From cfb9c2421bd0836e643cf5ee5e0ab98eed7117ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Wed, 20 Nov 2024 14:35:09 +0000 Subject: [PATCH 01/11] update module structure --- .../create_annotated_tables/environment.yml | 8 +++++++ .../create_annotated_tables/main.nf} | 24 +++++++++++++++---- 2 files changed, 27 insertions(+), 5 deletions(-) create mode 100644 modules/local/nacho/create_annotated_tables/environment.yml rename modules/local/{create_annotated_tables.nf => nacho/create_annotated_tables/main.nf} (55%) diff --git a/modules/local/nacho/create_annotated_tables/environment.yml b/modules/local/nacho/create_annotated_tables/environment.yml new file mode 100644 index 0000000..6af817c --- /dev/null +++ b/modules/local/nacho/create_annotated_tables/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge +dependencies: + - conda-forge::r-dplyr=1.1.4 + - conda-forge::r-ggplot2=3.4.4 + - conda-forge::r-readr=2.1.5 + - conda-forge::r-stringr=1.5.0 + - conda-forge::r-tidyr=1.3.0 diff --git a/modules/local/create_annotated_tables.nf b/modules/local/nacho/create_annotated_tables/main.nf similarity index 55% rename from modules/local/create_annotated_tables.nf rename to modules/local/nacho/create_annotated_tables/main.nf index a9e6772..fbe2b24 100644 --- a/modules/local/create_annotated_tables.nf +++ b/modules/local/nacho/create_annotated_tables/main.nf @@ -1,10 +1,9 @@ process CREATE_ANNOTATED_TABLES { + tag "$sample_sheet" label 'process_single' - conda "r-tidyr=1.3.0 r-ggplot2=3.4.4 r-dplyr=1.1.4 r-stringr=1.5.0 r-readr=2.1.5" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-5ff8b00c2d7f6173e034c115dfe295627ff99689:beb0ad5f49ec2904f79edffacd41bba38492e881-0' : - 'biocontainers/mulled-v2-5ff8b00c2d7f6173e034c115dfe295627ff99689:beb0ad5f49ec2904f79edffacd41bba38492e881-0' }" + conda "${moduleDir}/environment.yml" + container "community.wave.seqera.io/library/r-dplyr_r-ggplot2_r-readr_r-stringr_r-tidyr:44c4e4fe69e11c2f" input: path counts @@ -32,5 +31,20 @@ process CREATE_ANNOTATED_TABLES { r-readr: \$(Rscript -e "library(readr); cat(as.character(packageVersion('readr')))") END_VERSIONS """ -} + stub: + def args = task.ext.args ?: '' + """ + touch ENDO.tsv + touch HK.tsv + touch mqc.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') + r-ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot')))") + r-dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") + r-readr: \$(Rscript -e "library(readr); cat(as.character(packageVersion('readr')))") + END_VERSIONS + """ +} From 1ec112969e71077a14b7186932a4336f89c3fb7c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Wed, 20 Nov 2024 14:36:02 +0000 Subject: [PATCH 02/11] update include statement --- workflows/nanostring.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/nanostring.nf b/workflows/nanostring.nf index 62ba3ad..4e8ec81 100644 --- a/workflows/nanostring.nf +++ b/workflows/nanostring.nf @@ -23,7 +23,7 @@ include { NORMALIZE } from '../subworkflows/local/normalize' // // MODULES // -include { CREATE_ANNOTATED_TABLES } from '../modules/local/create_annotated_tables' +include { CREATE_ANNOTATED_TABLES } from '../modules/local/nacho/create_annotated_tables/main' include { COMPUTE_GENE_SCORES } from '../modules/local/compute_gene_scores' include { CREATE_GENE_HEATMAP } from '../modules/local/create_gene_heatmap' From ed60a5112e0ef6d3d41c77c8f3c5138a1ba7b1a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Wed, 20 Nov 2024 14:36:18 +0000 Subject: [PATCH 03/11] create test --- .../tests/main.nf.test | 31 +++++++++++++ .../tests/main.nf.test.snap | 43 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 modules/local/nacho/create_annotated_tables/tests/main.nf.test create mode 100644 modules/local/nacho/create_annotated_tables/tests/main.nf.test.snap diff --git a/modules/local/nacho/create_annotated_tables/tests/main.nf.test b/modules/local/nacho/create_annotated_tables/tests/main.nf.test new file mode 100644 index 0000000..5af36f9 --- /dev/null +++ b/modules/local/nacho/create_annotated_tables/tests/main.nf.test @@ -0,0 +1,31 @@ +nextflow_process { + + name "Test Process CREATE_ANNOTATED_TABLES" + script "../main.nf" + process "CREATE_ANNOTATED_TABLES" + tag "module" + + test("Should run without failures") { + + when { + process { + """ + // Normalized file + input[0] = file(params.pipelines_testdata_base_path + 'nanostring/modules_test_data/test_profile/normalized_counts.tsv', checkIfExists: true) + + // Sample sheet + input[1] = file(params.pipelines_testdata_base_path + 'nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/local/nacho/create_annotated_tables/tests/main.nf.test.snap b/modules/local/nacho/create_annotated_tables/tests/main.nf.test.snap new file mode 100644 index 0000000..6c066db --- /dev/null +++ b/modules/local/nacho/create_annotated_tables/tests/main.nf.test.snap @@ -0,0 +1,43 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "counts_Norm_GEX_ENDO.tsv:md5,5992886680cb6fc6f3e901e79752d544" + ], + "1": [ + "counts_Norm_GEX_HK.tsv:md5,9d8a0503df864a82990648348131be21" + ], + "2": [ + [ + "Norm_GEX_ENDO_mqc.tsv:md5,5992886680cb6fc6f3e901e79752d544", + "Norm_GEX_HK_mqc.tsv:md5,9d8a0503df864a82990648348131be21" + ] + ], + "3": [ + "versions.yml:md5,43b871def59fb08862ac85e636101fe5" + ], + "annotated_data_mqc": [ + [ + "Norm_GEX_ENDO_mqc.tsv:md5,5992886680cb6fc6f3e901e79752d544", + "Norm_GEX_HK_mqc.tsv:md5,9d8a0503df864a82990648348131be21" + ] + ], + "annotated_endo_data": [ + "counts_Norm_GEX_ENDO.tsv:md5,5992886680cb6fc6f3e901e79752d544" + ], + "annotated_hk_data": [ + "counts_Norm_GEX_HK.tsv:md5,9d8a0503df864a82990648348131be21" + ], + "versions": [ + "versions.yml:md5,43b871def59fb08862ac85e636101fe5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-20T14:10:50.997813905" + } +} \ No newline at end of file From 492e28572352b4d761b36e47467481bbe1cf8046 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 21 Nov 2024 12:50:53 +0000 Subject: [PATCH 04/11] correct module name --- .../local/{nacho => }/create_annotated_tables/environment.yml | 0 modules/local/{nacho => }/create_annotated_tables/main.nf | 0 .../{nacho => }/create_annotated_tables/tests/main.nf.test | 0 .../{nacho => }/create_annotated_tables/tests/main.nf.test.snap | 0 workflows/nanostring.nf | 2 +- 5 files changed, 1 insertion(+), 1 deletion(-) rename modules/local/{nacho => }/create_annotated_tables/environment.yml (100%) rename modules/local/{nacho => }/create_annotated_tables/main.nf (100%) rename modules/local/{nacho => }/create_annotated_tables/tests/main.nf.test (100%) rename modules/local/{nacho => }/create_annotated_tables/tests/main.nf.test.snap (100%) diff --git a/modules/local/nacho/create_annotated_tables/environment.yml b/modules/local/create_annotated_tables/environment.yml similarity index 100% rename from modules/local/nacho/create_annotated_tables/environment.yml rename to modules/local/create_annotated_tables/environment.yml diff --git a/modules/local/nacho/create_annotated_tables/main.nf b/modules/local/create_annotated_tables/main.nf similarity index 100% rename from modules/local/nacho/create_annotated_tables/main.nf rename to modules/local/create_annotated_tables/main.nf diff --git a/modules/local/nacho/create_annotated_tables/tests/main.nf.test b/modules/local/create_annotated_tables/tests/main.nf.test similarity index 100% rename from modules/local/nacho/create_annotated_tables/tests/main.nf.test rename to modules/local/create_annotated_tables/tests/main.nf.test diff --git a/modules/local/nacho/create_annotated_tables/tests/main.nf.test.snap b/modules/local/create_annotated_tables/tests/main.nf.test.snap similarity index 100% rename from modules/local/nacho/create_annotated_tables/tests/main.nf.test.snap rename to modules/local/create_annotated_tables/tests/main.nf.test.snap diff --git a/workflows/nanostring.nf b/workflows/nanostring.nf index 4e8ec81..62ba3ad 100644 --- a/workflows/nanostring.nf +++ b/workflows/nanostring.nf @@ -23,7 +23,7 @@ include { NORMALIZE } from '../subworkflows/local/normalize' // // MODULES // -include { CREATE_ANNOTATED_TABLES } from '../modules/local/nacho/create_annotated_tables/main' +include { CREATE_ANNOTATED_TABLES } from '../modules/local/create_annotated_tables' include { COMPUTE_GENE_SCORES } from '../modules/local/compute_gene_scores' include { CREATE_GENE_HEATMAP } from '../modules/local/create_gene_heatmap' From 84bb5196b926f73e86604749131f88ffbdd786cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 21 Nov 2024 12:56:52 +0000 Subject: [PATCH 05/11] update snaps --- tests/test.nf.test.snap | 6 +++--- tests/test_samples.nf.test.snap | 24 ++++++++++++------------ tests/test_scores.nf.test.snap | 6 +++--- 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 566c02d..2b3952b 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -4,7 +4,7 @@ 5, { "CREATE_ANNOTATED_TABLES": { - "r-base": "4.3.2", + "r-base": "4.3.3", "r-ggplot2": null, "r-dplyr": "1.1.4", "r-readr": "2.1.5" @@ -115,6 +115,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-19T21:23:55.334879021" + "timestamp": "2024-11-21T12:52:19.83780821" } -} +} \ No newline at end of file diff --git a/tests/test_samples.nf.test.snap b/tests/test_samples.nf.test.snap index 255eddc..5050a2f 100644 --- a/tests/test_samples.nf.test.snap +++ b/tests/test_samples.nf.test.snap @@ -4,7 +4,7 @@ 5, { "CREATE_ANNOTATED_TABLES": { - "r-base": "4.3.2", + "r-base": "4.3.3", "r-ggplot2": null, "r-dplyr": "1.1.4", "r-readr": "2.1.5" @@ -67,11 +67,11 @@ "QC/NACHO/png/plot_normf_mqc.png", "annotated_tables", "gene_heatmaps", - "gene_heatmaps/gene_heatmap_mqc.png", + "gene_heatmaps/wo_HKnorm_gene_heatmap_mqc.png", "multiqc", "multiqc/multiqc_data", - "multiqc/multiqc_data/multiqc_Norm_GEX_ENDO-section-plot.txt", - "multiqc/multiqc_data/multiqc_Norm_GEX_HK-section-plot.txt", + "multiqc/multiqc_data/multiqc_No_HK_Norm_GEX_ENDO-section-plot.txt", + "multiqc/multiqc_data/multiqc_No_HK_Norm_GEX_HK-section-plot.txt", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_normalized_qc-section-plot.txt", @@ -79,16 +79,16 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/Norm_GEX_ENDO-section-plot.pdf", - "multiqc/multiqc_plots/pdf/Norm_GEX_HK-section-plot.pdf", + "multiqc/multiqc_plots/pdf/No_HK_Norm_GEX_ENDO-section-plot.pdf", + "multiqc/multiqc_plots/pdf/No_HK_Norm_GEX_HK-section-plot.pdf", "multiqc/multiqc_plots/pdf/normalized_qc-section-plot.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/Norm_GEX_ENDO-section-plot.png", - "multiqc/multiqc_plots/png/Norm_GEX_HK-section-plot.png", + "multiqc/multiqc_plots/png/No_HK_Norm_GEX_ENDO-section-plot.png", + "multiqc/multiqc_plots/png/No_HK_Norm_GEX_HK-section-plot.png", "multiqc/multiqc_plots/png/normalized_qc-section-plot.png", "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/Norm_GEX_ENDO-section-plot.svg", - "multiqc/multiqc_plots/svg/Norm_GEX_HK-section-plot.svg", + "multiqc/multiqc_plots/svg/No_HK_Norm_GEX_ENDO-section-plot.svg", + "multiqc/multiqc_plots/svg/No_HK_Norm_GEX_HK-section-plot.svg", "multiqc/multiqc_plots/svg/normalized_qc-section-plot.svg", "multiqc/multiqc_report.html", "normalized_counts", @@ -115,6 +115,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-19T21:24:55.10531256" + "timestamp": "2024-11-21T12:53:40.202730569" } -} +} \ No newline at end of file diff --git a/tests/test_scores.nf.test.snap b/tests/test_scores.nf.test.snap index 01bbf1a..187889a 100644 --- a/tests/test_scores.nf.test.snap +++ b/tests/test_scores.nf.test.snap @@ -15,7 +15,7 @@ "r-matrixstats": null }, "CREATE_ANNOTATED_TABLES": { - "r-base": "4.3.2", + "r-base": "4.3.3", "r-ggplot2": null, "r-dplyr": "1.1.4", "r-readr": "2.1.5" @@ -141,6 +141,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-19T21:26:05.626984239" + "timestamp": "2024-11-21T12:55:12.430646745" } -} +} \ No newline at end of file From cec62c6c7dc09952ba77b5ca9f52391227bcbc51 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 21 Nov 2024 13:02:38 +0000 Subject: [PATCH 06/11] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index feb4e77..3d6d3cb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#100](https://github.com/nf-core/nanostring/pull/100) - Added nf-tests for local module `NACHO_QC`. - [#101](https://github.com/nf-core/nanostring/pull/101) - Added nf-tests for local module `COMPUTE_GENE_SCORES`. - [#102](https://github.com/nf-core/nanostring/pull/102) - Added nf-tests for local module `CREATE_GENE_HEATMAP`. +- [#103](https://github.com/nf-core/nanostring/pull/103) - Added nf-tests for local module `CREATE_ANNOTATED_TABLES`. ### `Fixed` From 77b7ece5800eacad9aa967b1dfbd4611ee9e0ffd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 21 Nov 2024 13:07:48 +0000 Subject: [PATCH 07/11] Update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d6d3cb..332149d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#94](https://github.com/nf-core/nanostring/pull/94) - Added nf-tests for local subworkflows `NORMALIZE` and `QUALITY_CONTROL`. +- [#99](https://github.com/nf-core/nanostring/pull/99) - Added nf-tests for local module `NACHO_NORMALIZE`. - [#100](https://github.com/nf-core/nanostring/pull/100) - Added nf-tests for local module `NACHO_QC`. - [#101](https://github.com/nf-core/nanostring/pull/101) - Added nf-tests for local module `COMPUTE_GENE_SCORES`. - [#102](https://github.com/nf-core/nanostring/pull/102) - Added nf-tests for local module `CREATE_GENE_HEATMAP`. @@ -20,7 +21,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#82](https://github.com/nf-core/nanostring/pull/82) - Updated to nf-core template 3.0.2 - [#95](https://github.com/nf-core/nanostring/pull/95) - Add pipeline level nf-tests. - [#96](https://github.com/nf-core/nanostring/pull/96) - Remove timestamp suffix from nacho_norm.R and write_out_prepared_gex.R -- [#99](https://github.com/nf-core/nanostring/pull/99) - Add nf-test for local module nacho_normalize. ### `Dependencies` From 78d74789113f5ab6995d772edf28e8860da9bf2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 21 Nov 2024 19:39:55 +0000 Subject: [PATCH 08/11] remove normalize.nf subworkflow --- subworkflows/local/normalize.nf | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 subworkflows/local/normalize.nf diff --git a/subworkflows/local/normalize.nf b/subworkflows/local/normalize.nf deleted file mode 100644 index fb1453f..0000000 --- a/subworkflows/local/normalize.nf +++ /dev/null @@ -1,19 +0,0 @@ -// -// Perform normalizations (currently using Nacho) -// - -include { NACHO_NORMALIZE } from '../../modules/local/nacho/normalize/main' - -workflow NORMALIZE { - take: - counts // channel: [ meta, path(rcc) ] - samplesheet // file: /path/to/samplesheet.csv - - main: - NACHO_NORMALIZE ( counts, samplesheet ) - - emit: - normalized_counts = NACHO_NORMALIZE.out.normalized_counts // channel: [ val(meta), [ counts ] ] - normalized_counts_wo_HK = NACHO_NORMALIZE.out.normalized_counts_wo_HK // channel: [ samplesheet.valid.csv ] - versions = NACHO_NORMALIZE.out.versions // channel: [ versions.yml ] -} From 68ef4dc6a57ae162351443a37a449d3b85bd978f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 21 Nov 2024 19:40:29 +0000 Subject: [PATCH 09/11] sort create_annotated_table input to solve consistency --- workflows/nanostring.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/nanostring.nf b/workflows/nanostring.nf index 62ba3ad..9c3f218 100644 --- a/workflows/nanostring.nf +++ b/workflows/nanostring.nf @@ -91,7 +91,7 @@ workflow NANOSTRING { // MODULE: Annotate normalized counts with metadata from the samplesheet // CREATE_ANNOTATED_TABLES ( - NORMALIZE.out.normalized_counts.mix(NORMALIZE.out.normalized_counts_wo_HK), + NORMALIZE.out.normalized_counts.mix(NORMALIZE.out.normalized_counts_wo_HK).toSortedList().flatten(), samplesheet_path ) ch_versions = ch_versions.mix(CREATE_ANNOTATED_TABLES.out.versions) From 4e395de09af626117659172c53d983070065534f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 21 Nov 2024 19:40:41 +0000 Subject: [PATCH 10/11] update pipeline snapshot --- tests/test_samples.nf.test.snap | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/tests/test_samples.nf.test.snap b/tests/test_samples.nf.test.snap index 3134eba..bb4a735 100644 --- a/tests/test_samples.nf.test.snap +++ b/tests/test_samples.nf.test.snap @@ -67,11 +67,11 @@ "QC/NACHO/png/plot_normf_mqc.png", "annotated_tables", "gene_heatmaps", - "gene_heatmaps/wo_HKnorm_gene_heatmap_mqc.png", + "gene_heatmaps/gene_heatmap_mqc.png", "multiqc", "multiqc/multiqc_data", - "multiqc/multiqc_data/multiqc_No_HK_Norm_GEX_ENDO-section-plot.txt", - "multiqc/multiqc_data/multiqc_No_HK_Norm_GEX_HK-section-plot.txt", + "multiqc/multiqc_data/multiqc_Norm_GEX_ENDO-section-plot.txt", + "multiqc/multiqc_data/multiqc_Norm_GEX_HK-section-plot.txt", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_normalized_qc-section-plot.txt", @@ -79,16 +79,16 @@ "multiqc/multiqc_data/multiqc_sources.txt", "multiqc/multiqc_plots", "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/No_HK_Norm_GEX_ENDO-section-plot.pdf", - "multiqc/multiqc_plots/pdf/No_HK_Norm_GEX_HK-section-plot.pdf", + "multiqc/multiqc_plots/pdf/Norm_GEX_ENDO-section-plot.pdf", + "multiqc/multiqc_plots/pdf/Norm_GEX_HK-section-plot.pdf", "multiqc/multiqc_plots/pdf/normalized_qc-section-plot.pdf", "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/No_HK_Norm_GEX_ENDO-section-plot.png", - "multiqc/multiqc_plots/png/No_HK_Norm_GEX_HK-section-plot.png", + "multiqc/multiqc_plots/png/Norm_GEX_ENDO-section-plot.png", + "multiqc/multiqc_plots/png/Norm_GEX_HK-section-plot.png", "multiqc/multiqc_plots/png/normalized_qc-section-plot.png", "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/No_HK_Norm_GEX_ENDO-section-plot.svg", - "multiqc/multiqc_plots/svg/No_HK_Norm_GEX_HK-section-plot.svg", + "multiqc/multiqc_plots/svg/Norm_GEX_ENDO-section-plot.svg", + "multiqc/multiqc_plots/svg/Norm_GEX_HK-section-plot.svg", "multiqc/multiqc_plots/svg/normalized_qc-section-plot.svg", "multiqc/multiqc_report.html", "normalized_counts", @@ -115,6 +115,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-21T12:53:40.202730569" + "timestamp": "2024-11-21T18:48:26.062894171" } } \ No newline at end of file From c1eaaa225faa203afb1f7150cedbe8d5064b6506 Mon Sep 17 00:00:00 2001 From: alanmmobbs93 Date: Fri, 22 Nov 2024 11:40:00 -0300 Subject: [PATCH 11/11] fix nacho_normalize test snaps --- modules/local/nacho/normalize/tests/main.nf.test | 2 +- modules/local/nacho/normalize/tests/main.nf.test.snap | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/nacho/normalize/tests/main.nf.test b/modules/local/nacho/normalize/tests/main.nf.test index 346cb4c..5931be5 100644 --- a/modules/local/nacho/normalize/tests/main.nf.test +++ b/modules/local/nacho/normalize/tests/main.nf.test @@ -8,7 +8,6 @@ nextflow_process { test("Should run without failures") { when { - process { """ // RCC Files: Collect from sample sheet @@ -30,4 +29,5 @@ nextflow_process { ) } } + } diff --git a/modules/local/nacho/normalize/tests/main.nf.test.snap b/modules/local/nacho/normalize/tests/main.nf.test.snap index 0cdce8c..9833071 100644 --- a/modules/local/nacho/normalize/tests/main.nf.test.snap +++ b/modules/local/nacho/normalize/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e" ], "2": [ - "versions.yml:md5,dd0bb0b151596e1316c29a51f38f5a2e" + "versions.yml:md5,0b8556f7dd763f21894470ecc737ca3b" ], "normalized_counts": [ "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f" @@ -18,7 +18,7 @@ "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e" ], "versions": [ - "versions.yml:md5,dd0bb0b151596e1316c29a51f38f5a2e" + "versions.yml:md5,0b8556f7dd763f21894470ecc737ca3b" ] } ], @@ -26,6 +26,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-19T15:00:56.669733561" + "timestamp": "2024-11-19T19:00:09.938938106" } } \ No newline at end of file