc-1_per_base_n_content_plot.txt:md5,c0d889e3447bb580a91c26d58367ea3d", + "fastqc-1_per_base_sequence_quality_plot.txt:md5,fc98fee907d0942dc1e0a2c046e697fc", + "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,d76e3dbdcdcbb0c5dc60912c275be5e1", + "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,727231c2c86c657e506296c2fda2025d", + "fastqc-1_per_sequence_quality_scores_plot.txt:md5,89cb687875c238d4920f01401635edd4", + "fastqc-1_sequence_counts_plot.txt:md5,020f9eacc4ddf1eef1f4187a3cf0122e", + "fastqc-1_sequence_duplication_levels_plot.txt:md5,3c42607c5bda6eb3d39f45982f1c8e53", + "fastqc-1_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "fastqc-2_per_base_n_content_plot.txt:md5,dee7d9c094c60dc3a67c4da1954303f2", + "fastqc-2_per_base_sequence_quality_plot.txt:md5,5d63f6647b7589d04bf2f2f9db88f584", + "fastqc-2_per_sequence_gc_content_plot_Counts.txt:md5,ae1a7e984622d704f03cb658d5f160f5", + "fastqc-2_per_sequence_gc_content_plot_Percentages.txt:md5,7ade5018e5188777fddc82e35b06ef3f", + "fastqc-2_per_sequence_quality_scores_plot.txt:md5,5d1d91faa379b3551b27a9b5c39ce5b0", + "fastqc-2_sequence_counts_plot.txt:md5,1d5fa5876e4261235b9fa8650ee3ff7f", + "fastqc-2_sequence_duplication_levels_plot.txt:md5,a524a5e16ed509a3615ea05aa6d36bd0", + "fastqc-2_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_citations.txt:md5,d35df50e9903a96a2b3bce3c1fbc8ad2", "sim-data.csv:md5,a5ea0ad63c5df73b5fc2436dd8d9dbfe", "Undetermined_S25_L001.fastp.json:md5,577922aa75bb6ab549ed7699ae45becc", "metrics.tsv:md5,7627e4bd2a56ea551fd74b4a2b5cb4b2", @@ -403,6 +582,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T19:04:04.078111423" + "timestamp": "2024-10-18T00:54:45.989490742" } } \ No newline at end of file From ba3a26157f8f444ebfc76cc8ca5ed9c86d8a4ac5 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 18 Oct 2024 15:06:26 +0000 Subject: [PATCH 10/12] add pipeline tag --- tests/fqtk.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/fqtk.nf.test b/tests/fqtk.nf.test index 3dea13d8..cd1841a1 100644 --- a/tests/fqtk.nf.test +++ b/tests/fqtk.nf.test @@ -4,6 +4,7 @@ nextflow_pipeline { script "../main.nf" profile "test_fqtk" tag "fqtk" + tag "pipeline" test("FQTK") { From f5b7c9101b7fbf3a3bf8e3f9b2099c19ae554ff3 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 18 Oct 2024 15:06:47 +0000 Subject: [PATCH 11/12] remove debug/verbose from ci temporarily --- .github/workflows/ci.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6fef5f23..ad8124b9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -102,8 +102,6 @@ jobs: - name: Run Tests (Shard ${{ matrix.shard }}/6) run: | nf-test test \ - --debug \ - --verbose \ --ci \ --shard ${{ matrix.shard }}/6 \ --changed-since HEAD^ \ From 825e1555f93a26f8a9967f8bd23921d4ca6f9312 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 18 Oct 2024 15:07:13 +0000 Subject: [PATCH 12/12] test with stable nextflow version --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ad8124b9..df00beb4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,7 +33,7 @@ jobs: matrix: NXF_VER: - "24.04.2" - - "latest-everything" + - "latest-stable" profile: - "docker" - "singularity"