From efd25a2135d9aec52d4c0384170131e122d68e81 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 24 Jan 2025 16:18:13 +0000 Subject: [PATCH 01/16] feat: add MultiQC AI summaries support Add support for MultiQC's AI-powered summaries feature via new parameter: - Add enable_multiqc_ai boolean parameter to schema - Add --ai flag to MultiQC args when enabled - Use nf-core standard array syntax for MultiQC args --- modules/nf-core/multiqc/nextflow.config | 5 ++++- nextflow_schema.json | 7 +++++++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config index ac178787c..22c8318e4 100644 --- a/modules/nf-core/multiqc/nextflow.config +++ b/modules/nf-core/multiqc/nextflow.config @@ -1,7 +1,10 @@ if (!params.skip_multiqc) { process { withName: 'MULTIQC' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + ext.args = { [ + ((params.multiqc_title == null) ? '' : "--title \"${params.multiqc_title}\""), + (params.enable_multiqc_ai ? '--ai' : '') + ].join(' ').trim() } ext.prefix = "multiqc_report" publishDir = [ path: { [ diff --git a/nextflow_schema.json b/nextflow_schema.json index 5bd25ca0d..573883324 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -40,6 +40,13 @@ "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", "fa_icon": "fas fa-file-signature" + }, + "enable_multiqc_ai": { + "type": "boolean", + "description": "Enable AI-powered summaries in MultiQC report", + "fa_icon": "fas fa-robot", + "default": false, + "help_text": "When enabled, MultiQC will use AI to generate summaries of the quality control results." } } }, From 41b2187f660bb461ee502d90046459b4c378529b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 24 Jan 2025 16:22:55 +0000 Subject: [PATCH 02/16] feat: Add MultiQC AI summary options with type selection --- modules/nf-core/multiqc/nextflow.config | 2 +- nextflow.config | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config index 22c8318e4..fe5b89b2c 100644 --- a/modules/nf-core/multiqc/nextflow.config +++ b/modules/nf-core/multiqc/nextflow.config @@ -3,7 +3,7 @@ if (!params.skip_multiqc) { withName: 'MULTIQC' { ext.args = { [ ((params.multiqc_title == null) ? '' : "--title \"${params.multiqc_title}\""), - (params.enable_multiqc_ai ? '--ai' : '') + (params.enable_multiqc_ai ? (params.multiqc_ai_type == 'full' ? '--ai-summary-full' : '--ai') : '') ].join(' ').trim() } ext.prefix = "multiqc_report" publishDir = [ diff --git a/nextflow.config b/nextflow.config index 61400efa7..d0b802b5b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -112,6 +112,8 @@ params { multiqc_logo = null max_multiqc_email_size = '25.MB' multiqc_methods_description = null + enable_multiqc_ai = false + multiqc_ai_type = 'concise' // 'concise' or 'full' // Boilerplate options outdir = null From fade208e43e669b4b65d10bc11b9c1e8e8364e64 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 24 Jan 2025 16:34:55 +0000 Subject: [PATCH 03/16] feat: Add Seqera access token configuration for MultiQC AI --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index d0b802b5b..5f5ccc9c4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -296,6 +296,7 @@ env { R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" JULIA_DEPOT_PATH = "/usr/local/share/julia" + SEQERA_ACCESS_TOKEN = { params.enable_multiqc_ai ? System.getenv('SEQERA_ACCESS_TOKEN') : null } } // Set bash options From b66571f394051f0b6c29e171a8b28a996ebaea3c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 10:33:03 +0000 Subject: [PATCH 04/16] bump multiqc --- modules.json | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 ++-- modules/nf-core/multiqc/tests/main.nf.test | 5 ++++ .../nf-core/multiqc/tests/main.nf.test.snap | 24 +++++++++---------- 5 files changed, 21 insertions(+), 16 deletions(-) diff --git a/modules.json b/modules.json index 320f2c245..7d151208c 100644 --- a/modules.json +++ b/modules.json @@ -110,7 +110,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", + "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", "installed_by": ["modules"] }, "picard/markduplicates": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 6f5b867b7..a27122ce1 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.25.1 + - bioconda::multiqc=1.27 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index cc0643e1d..58d9313c6 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : + 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f815b6de3..33316a7dd 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,6 +3,11 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + + tag "modules" + tag "modules_nfcore" + tag "multiqc" + config "./nextflow.config" test("sarscov2 single-end [fastqc]") { diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 2fcbb5ff7..7b7c13220 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:51:46.317523" + "timestamp": "2025-01-27T09:29:57.631982377" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:20.680978" + "timestamp": "2025-01-27T09:30:34.743726958" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:09.185842" + "timestamp": "2025-01-27T09:30:21.44383553" } } \ No newline at end of file From 68ee86c1c1821ce0629a9af8ba881a023c90bd5d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 10:42:24 +0000 Subject: [PATCH 05/16] fix schema --- nextflow_schema.json | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 573883324..e26cfa2bf 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -45,8 +45,14 @@ "type": "boolean", "description": "Enable AI-powered summaries in MultiQC report", "fa_icon": "fas fa-robot", - "default": false, "help_text": "When enabled, MultiQC will use AI to generate summaries of the quality control results." + }, + "multiqc_ai_type": { + "type": "string", + "default": "concise", + "description": "Seqera AI summary type.", + "fa_icon": "fas fa-font", + "enum": ["concise", "full"] } } }, From 2b054b97df7d645f66a00e4008eefde15b07d985 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 11:52:48 +0000 Subject: [PATCH 06/16] Simplify env var porting --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 5f5ccc9c4..cafc190f6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -296,7 +296,7 @@ env { R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" JULIA_DEPOT_PATH = "/usr/local/share/julia" - SEQERA_ACCESS_TOKEN = { params.enable_multiqc_ai ? System.getenv('SEQERA_ACCESS_TOKEN') : null } + SEQERA_ACCESS_TOKEN = "$SEQERA_ACCESS_TOKEN" } // Set bash options From 17ccfa48ed90f01de6036574efaaefaa7d526178 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 13:10:56 +0000 Subject: [PATCH 07/16] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a9c12a685..f70ac1713 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1482](https://github.com/nf-core/rnaseq/pull/1482) - Update trimgalore module for save_unpaired fix - [PR #1486](https://github.com/nf-core/rnaseq/pull/1486) - Bump STAR build for multiprocessing fix - [PR #1490](https://github.com/nf-core/rnaseq/pull/1490) - Make genomic FASTA input optional +- [PR #1495](https://github.com/nf-core/rnaseq/pull/1495) - Activate multiqc AI summaries # 3.18.0 - 2024-12-19 From 1747b1b947b0a670f429357e0b74ce930f3b7d7f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 13:11:28 +0000 Subject: [PATCH 08/16] Account for other providers, move keys to secrets --- nextflow.config | 22 +++++++++++++--------- nextflow_schema.json | 9 ++++++++- 2 files changed, 21 insertions(+), 10 deletions(-) diff --git a/nextflow.config b/nextflow.config index cafc190f6..19c554fb5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -113,7 +113,8 @@ params { max_multiqc_email_size = '25.MB' multiqc_methods_description = null enable_multiqc_ai = false - multiqc_ai_type = 'concise' // 'concise' or 'full' + multiqc_ai_type = 'concise' + multiqc_ai_provider = 'seqera' // Boilerplate options outdir = null @@ -287,16 +288,19 @@ charliecloud.registry = 'quay.io' // Load igenomes.config if required includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' -// Export these variables to prevent local Python/R libraries from conflicting with those in the container -// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. -// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. - env { + // Export these variables to prevent local Python/R libraries from conflicting with those in the container + // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. + // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. PYTHONNOUSERSITE = 1 - R_PROFILE_USER = "/.Rprofile" - R_ENVIRON_USER = "/.Renviron" - JULIA_DEPOT_PATH = "/usr/local/share/julia" - SEQERA_ACCESS_TOKEN = "$SEQERA_ACCESS_TOKEN" + R_PROFILE_USER = "/.Rprofile" + R_ENVIRON_USER = "/.Renviron" + JULIA_DEPOT_PATH = "/usr/local/share/julia" + + // Pass AI summary keys to MULTIQC + SEQERA_ACCESS_TOKEN = (secrets.SEQERA_ACCESS_TOKEN ?: '') + OPENAI_API_KEY = (secrets.OPENAI_API_KEY ?: '') + ANTHROPIC_API_KEY = (secrets.ANTHROPIC_API_KEY ?: '') } // Set bash options diff --git a/nextflow_schema.json b/nextflow_schema.json index e26cfa2bf..ce890cdc2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -50,9 +50,16 @@ "multiqc_ai_type": { "type": "string", "default": "concise", - "description": "Seqera AI summary type.", + "description": "MultiQC AI summary type.", "fa_icon": "fas fa-font", "enum": ["concise", "full"] + }, + "multiqc_ai_provider": { + "type": "string", + "default": "concise", + "description": "MultiQC AI summary provider.", + "fa_icon": "fas fa-font", + "enum": ["seqera", "openai", "anthropic"] } } }, From 67cb1dc48874ab88842397af52cb9aecd9fa9a59 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 14:44:13 +0000 Subject: [PATCH 09/16] Use env after all --- nextflow.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index 19c554fb5..8db704cc7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -297,10 +297,10 @@ env { R_ENVIRON_USER = "/.Renviron" JULIA_DEPOT_PATH = "/usr/local/share/julia" - // Pass AI summary keys to MULTIQC - SEQERA_ACCESS_TOKEN = (secrets.SEQERA_ACCESS_TOKEN ?: '') - OPENAI_API_KEY = (secrets.OPENAI_API_KEY ?: '') - ANTHROPIC_API_KEY = (secrets.ANTHROPIC_API_KEY ?: '') + // Propagate API keys to MultiQC + SEQERA_ACCESS_TOKEN = "$SEQERA_ACCESS_TOKEN" + OPENAI_API_KEY = "$OPENAI_API_KEY" + ANTHROPIC_API_KEY = "$ANTHROPIC_API_KEY" } // Set bash options From 8de61775263a4dada2d9dd3526ad69d31812b9ec Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 14:55:33 +0000 Subject: [PATCH 10/16] Update docs --- docs/usage.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 74fd92290..f388c69e7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -319,6 +319,20 @@ It is important to note that the accuracy of Kraken2 is [highly dependent on the While Kraken2 is capable of detecting low-abundance contaminants in a sample, false positives can occur. Therefore, if only a very small number of reads from a contaminating species are detected, these results should be interpreted with caution. +## AI summaries with MultiQC + +As of version 1.27, MultiQC has [AI-driven summarisation functionality](https://docs.seqera.io/multiqc/ai). You can activate this functionality in this workflow by passing `--enable_multiqc_ai`. + +You use any of Seqera AI, OpenAI, or Anthropic as your provider of AI services, setting `--multiqc_ai_provider` correctly and defining the appropriate environment variable to provide the API key: + +| `--multiqc_ai_provider` | Environment variable | +| ----------------------- | -------------------- | +| seqera | SEQERA_ACCESS_TOKEN | +| openai | OPENAI_API_KEY | +| anthropic | ANTHROPIC_API_KEY | + +Default behaviour is a concise summary, you can opt for a fuller summary by setting `--multiqc_ai_type` to 'full'. + ## Running the pipeline The typical command for running the pipeline is as follows: From f00047954a15df65e9976e304dec9aa63bdad1a9 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 14:58:00 +0000 Subject: [PATCH 11/16] Add new params to changelog --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f70ac1713..10c724b32 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1490](https://github.com/nf-core/rnaseq/pull/1490) - Make genomic FASTA input optional - [PR #1495](https://github.com/nf-core/rnaseq/pull/1495) - Activate multiqc AI summaries +## Parameters + +| Old parameter | New parameter | +| ------------- | ----------------------- | +| | `--enable_multiqc_ai` | +| | `--multiqc_ai_type` | +| | `--multiqc_ai_provider` | + # 3.18.0 - 2024-12-19 ### Credits From 9260b70bc68dc910957860a7a151b3962b6a7937 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 15:01:30 +0000 Subject: [PATCH 12/16] Fix schema --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index ce890cdc2..4e7a374f5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -56,7 +56,7 @@ }, "multiqc_ai_provider": { "type": "string", - "default": "concise", + "default": "seqera", "description": "MultiQC AI summary provider.", "fa_icon": "fas fa-font", "enum": ["seqera", "openai", "anthropic"] From 81f6bb436bf9b9bb4ab4eff4a5f82d2b6fa1fd9b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 15:43:06 +0000 Subject: [PATCH 13/16] what happens if I disable the tower var passthrough? --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 8db704cc7..57fc1cd77 100644 --- a/nextflow.config +++ b/nextflow.config @@ -298,7 +298,7 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" // Propagate API keys to MultiQC - SEQERA_ACCESS_TOKEN = "$SEQERA_ACCESS_TOKEN" + //SEQERA_ACCESS_TOKEN = "$SEQERA_ACCESS_TOKEN" OPENAI_API_KEY = "$OPENAI_API_KEY" ANTHROPIC_API_KEY = "$ANTHROPIC_API_KEY" } From d94575850ad46205cfb98d7394c02ac64b3801c9 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 16:45:53 +0000 Subject: [PATCH 14/16] Revert "what happens if I disable the tower var passthrough?" This reverts commit 81f6bb436bf9b9bb4ab4eff4a5f82d2b6fa1fd9b. --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 57fc1cd77..8db704cc7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -298,7 +298,7 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" // Propagate API keys to MultiQC - //SEQERA_ACCESS_TOKEN = "$SEQERA_ACCESS_TOKEN" + SEQERA_ACCESS_TOKEN = "$SEQERA_ACCESS_TOKEN" OPENAI_API_KEY = "$OPENAI_API_KEY" ANTHROPIC_API_KEY = "$ANTHROPIC_API_KEY" } From 42756fbd2d42f0e2eebd87b3dc97ecc7e3ac3923 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Jan 2025 18:14:28 +0000 Subject: [PATCH 15/16] Don't env empty things --- nextflow.config | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index 8db704cc7..f14a5aec2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -298,9 +298,10 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" // Propagate API keys to MultiQC - SEQERA_ACCESS_TOKEN = "$SEQERA_ACCESS_TOKEN" - OPENAI_API_KEY = "$OPENAI_API_KEY" - ANTHROPIC_API_KEY = "$ANTHROPIC_API_KEY" + System.getenv('SEQERA_ACCESS_TOKEN')?.with { SEQERA_ACCESS_TOKEN = it } + System.getenv('TOWER_ACCESS_TOKEN')?.with { TOWER_ACCESS_TOKEN = it } + System.getenv('OPENAI_API_KEY')?.with { OPENAI_API_KEY = it } + System.getenv('ANTHROPIC_API_KEY')?.with { ANTHROPIC_API_KEY = it } } // Set bash options From ae15852070e342111427e2aa394c4e7f2659f473 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 28 Jan 2025 15:45:34 +0000 Subject: [PATCH 16/16] update snaps --- tests/default.nf.test.snap | 28 ++++++++++----------- tests/featurecounts_group_type.nf.test.snap | 26 +++++++++---------- tests/hisat2.nf.test.snap | 28 ++++++++++----------- tests/kallisto.nf.test.snap | 14 +++++------ tests/min_mapped_reads.nf.test.snap | 28 ++++++++++----------- tests/nofasta.nf.test.snap | 2 +- tests/remove_ribo_rna.nf.test.snap | 28 ++++++++++----------- tests/salmon.nf.test.snap | 14 +++++------ tests/skip_qc.nf.test.snap | 26 +++++++++---------- tests/skip_trimming.nf.test.snap | 20 +++++++-------- tests/star_rsem.nf.test.snap | 28 ++++++++++----------- tests/umi.nf.test.snap | 18 ++++++------- 12 files changed, 130 insertions(+), 130 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 6c81ba445..353b5832e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -98,10 +98,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T12:26:32.825018567" + "timestamp": "2025-01-28T13:26:07.890871152" }, "Params: default": { "content": [ @@ -367,10 +367,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1346,11 +1346,11 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d", + "multiqc_featurecounts_biotype_plot.txt:md5,fb9db2fca737fbdcd1a921e683805d77", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882", "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5", "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405", @@ -1490,9 +1490,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T12:39:04.406597796" + "timestamp": "2025-01-28T13:24:46.099038947" } -} +} \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 8dc553d3c..8dc50d747 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -98,10 +98,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:26:42.742119846" + "timestamp": "2025-01-28T13:38:47.824968389" }, "Params: --featurecounts_group_type false": { "content": [ @@ -360,10 +360,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1313,9 +1313,9 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882", "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5", "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405", @@ -1440,9 +1440,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:25:47.179044158" + "timestamp": "2025-01-28T13:38:00.766111515" } -} +} \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 6c636a54a..4669ca38d 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -99,10 +99,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:39:53.585492305" + "timestamp": "2025-01-28T13:46:14.476085587" }, "Params: --aligner hisat2": { "content": [ @@ -834,10 +834,10 @@ "multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt", "multiqc/hisat2/multiqc_report_data/multiqc_sources.txt", + "multiqc/hisat2/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/hisat2/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/hisat2/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/hisat2/multiqc_report_data/picard_deduplication.txt", - "multiqc/hisat2/multiqc_report_data/picard_histogram.txt", - "multiqc/hisat2/multiqc_report_data/picard_histogram_1.txt", - "multiqc/hisat2/multiqc_report_data/picard_histogram_2.txt", "multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1293,11 +1293,11 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,d784fc4b2dce860c8f88cc3e936e589e", + "multiqc_featurecounts_biotype_plot.txt:md5,6d251bec0231afccd0682e454a3b17bc", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,f3b9bb1902af4c7b5e04c0830ded2c02", "qualimap_gene_coverage_profile_Normalised.txt:md5,ebcedec8e5c959414a4e89ccae3fc07e", "qualimap_rnaseq_cov_hist.txt:md5,b78ff616f267f9b061b3297b767e88fb", @@ -1340,9 +1340,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:38:50.917761241" + "timestamp": "2025-01-28T13:45:28.520702162" } -} +} \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 3be9c4e1c..796efdfd9 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -273,10 +273,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:48:16.536464395" + "timestamp": "2025-01-28T13:49:54.341502957" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -360,9 +360,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:49:02.306667165" + "timestamp": "2025-01-28T13:50:34.753130451" } -} +} \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 198ebc1ae..f2f43f748 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -264,10 +264,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1077,11 +1077,11 @@ "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476", + "multiqc_featurecounts_biotype_plot.txt:md5,7023aeba8868687d17107a265791f096", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,6d377444d29c3d4135980982ab1df2fb", "qualimap_gene_coverage_profile_Normalised.txt:md5,dc8b4f9fddc08e06668f9ee87faac008", "qualimap_rnaseq_cov_hist.txt:md5,a409821701f60811027daef4e7f3ebee", @@ -1195,10 +1195,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:57:05.836924025" + "timestamp": "2025-01-28T13:58:04.624400317" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1299,9 +1299,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:57:59.273391037" + "timestamp": "2025-01-28T13:58:55.550749008" } -} +} \ No newline at end of file diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap index f3593cdb6..5e9ec37d0 100644 --- a/tests/nofasta.nf.test.snap +++ b/tests/nofasta.nf.test.snap @@ -424,6 +424,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-21T18:27:30.970398934" + "timestamp": "2025-01-28T14:01:08.126903467" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 0cb05e4df..b543e52a4 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -270,10 +270,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1262,11 +1262,11 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,f4de303d3277d862031df94b509527ba", + "multiqc_featurecounts_biotype_plot.txt:md5,4ae746bfab7f24c39085661271ab3c57", "multiqc_samtools_idxstats.txt:md5,58f19b28617037a2825f812d58d55e2e", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,286d47f67e1d034a88e122091ae30f3d", "qualimap_gene_coverage_profile_Normalised.txt:md5,3297068282f57506f40070b8bc6ad1b5", "qualimap_rnaseq_cov_hist.txt:md5,a523cfcb52fe8f2d5902d933568a790d", @@ -1406,10 +1406,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:13:03.469655405" + "timestamp": "2025-01-28T14:14:14.995102985" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1513,9 +1513,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:13:56.979730403" + "timestamp": "2025-01-28T14:15:07.900489704" } -} +} \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index f95d31988..09d20feb7 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -349,10 +349,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T19:45:33.529844191" + "timestamp": "2025-01-28T14:18:40.084965809" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -433,9 +433,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T19:46:22.63337267" + "timestamp": "2025-01-28T14:19:20.666237815" } -} +} \ No newline at end of file diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index ff35f4743..c2b30f4a2 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -84,10 +84,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:20:52.010478721" + "timestamp": "2025-01-28T14:26:25.392367126" }, "Params: --skip_qc": { "content": [ @@ -267,10 +267,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/salmon_plot.txt", "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt", "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt", @@ -727,9 +727,9 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", @@ -818,9 +818,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:20:07.800214285" + "timestamp": "2025-01-28T14:25:33.060222508" } -} +} \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 78f2d0096..15f1425d2 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -219,10 +219,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1126,11 +1126,11 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_featurecounts_biotype_plot.txt:md5,91d4ea5a6d4b02091be666eeab952443", + "multiqc_featurecounts_biotype_plot.txt:md5,2fffc21e7bef2a357f5651ba64bb6cd4", "multiqc_samtools_idxstats.txt:md5,adf5f32fa1485ad0f4dacdfedc7b4bbc", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,b16bc0437cb340aaf6fa1472888b6930", "qualimap_gene_coverage_profile_Normalised.txt:md5,209b0020fcd4c3c497e3abbd1f8cd593", "qualimap_rnaseq_cov_hist.txt:md5,3be7bc41531ce84b42092a742bfeb0ab", @@ -1270,9 +1270,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:28:59.906095781" + "timestamp": "2025-01-28T14:35:13.246904514" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 31bf3c782..b2752af74 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -263,10 +263,10 @@ "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt", + "multiqc/star_rsem/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_rsem/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_rsem/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_rsem/multiqc_report_data/picard_histogram.txt", - "multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_rsem/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_rsem/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1173,11 +1173,11 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,aef45c9c7814f3127cd3e9b77a5ed676", + "multiqc_featurecounts_biotype_plot.txt:md5,16081809f893eca4d9914fd370e7fbd7", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,387c07f2a93e3d13048c4cd788d1fcc3", "qualimap_gene_coverage_profile_Normalised.txt:md5,35f0b71796622269bc51cf1e7a0650ab", "qualimap_rnaseq_cov_hist.txt:md5,a620cb9d1878e86e10e87500e98122f1", @@ -1290,10 +1290,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:37:23.242230621" + "timestamp": "2025-01-28T14:45:42.416394727" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1392,9 +1392,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:38:21.04782292" + "timestamp": "2025-01-28T14:46:52.666136139" } -} +} \ No newline at end of file diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap index b8376d44f..f7aba4613 100644 --- a/tests/umi.nf.test.snap +++ b/tests/umi.nf.test.snap @@ -1323,7 +1323,7 @@ "multiqc_cutadapt.txt:md5,0937983d3ddfeccd4ccc5b0d74477558", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a8a003b61b03295c416f3eb66c1cca65", - "multiqc_featurecounts_biotype_plot.txt:md5,5d1c33f3ff898b9bb95ed161e4235011", + "multiqc_featurecounts_biotype_plot.txt:md5,263834175c1a124e529c686b433fd005", "multiqc_samtools_idxstats.txt:md5,bdf185faa6d15d22efedb39d38c84943", "multiqc_umitools_dedup.txt:md5,bad73f567baddb2272488b0e78e208cb", "multiqc_umitools_extract.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1507,9 +1507,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2024-12-20T00:02:04.611696704" + "timestamp": "2025-01-28T15:37:17.975884153" }, "Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": { "content": [ @@ -2692,7 +2692,7 @@ "multiqc_cutadapt.txt:md5,0937983d3ddfeccd4ccc5b0d74477558", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a8a003b61b03295c416f3eb66c1cca65", - "multiqc_featurecounts_biotype_plot.txt:md5,078841c35fb163ad1e7c99393015ecac", + "multiqc_featurecounts_biotype_plot.txt:md5,aa03c08d5d2fba14d6770085bc042dbc", "multiqc_samtools_idxstats.txt:md5,35fe3b73df5ab19b53c117d3269e7e72", "qualimap_gene_coverage_profile_Counts.txt:md5,54613117acef91c2271327e31203242c", "qualimap_gene_coverage_profile_Normalised.txt:md5,f2884314cb4296877eb6ffd03a12a5b8", @@ -2745,9 +2745,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2024-12-19T22:33:42.012684597" + "timestamp": "2025-01-28T15:28:11.592812818" }, "--umi_dedup_tool 'umitools - stub": { "content": [ @@ -2858,8 +2858,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2024-12-19T23:28:01.570835895" + "timestamp": "2025-01-28T15:38:40.145569546" } -} +} \ No newline at end of file