From 2cfe373f6556981ee6da1f6e02fdd8c3bc023894 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sun, 13 Oct 2024 18:31:03 -0500 Subject: [PATCH 1/6] chore: Use assertAll in all tests --- .../grohmm/parametertuning/tests/main.nf.test | 5 ++++- .../transcriptcalling/tests/main.nf.test | 6 +++-- subworkflows/local/grohmm/tests/main.nf.test | 18 ++++++++++----- workflows/tests/aligner/bwa.nf.test | 22 ++++++++++++------- 4 files changed, 34 insertions(+), 17 deletions(-) diff --git a/modules/local/grohmm/parametertuning/tests/main.nf.test b/modules/local/grohmm/parametertuning/tests/main.nf.test index 36925575..c80c61b4 100644 --- a/modules/local/grohmm/parametertuning/tests/main.nf.test +++ b/modules/local/grohmm/parametertuning/tests/main.nf.test @@ -28,7 +28,10 @@ nextflow_process { then { // FIXME Broken test - assert process.failed + assertAll( + { assert process.failed }, + { assert snapshot(process.out).match() } + ) } } diff --git a/modules/local/grohmm/transcriptcalling/tests/main.nf.test b/modules/local/grohmm/transcriptcalling/tests/main.nf.test index 21fdb8af..6b088542 100644 --- a/modules/local/grohmm/transcriptcalling/tests/main.nf.test +++ b/modules/local/grohmm/transcriptcalling/tests/main.nf.test @@ -27,8 +27,10 @@ nextflow_process { } then { - // FIXME Broken test - assert process.failed + assertAll( + { assert process.failed }, + { assert snapshot(process.out).match() } + ) } } diff --git a/subworkflows/local/grohmm/tests/main.nf.test b/subworkflows/local/grohmm/tests/main.nf.test index c54ce88a..59b159d0 100644 --- a/subworkflows/local/grohmm/tests/main.nf.test +++ b/subworkflows/local/grohmm/tests/main.nf.test @@ -27,8 +27,10 @@ nextflow_workflow { } then { - assert workflow.success - assert snapshot(workflow.out).match() + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) } } @@ -55,8 +57,10 @@ nextflow_workflow { } then { - assert workflow.success - assert snapshot(workflow.out).match() + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) } } @@ -84,8 +88,10 @@ nextflow_workflow { } then { - assert workflow.success - assert snapshot(workflow.out).match() + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) } } diff --git a/workflows/tests/aligner/bwa.nf.test b/workflows/tests/aligner/bwa.nf.test index b8833f01..9add36bd 100644 --- a/workflows/tests/aligner/bwa.nf.test +++ b/workflows/tests/aligner/bwa.nf.test @@ -71,10 +71,13 @@ nextflow_pipeline { } then { - assert workflow.success - assert snapshot( - workflow.trace.tasks().size(), - ).match() + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.trace.tasks().size(), + ).match() + } + ) } } @@ -91,10 +94,13 @@ nextflow_pipeline { } then { - assert workflow.success - assert snapshot( - workflow.trace.tasks().size(), - ).match() + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.trace.tasks().size(), + ).match() + } + ) } } From 9e945e1b6db694279bced7e847354e279be4bf61 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sun, 13 Oct 2024 20:30:15 -0500 Subject: [PATCH 2/6] fix(multiqc): Update groHMM plot fn --- assets/multiqc_config.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 44c6bde6..71bf88ba 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -30,9 +30,11 @@ module_order: custom_data: grohmm_plot: section_name: "groHMM TD Plot" + description: "Transcription direction (TD) plot generated by groHMM" + plot_type: "image" sp: - my_custom_content_image: - fn: "./grohmm/*.tdplot.jpg" + grohmm_plot: + fn: "*.tdplot_mqc.jpg" ignore_images: false export_plots: true From a86ea1807512bd1e2238550d5e9092ce1f79f928 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 14 Oct 2024 09:13:58 -0500 Subject: [PATCH 3/6] fix: Remove custom FastQC section https://github.com/nf-core/rnaseq/issues/1303 --- assets/multiqc_config.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 71bf88ba..525f129a 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -20,13 +20,6 @@ run_modules: - featureCounts - homer -module_order: - - fastqc: - name: "FastQC (raw)" - info: "This section of the report shows FastQC results before adapter trimming." - path_filters: - - "./fastqc/*.zip" - custom_data: grohmm_plot: section_name: "groHMM TD Plot" From 252d59dd7e57e77a0aa8410b042112c080a2023d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 14 Oct 2024 12:31:25 -0500 Subject: [PATCH 4/6] chore(multiqc): Copy RNA-seq report order --- assets/multiqc_config.yml | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 525f129a..c2263ca3 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,6 +3,29 @@ report_comment: > analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: + fastqc: + order: 4004 + fastp: + order: 4003 + star: + order: 3000 + hisat2: + order: 3000 + samtools: + order: 3000 + featurecounts_biotype: + order: 3000 + picard: + order: 3000 + preseq: + order: 3000 + qualimap: + order: 3000 + rseqc: + order: 3000 + umitools: + order: 3000 + # Summaries "nf-core-nascent-methods-description": order: -1000 software_versions: From 64a51c283fdc3c25f4ff854eab59a280a60d2359 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 14 Oct 2024 13:08:57 -0500 Subject: [PATCH 5/6] chore: Add test profile as default to nf-test --- nf-test.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nf-test.config b/nf-test.config index 261ec1c2..d8258c96 100644 --- a/nf-test.config +++ b/nf-test.config @@ -3,6 +3,7 @@ config { testsDir "." workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" configFile "tests/nextflow.config" + profile "test" plugins { load "nft-bam@0.3.0" } From a989636e7d72d96fbe83e959c72862ff42880e48 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sun, 20 Oct 2024 14:53:17 -0500 Subject: [PATCH 6/6] chore: Update Changelog --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 07e1c640..684accc5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,10 +13,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#142](https://github.com/nf-core/nascent/pull/142) - Add STAR aligner - [#149](https://github.com/nf-core/nascent/pull/149) - Add Software citations to MultiQC +### Fixed + +- [#171](https://github.com/nf-core/nascent/pull/171) - Clean up MultiQC report + ### Changed - [#137](https://github.com/nf-core/nascent/pull/137) - Use singularity containers for PINTS - [#142](https://github.com/nf-core/nascent/pull/142) - Updated CHM13 references +- [#171](https://github.com/nf-core/nascent/pull/171) - Use assertAll in tests ## v2.2.0 - 2024-03-05