From f8fccf986856f62bd91a17ea08fe7c6a3fb6e715 Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 24 Oct 2023 15:29:09 +0200 Subject: [PATCH 01/15] Post-release version bump --- CHANGELOG.md | 8 ++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 11 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 991a6b02..a40ebde2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,14 @@ 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). +## v1.4.0dev + +### `Added` + +### `Fixed` + +### `Changed` + ## v1.3.0 - 2023-10-25 ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 15a57fd3..211358cb 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/differentialabundance + This report has been generated by the nf-core/differentialabundance analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-differentialabundance-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 3912922d..18f335ae 100644 --- a/nextflow.config +++ b/nextflow.config @@ -384,7 +384,7 @@ manifest { description = 'Differential abundance analysis' mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.3.0' + version = '1.4.0dev' doi = '10.5281/zenodo.7568000' } From 94dbc6535f5e95222e8ad23aadda7d7719adf28a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 24 Oct 2023 15:15:36 +0100 Subject: [PATCH 02/15] Update README.md to fix Jon's employer --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 94a82262..0e19f064 100644 --- a/README.md +++ b/README.md @@ -100,7 +100,7 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning is an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project. +nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning (now at Seqera) initially built this workflow as an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project. We thank the many members of the nf-core community who assisted with this pipeline, often by reviewing module pull requests including but not limited to: From 46524104277c8d7b2ef11c4d3549cdc5f65be4df Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 24 Oct 2023 23:41:23 +0100 Subject: [PATCH 03/15] Fix logging for dendrograms --- assets/differentialabundance_report.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index d6b654b8..70ce31dd 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -255,9 +255,9 @@ assay_data <- lapply(assay_files, function(x) { if (!is.null(params$features_log2_assays)) { # Remove brackets from assay list. TODO: Remove if this is added to cond_log2_transform_assays - features_log2_assays <- gsub('\\]$', '', gsub('^\\[', '', params$features_log2_assays)) - assay_data <- cond_log2_transform_assays(assay_data, features_log2_assays) + params$features_log2_assays <- gsub('\\]$', '', gsub('^\\[', '', params$features_log2_assays)) } +assay_data <- cond_log2_transform_assays(assay_data, params$features_log2_assays) # Now we can rename the observations rows using the title field rownames(observations) <- observations[[params$observations_name_col]] From 4821e7944399b353f05c053d4c6f5a4fdbe6910b Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 25 Oct 2023 07:57:48 +0200 Subject: [PATCH 04/15] realigned version --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 18f335ae..68ac9500 100644 --- a/nextflow.config +++ b/nextflow.config @@ -384,7 +384,7 @@ manifest { description = 'Differential abundance analysis' mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.4.0dev' + version = '1.4.0dev' doi = '10.5281/zenodo.7568000' } From 8a4408569cefd5ec150059c4922a2d809ec991c3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 25 Oct 2023 10:28:33 +0100 Subject: [PATCH 05/15] Poke CI --- assets/differentialabundance_report.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 70ce31dd..34521ad2 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -254,7 +254,7 @@ assay_data <- lapply(assay_files, function(x) { }) if (!is.null(params$features_log2_assays)) { - # Remove brackets from assay list. TODO: Remove if this is added to cond_log2_transform_assays + # Remove brackets from assay list. TODO: remove if this is added to cond_log2_transform_assays params$features_log2_assays <- gsub('\\]$', '', gsub('^\\[', '', params$features_log2_assays)) } assay_data <- cond_log2_transform_assays(assay_data, params$features_log2_assays) From 5f049f54434ea7ba6f059923332b858e94fc6c70 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 25 Oct 2023 10:32:18 +0100 Subject: [PATCH 06/15] authorship nuance --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0e19f064..6e3b24a7 100644 --- a/README.md +++ b/README.md @@ -100,7 +100,7 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning (now at Seqera) initially built this workflow as an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project. +nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning (now at Seqera) initially worked on this workflow as an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project. We thank the many members of the nf-core community who assisted with this pipeline, often by reviewing module pull requests including but not limited to: From bd80954834e8b8146a25215a032cdb41ed2fa12c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 09:06:09 +0100 Subject: [PATCH 07/15] Fix changelog --- CHANGELOG.md | 4 ++++ modules.json | 2 +- modules/nf-core/custom/dumpsoftwareversions/meta.yml | 5 +++-- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a40ebde2..61ff3516 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,8 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [[#183](https://github.com/nf-core/differentialabundance/pull/183)] - Fix logging for dendrograms ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) + ### `Changed` +- [[#182](https://github.com/nf-core/differentialabundance/pull/182) - Fixed Jon's employer ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) + ## v1.3.0 - 2023-10-25 ### `Added` diff --git a/modules.json b/modules.json index ff601367..fb9c03b7 100644 --- a/modules.json +++ b/modules.json @@ -17,7 +17,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5", + "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", "installed_by": ["modules"] }, "custom/matrixfilter": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..9414c32d 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" From 2c866113fb418336c06a71a5869d4087ee42c1f7 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 09:07:27 +0100 Subject: [PATCH 08/15] Fix changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 61ff3516..7e7f2d57 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [[#182](https://github.com/nf-core/differentialabundance/pull/182) - Fixed Jon's employer ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) +- [[#182](https://github.com/nf-core/differentialabundance/pull/182)] - Fixed Jon's employer ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) ## v1.3.0 - 2023-10-25 @@ -23,7 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#129](https://github.com/nf-core/differentialabundance/pull/129)] - Module updates to fit with recent registry changes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse), [@adamrtalbot](https://github.com/adamrtalbot)) - [[#130](https://github.com/nf-core/differentialabundance/pull/130)] - Document reasons for lack of differential expression ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jfy133](https://github.com/jfy133)) - [[#131](https://github.com/nf-core/differentialabundance/pull/131)] - Improve gtf to table configurability ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) -- [# 136](https://github.com/nf-core/differentialabundance/pull/136)] - Added support for non-Affymetrix arrays via automatic download of SOFT matrices in GEO ([@azedinez](https://github.com/azedinez), review by [@pinin4fjords](https://github.com/pinin4fjords)) +- [[#136](https://github.com/nf-core/differentialabundance/pull/136)] - Added support for non-Affymetrix arrays via automatic download of SOFT matrices in GEO ([@azedinez](https://github.com/azedinez), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#137](https://github.com/nf-core/differentialabundance/pull/137)] - Add `--sizefactors_from_controls` and `--gene_id_col` for DESeq2 module to modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#145](https://github.com/nf-core/differentialabundance/pull/145)] - Template update for nf-core/tools v2.9 ([@nf-core-bot](https://github.com/nf-core-bot), review by [@pinin4fjords](https://github.com/pinin4fjords), [@WackerO](https://github.com/WackerO)) - [[#147](https://github.com/nf-core/differentialabundance/pull/147)] - Add Maxquant analysis module ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) From f7dc1330c4d97cbde6c42144b0885afc4411f88e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 09:51:50 +0100 Subject: [PATCH 09/15] Bump modules --- modules.json | 38 +++++++++---------- modules/nf-core/affy/justrma/main.nf | 2 +- modules/nf-core/affy/justrma/meta.yml | 5 +-- .../gtf2featureannotation/main.nf | 2 +- .../gtf2featureannotation/meta.yml | 5 +-- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/custom/matrixfilter/main.nf | 2 +- modules/nf-core/custom/matrixfilter/meta.yml | 8 ++-- .../nf-core/custom/tabulartogseacls/main.nf | 2 +- .../nf-core/custom/tabulartogseacls/meta.yml | 8 ++-- .../nf-core/custom/tabulartogseagct/main.nf | 2 +- .../nf-core/custom/tabulartogseagct/meta.yml | 8 ++-- modules/nf-core/deseq2/differential/main.nf | 2 +- modules/nf-core/deseq2/differential/meta.yml | 6 +-- modules/nf-core/geoquery/getgeo/main.nf | 2 +- modules/nf-core/geoquery/getgeo/meta.yml | 7 ++-- modules/nf-core/gsea/gsea/main.nf | 2 +- modules/nf-core/gsea/gsea/meta.yml | 29 +++++--------- modules/nf-core/gunzip/main.nf | 2 +- modules/nf-core/gunzip/meta.yml | 4 ++ modules/nf-core/limma/differential/main.nf | 2 +- modules/nf-core/limma/differential/meta.yml | 9 ++--- .../nf-core/proteus/readproteingroups/main.nf | 2 +- .../proteus/readproteingroups/meta.yml | 5 +-- modules/nf-core/rmarkdownnotebook/main.nf | 2 +- modules/nf-core/rmarkdownnotebook/meta.yml | 7 +--- modules/nf-core/shinyngs/app/main.nf | 2 +- modules/nf-core/shinyngs/app/meta.yml | 6 +-- .../shinyngs/staticdifferential/main.nf | 2 +- .../shinyngs/staticdifferential/meta.yml | 4 +- .../shinyngs/staticexploratory/main.nf | 2 +- .../shinyngs/staticexploratory/meta.yml | 4 +- .../shinyngs/validatefomcomponents/main.nf | 2 +- .../shinyngs/validatefomcomponents/meta.yml | 7 +--- modules/nf-core/untar/main.nf | 2 +- modules/nf-core/untar/meta.yml | 5 +++ modules/nf-core/zip/main.nf | 2 +- modules/nf-core/zip/meta.yml | 6 +-- 38 files changed, 92 insertions(+), 117 deletions(-) diff --git a/modules.json b/modules.json index fb9c03b7..98294844 100644 --- a/modules.json +++ b/modules.json @@ -7,97 +7,97 @@ "nf-core": { "affy/justrma": { "branch": "master", - "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "atlasgeneannotationmanipulation/gtf2featureannotation": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "custom/matrixfilter": { "branch": "master", - "git_sha": "e432a05dc59832d55307442264ad2b70039f5e3a", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "custom/tabulartogseacls": { "branch": "master", - "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "custom/tabulartogseagct": { "branch": "master", - "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "deseq2/differential": { "branch": "master", - "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "geoquery/getgeo": { "branch": "master", - "git_sha": "6814b0659c51e447684a58c2b834a9f3b530540d", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "gsea/gsea": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "8663c9d215573d4bd0417c93dbc310aa9e6720a4", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "limma/differential": { "branch": "master", - "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "proteus/readproteingroups": { "branch": "master", - "git_sha": "685765c4a5e3423d20f74aa9c4405ef0b8c4748d", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "rmarkdownnotebook": { "branch": "master", - "git_sha": "4e640839b1076da7c2a2a4a8f160815e00eedfba", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "shinyngs/app": { "branch": "master", - "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "shinyngs/staticdifferential": { "branch": "master", - "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "shinyngs/staticexploratory": { "branch": "master", - "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "shinyngs/validatefomcomponents": { "branch": "master", - "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] }, "zip": { "branch": "master", - "git_sha": "9ba4f5972ae27474f752ddb20e855f48047aa6c8", + "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", "installed_by": ["modules"] } } diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf index d0da7129..6dcfdf29 100644 --- a/modules/nf-core/affy/justrma/main.nf +++ b/modules/nf-core/affy/justrma/main.nf @@ -2,7 +2,7 @@ process AFFY_JUSTRMA { tag "$meta.id" label 'process_single' - conda "bioconda::bioconductor-affy=1.78.0" + conda 'modules/nf-core/affy/justrma/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-affy:1.78.0--r43ha9d7317_1': 'biocontainers/bioconductor-affy:1.78.0--r43ha9d7317_1' }" diff --git a/modules/nf-core/affy/justrma/meta.yml b/modules/nf-core/affy/justrma/meta.yml index 1f57087f..8b1685fc 100644 --- a/modules/nf-core/affy/justrma/meta.yml +++ b/modules/nf-core/affy/justrma/meta.yml @@ -13,7 +13,6 @@ tools: tool_dev_url: "https://github.com/Bioconductor/affy" doi: "10.1093/bioinformatics/btg405" licence: "['LGPL >=2.0']" - input: - meta: type: map @@ -32,7 +31,6 @@ input: type: file description: | Optional description file in MIAME format - output: - meta: type: map @@ -55,6 +53,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf index 42c6755d..c71e0f7f 100644 --- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf @@ -2,7 +2,7 @@ process ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION { tag "${meta.id}" label 'process_single' - conda "bioconda::atlas-gene-annotation-manipulation=1.1.0" + conda 'modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/atlas-gene-annotation-manipulation%3A1.1.0--hdfd78af_0': 'biocontainers/atlas-gene-annotation-manipulation:1.1.0--hdfd78af_0' }" diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml index b8c0742c..10aa5366 100644 --- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml @@ -10,7 +10,6 @@ tools: documentation: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" tool_dev_url: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" licence: "['Apache-2.0']" - input: - meta: type: map @@ -31,7 +30,6 @@ input: description: | An optional cDNA file for extracting meta info and/or filtering. pattern: "*.{gtf}" - output: - versions: type: file @@ -50,6 +48,7 @@ output: --dummy-from-cdnas only). See documentation at https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. pattern: "*.{tsv}" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c9d014b1..60a19e0e 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.15" + conda 'modules/nf-core/custom/dumpsoftwareversions/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" diff --git a/modules/nf-core/custom/matrixfilter/main.nf b/modules/nf-core/custom/matrixfilter/main.nf index 137918d7..db603c43 100644 --- a/modules/nf-core/custom/matrixfilter/main.nf +++ b/modules/nf-core/custom/matrixfilter/main.nf @@ -1,7 +1,7 @@ process CUSTOM_MATRIXFILTER { tag "$meta" label 'process_single' - conda "conda-forge::r-base=4.2.1" + conda 'modules/nf-core/custom/matrixfilter/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-base:4.2.1' : 'biocontainers/r-base:4.2.1' }" diff --git a/modules/nf-core/custom/matrixfilter/meta.yml b/modules/nf-core/custom/matrixfilter/meta.yml index 9911efce..3ba2d0cb 100644 --- a/modules/nf-core/custom/matrixfilter/meta.yml +++ b/modules/nf-core/custom/matrixfilter/meta.yml @@ -1,6 +1,5 @@ name: "custom_matrixfilter" -description: filter a matrix based on a minimum value and numbers of samples - that must pass. +description: filter a matrix based on a minimum value and numbers of samples that must pass. keywords: - matrix - filter @@ -10,7 +9,6 @@ tools: - "matrixfilter": description: "filter a matrix based on a minimum value and numbers of samples" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/matrixfilter/main.nf" - input: - meta: type: map @@ -74,7 +72,6 @@ input: Minimum observations that must have a numeric value (not be NA) to retain the row/ feature (e.g. gene). Supplied via task.ext.args as --minimum_samples_not_na. Overrides minimum_proportion_not_na - output: - versions: type: file @@ -93,6 +90,7 @@ output: type: file description: Boolean matrix with pass/ fail status for each test on each feature pattern: "*.tests.tsv" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/custom/tabulartogseacls/main.nf b/modules/nf-core/custom/tabulartogseacls/main.nf index 0df0eb1d..58fb5d08 100644 --- a/modules/nf-core/custom/tabulartogseacls/main.nf +++ b/modules/nf-core/custom/tabulartogseacls/main.nf @@ -2,7 +2,7 @@ process CUSTOM_TABULARTOGSEACLS { tag "$meta.id" label 'process_single' - conda "conda-forge::coreutils=9.1" + conda 'modules/nf-core/custom/tabulartogseacls/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/custom/tabulartogseacls/meta.yml b/modules/nf-core/custom/tabulartogseacls/meta.yml index 20b0122b..2d1ec0b8 100644 --- a/modules/nf-core/custom/tabulartogseacls/meta.yml +++ b/modules/nf-core/custom/tabulartogseacls/meta.yml @@ -9,7 +9,6 @@ tools: - custom: description: "Make a GSEA class file (.cls) from tabular inputs" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseacls/main.nf" - input: - meta: type: map @@ -23,10 +22,8 @@ input: compulsory here). - samples: type: file - description: Tabular (e.g. TSV/CSV) samples file with sample IDs by row - and variables by column. + description: Tabular (e.g. TSV/CSV) samples file with sample IDs by row and variables by column. pattern: "*.{csv,tsv}" - output: - meta: type: map @@ -43,6 +40,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/custom/tabulartogseagct/main.nf b/modules/nf-core/custom/tabulartogseagct/main.nf index c128fe36..214ea61e 100644 --- a/modules/nf-core/custom/tabulartogseagct/main.nf +++ b/modules/nf-core/custom/tabulartogseagct/main.nf @@ -2,7 +2,7 @@ process CUSTOM_TABULARTOGSEAGCT { tag "$meta.id" label 'process_single' - conda "conda-forge::coreutils=9.1" + conda 'modules/nf-core/custom/tabulartogseagct/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/custom/tabulartogseagct/meta.yml b/modules/nf-core/custom/tabulartogseagct/meta.yml index 14274b60..4f4a8064 100644 --- a/modules/nf-core/custom/tabulartogseagct/meta.yml +++ b/modules/nf-core/custom/tabulartogseagct/meta.yml @@ -8,7 +8,6 @@ tools: - tabulartogseagct: description: "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseagct/main.nf" - input: - meta: type: map @@ -17,10 +16,8 @@ input: e.g. [ id:'test' ] - tabular: type: file - description: Tabular (e.g. TSV or CSV file) containing a numeric matrix - with features (e.g. genes) by row and samples by column. + description: Tabular (e.g. TSV or CSV file) containing a numeric matrix with features (e.g. genes) by row and samples by column. pattern: "*.{tsv,csv}" - output: - meta: type: map @@ -35,6 +32,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf index bad536b2..19ea2b3f 100644 --- a/modules/nf-core/deseq2/differential/main.nf +++ b/modules/nf-core/deseq2/differential/main.nf @@ -2,7 +2,7 @@ process DESEQ2_DIFFERENTIAL { tag "$meta" label 'process_medium' - conda "bioconda::bioconductor-deseq2=1.34.0" + conda 'modules/nf-core/deseq2/differential/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-deseq2:1.34.0--r41hc247a5b_3' : 'biocontainers/bioconductor-deseq2:1.34.0--r41hc247a5b_3' }" diff --git a/modules/nf-core/deseq2/differential/meta.yml b/modules/nf-core/deseq2/differential/meta.yml index a32c3cb8..bed638e3 100644 --- a/modules/nf-core/deseq2/differential/meta.yml +++ b/modules/nf-core/deseq2/differential/meta.yml @@ -5,7 +5,6 @@ keywords: - expression - rna-seq - deseq2 - tools: - "deseq2": description: "Differential gene expression analysis based on the negative binomial distribution" @@ -14,7 +13,6 @@ tools: tool_dev_url: "https://github.com/mikelove/DESeq2" doi: "10.1186/s13059-014-0550-8" licence: "['LGPL >=3']" - input: - meta: type: map @@ -67,7 +65,6 @@ input: prevent bias in conventional normalisation (default), or used to generate the size factors (supplied via task.ext.args like '--sizefactors_from_controls TRUE'). - output: - results: type: file @@ -97,6 +94,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/geoquery/getgeo/main.nf b/modules/nf-core/geoquery/getgeo/main.nf index 39d12c26..2f9d6cd3 100644 --- a/modules/nf-core/geoquery/getgeo/main.nf +++ b/modules/nf-core/geoquery/getgeo/main.nf @@ -2,7 +2,7 @@ process GEOQUERY_GETGEO { tag "$meta.id" label 'process_single' - conda "bioconda::bioconductor-geoquery=2.66.0" + conda 'modules/nf-core/geoquery/getgeo/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-geoquery:2.66.0--r42hdfd78af_0' : 'biocontainers/bioconductor-geoquery:2.66.0--r42hdfd78af_0' }" diff --git a/modules/nf-core/geoquery/getgeo/meta.yml b/modules/nf-core/geoquery/getgeo/meta.yml index bbacbe04..ca0074c7 100644 --- a/modules/nf-core/geoquery/getgeo/meta.yml +++ b/modules/nf-core/geoquery/getgeo/meta.yml @@ -4,7 +4,6 @@ keywords: - geo - expression - microarray - tools: - "geoquery": description: "Get data from NCBI Gene Expression Omnibus (GEO)" @@ -13,7 +12,6 @@ tools: tool_dev_url: "https://github.com/seandavi/GEOquery" doi: "10.1093/bioinformatics/btm254" licence: "MIT" - input: - meta: type: map @@ -23,7 +21,6 @@ input: type: string description: | GSE identifier to pass to getGEO() - output: - rds: type: file @@ -41,7 +38,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@azedinez" - "@pinin4fjords" +maintainers: + - "@azedinez" + - "@pinin4fjords" diff --git a/modules/nf-core/gsea/gsea/main.nf b/modules/nf-core/gsea/gsea/main.nf index 479af5db..17f4a2e8 100644 --- a/modules/nf-core/gsea/gsea/main.nf +++ b/modules/nf-core/gsea/gsea/main.nf @@ -2,7 +2,7 @@ process GSEA_GSEA { tag "$meta.id" label 'process_single' - conda "bioconda::gsea=4.3.2" + conda 'modules/nf-core/gsea/gsea/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gsea:4.3.2--hdfd78af_0': 'biocontainers/gsea:4.3.2--hdfd78af_0' }" diff --git a/modules/nf-core/gsea/gsea/meta.yml b/modules/nf-core/gsea/gsea/meta.yml index a50b48be..0ff81518 100644 --- a/modules/nf-core/gsea/gsea/meta.yml +++ b/modules/nf-core/gsea/gsea/meta.yml @@ -12,7 +12,6 @@ tools: documentation: "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page" doi: "10.1073/pnas.0506580102" licence: "['BSD-3-clause']" - input: - meta: type: map @@ -46,7 +45,6 @@ input: optional Broad-style chip file mapping identifiers in gct to those in gene_sets pattern: "*.{chip}" - output: - meta: type: map @@ -70,8 +68,7 @@ output: pattern: "gsea_report_for_reference*.tsv" - report_htmls_ref: type: file - description: Main HTML results report file for the reference group. - sample groups + description: Main HTML results report file for the reference group. sample groups pattern: "gsea_report_for_reference*.html" - report_tsvs_target: type: file @@ -111,36 +108,27 @@ output: pattern: "ranked_list_corr_2.png" - gene_set_tsv: type: list - description: Where -make_sets is not set to false, TSV files, one file - for each gene set, with detail on - enrichment for each gene + description: Where -make_sets is not set to false, TSV files, one file for each gene set, with detail on enrichment for each gene pattern: "[!gene_set_size|gsea_report|ranked_gene_list]*.tsv" - gene_set_html: type: list - description: Where -make_sets is not set to false, HTML files, one file - for each gene set, with detail on enrichment for each gene + description: Where -make_sets is not set to false, HTML files, one file for each gene set, with detail on enrichment for each gene pattern: "[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html" - gene_set_heatmap: type: list - description: Where -make_sets is not set to false, PNG-format heatmaps, - one file for each gene set, showing - expression for each gene + description: Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene pattern: "[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png" - snapshot: type: list - description: HTML files, one each for positive and negative enrichment, - collecting elements of gene_set_enplot + description: HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot pattern: "*_snapshot*.html" - gene_set_enplot: type: list - description: Where -make_sets is not set to false, PNG-format enrichment - (barcode) plots, one file for each gene set, showing how genes - contribute to enrichment. + description: Where -make_sets is not set to false, PNG-format enrichment (barcode) plots, one file for each gene set, showing how genes contribute to enrichment. pattern: "enplot*.png" - gene_set_dist: type: list - description: Where -make_sets is not set to false, PNG-format enrichment - score distributions plots, one file for each gene set. + description: Where -make_sets is not set to false, PNG-format enrichment score distributions plots, one file for each gene set. pattern: "gset_rnd_es_dist*.png" - archive: type: file @@ -150,6 +138,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 73bf08cd..de9a3077 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -2,7 +2,7 @@ process GUNZIP { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7" + conda 'modules/nf-core/gunzip/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index 4cdcdf4c..231034f2 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -33,3 +33,7 @@ authors: - "@joseespinosa" - "@drpatelh" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf index 364c5a13..b41c173a 100644 --- a/modules/nf-core/limma/differential/main.nf +++ b/modules/nf-core/limma/differential/main.nf @@ -2,7 +2,7 @@ process LIMMA_DIFFERENTIAL { tag "$meta" label 'process_medium' - conda "bioconda::bioconductor-limma=3.54.0" + conda 'modules/nf-core/limma/differential/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-limma:3.54.0--r42hc0cfd56_0' : 'biocontainers/bioconductor-limma:3.54.0--r42hc0cfd56_0' }" diff --git a/modules/nf-core/limma/differential/meta.yml b/modules/nf-core/limma/differential/meta.yml index c3f5a64a..b9e43901 100644 --- a/modules/nf-core/limma/differential/meta.yml +++ b/modules/nf-core/limma/differential/meta.yml @@ -5,7 +5,6 @@ keywords: - expression - microarray - limma - tools: - "limma": description: "Linear Models for Microarray Data" @@ -14,7 +13,6 @@ tools: tool_dev_url: https://github.com/cran/limma"" doi: "10.18129/B9.bioc.limma" licence: "['LGPL >=3']" - input: - meta: type: map @@ -52,12 +50,10 @@ input: description: | Raw TSV or CSV format expression matrix with probes by row and samples by column - output: - results: type: file - description: TSV-format table of differential expression information as - output by Limma + description: TSV-format table of differential expression information as output by Limma pattern: "*.limma.results.tsv" - md_plot: type: file @@ -75,6 +71,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/proteus/readproteingroups/main.nf b/modules/nf-core/proteus/readproteingroups/main.nf index 37126cfe..34837410 100644 --- a/modules/nf-core/proteus/readproteingroups/main.nf +++ b/modules/nf-core/proteus/readproteingroups/main.nf @@ -2,7 +2,7 @@ process PROTEUS_READPROTEINGROUPS { tag "$meta.id" label 'process_single' - conda "conda-forge::r-base=4.2.1 bioconda::r-proteus-bartongroup=0.2.16 conda-forge::r-plotly=4.10.2 bioconda::bioconductor-limma=3.54.0" + conda 'modules/nf-core/proteus/readproteingroups/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-4e01206f2c47f56077f04e5d2d7b312f50513a1e:92abccefbeb09795ad6a93553b62a6ad3daaea48-0': 'biocontainers/mulled-v2-4e01206f2c47f56077f04e5d2d7b312f50513a1e:92abccefbeb09795ad6a93553b62a6ad3daaea48-0' }" diff --git a/modules/nf-core/proteus/readproteingroups/meta.yml b/modules/nf-core/proteus/readproteingroups/meta.yml index bed3dc68..8034770a 100644 --- a/modules/nf-core/proteus/readproteingroups/meta.yml +++ b/modules/nf-core/proteus/readproteingroups/meta.yml @@ -12,7 +12,6 @@ tools: tool_dev_url: "https://github.com/bartongroup/Proteus" doi: "10.1101/416511" licence: "['GPL v2']" - input: - meta: type: map @@ -34,7 +33,6 @@ input: type: string description: | The column in the sample sheet that should be used to define groups for comparison - output: - dendro_plot: type: file @@ -76,6 +74,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@WackerO" +maintainers: + - "@WackerO" diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf index 3eda8ee9..15e787df 100644 --- a/modules/nf-core/rmarkdownnotebook/main.nf +++ b/modules/nf-core/rmarkdownnotebook/main.nf @@ -7,7 +7,7 @@ process RMARKDOWNNOTEBOOK { //NB: You likely want to override this with a container containing all required //dependencies for your analysis. The container at least needs to contain the //yaml and rmarkdown R packages. - conda "conda-forge::r-base=4.1.0 conda-forge::r-rmarkdown=2.9 conda-forge::r-yaml=2.2.1" + conda 'modules/nf-core/rmarkdownnotebook/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' : 'biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }" diff --git a/modules/nf-core/rmarkdownnotebook/meta.yml b/modules/nf-core/rmarkdownnotebook/meta.yml index cdd16278..f84f0682 100644 --- a/modules/nf-core/rmarkdownnotebook/meta.yml +++ b/modules/nf-core/rmarkdownnotebook/meta.yml @@ -10,9 +10,7 @@ tools: homepage: https://rmarkdown.rstudio.com/ documentation: https://rmarkdown.rstudio.com/lesson-1.html tool_dev_url: https://github.com/rstudio/rmarkdown - licence: GPL-3 - params: - parametrize: type: boolean @@ -29,7 +27,6 @@ params: description: | If true, include a parameter `meta` which contains the information specified via the `meta` input channel. - input: - meta: type: map @@ -49,7 +46,6 @@ input: type: file description: One or multiple files serving as input data for the notebook. pattern: "*" - output: - meta: type: map @@ -68,6 +64,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@grst" +maintainers: + - "@grst" diff --git a/modules/nf-core/shinyngs/app/main.nf b/modules/nf-core/shinyngs/app/main.nf index 9cdf5cb1..d3ce2ffa 100644 --- a/modules/nf-core/shinyngs/app/main.nf +++ b/modules/nf-core/shinyngs/app/main.nf @@ -13,7 +13,7 @@ process SHINYNGS_APP { // // Those values must then be set in your Nextflow secrets. - conda "bioconda::r-shinyngs=1.8.4" + conda 'modules/nf-core/shinyngs/app/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" diff --git a/modules/nf-core/shinyngs/app/meta.yml b/modules/nf-core/shinyngs/app/meta.yml index 1c5cb831..e6ce81f8 100644 --- a/modules/nf-core/shinyngs/app/meta.yml +++ b/modules/nf-core/shinyngs/app/meta.yml @@ -5,7 +5,6 @@ keywords: - expression - rna-seq - deseq2 - tools: - "shinyngs": description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." @@ -13,7 +12,6 @@ tools: documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: "['AGPL v3']" - input: - meta: type: map @@ -45,7 +43,6 @@ input: type: file description: | List of TSV-format differential analysis outputs, one per row of the contrasts file - output: - meta: type: map @@ -67,6 +64,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf index e25edf5b..2166079f 100644 --- a/modules/nf-core/shinyngs/staticdifferential/main.nf +++ b/modules/nf-core/shinyngs/staticdifferential/main.nf @@ -2,7 +2,7 @@ process SHINYNGS_STATICDIFFERENTIAL { tag "$meta.id" label 'process_single' - conda "bioconda::r-shinyngs=1.8.4" + conda 'modules/nf-core/shinyngs/staticdifferential/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" diff --git a/modules/nf-core/shinyngs/staticdifferential/meta.yml b/modules/nf-core/shinyngs/staticdifferential/meta.yml index 84fe31de..9b92ccf7 100644 --- a/modules/nf-core/shinyngs/staticdifferential/meta.yml +++ b/modules/nf-core/shinyngs/staticdifferential/meta.yml @@ -43,7 +43,6 @@ input: description: | CSV or TSV matrix file to use alongside differential statistics in interpretation. Usually a normalised form. - output: - meta: type: map @@ -64,6 +63,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf index 4f5cbc33..4880095e 100644 --- a/modules/nf-core/shinyngs/staticexploratory/main.nf +++ b/modules/nf-core/shinyngs/staticexploratory/main.nf @@ -2,7 +2,7 @@ process SHINYNGS_STATICEXPLORATORY { tag "$meta.id" label 'process_single' - conda "bioconda::r-shinyngs=1.8.4" + conda 'modules/nf-core/shinyngs/staticexploratory/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" diff --git a/modules/nf-core/shinyngs/staticexploratory/meta.yml b/modules/nf-core/shinyngs/staticexploratory/meta.yml index 6f745da5..7bb6a61b 100644 --- a/modules/nf-core/shinyngs/staticexploratory/meta.yml +++ b/modules/nf-core/shinyngs/staticexploratory/meta.yml @@ -6,7 +6,6 @@ keywords: - boxplot - density - PCA - tools: - "shinyngs": description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." @@ -96,6 +95,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf index 0e63c89a..68943f1e 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/main.nf +++ b/modules/nf-core/shinyngs/validatefomcomponents/main.nf @@ -2,7 +2,7 @@ process SHINYNGS_VALIDATEFOMCOMPONENTS { tag "$sample" label 'process_single' - conda "bioconda::r-shinyngs=1.8.4" + conda 'modules/nf-core/shinyngs/validatefomcomponents/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" diff --git a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml index 7ad75968..fe1672a0 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml +++ b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml @@ -1,12 +1,10 @@ name: "shinyngs_validatefomcomponents" description: validate consistency of feature and sample annotations with matrices and contrasts - keywords: - expression - features - observations - validation - tools: - "shinyngs": description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." @@ -14,7 +12,6 @@ tools: documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: "['AGPL v3']" - input: - meta: type: map @@ -52,7 +49,6 @@ input: type: file description: | CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. - output: - meta: type: map @@ -80,6 +76,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 61461c39..04f5f1b2 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ process UNTAR { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" + conda 'modules/nf-core/untar/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index db241a6e..a9a2110f 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -39,3 +39,8 @@ authors: - "@drpatelh" - "@matthdsm" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@matthdsm" + - "@jfy133" diff --git a/modules/nf-core/zip/main.nf b/modules/nf-core/zip/main.nf index e281f2fa..53949e2f 100644 --- a/modules/nf-core/zip/main.nf +++ b/modules/nf-core/zip/main.nf @@ -2,7 +2,7 @@ process ZIP { tag "$prefix" label 'process_single' - conda "conda-forge::p7zip=16.02" + conda 'modules/nf-core/zip/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/p7zip:16.02' : 'biocontainers/p7zip:16.02' }" diff --git a/modules/nf-core/zip/meta.yml b/modules/nf-core/zip/meta.yml index 6aaf0aa4..c38a05cb 100644 --- a/modules/nf-core/zip/meta.yml +++ b/modules/nf-core/zip/meta.yml @@ -12,7 +12,6 @@ tools: documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" licence: ["LGPL-2.1-or-later"] - input: - meta: type: map @@ -22,7 +21,6 @@ input: - files: type: file description: File or list of files to be zipped - output: - meta: type: map @@ -37,7 +35,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@jfy133" - "@pinin4fjords" +maintainers: + - "@jfy133" + - "@pinin4fjords" From 22b7d64453af686e6611f323547407f6f7cb0a7a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 09:53:26 +0100 Subject: [PATCH 10/15] Add environment.yml files --- modules/nf-core/shinyngs/app/environment.yml | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 modules/nf-core/shinyngs/app/environment.yml diff --git a/modules/nf-core/shinyngs/app/environment.yml b/modules/nf-core/shinyngs/app/environment.yml new file mode 100644 index 00000000..3bf455c0 --- /dev/null +++ b/modules/nf-core/shinyngs/app/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::r-shinyngs=1.8.4 From 1e3a33bf4a02f4c47fd965644cfac31ddccd8801 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 09:56:31 +0100 Subject: [PATCH 11/15] Bump versions --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 211358cb..19b16027 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/differentialabundance + This report has been generated by the nf-core/differentialabundance analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-differentialabundance-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 68ac9500..0b1e93e5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -384,7 +384,7 @@ manifest { description = 'Differential abundance analysis' mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.4.0dev' + version = '1.3.1' doi = '10.5281/zenodo.7568000' } From 57bb0afc95b0d5b9126b62b093a726a0b21580b8 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 09:56:47 +0100 Subject: [PATCH 12/15] Add environment.yml files --- modules/nf-core/affy/justrma/environment.yml | 6 ++++++ .../gtf2featureannotation/environment.yml | 6 ++++++ .../nf-core/custom/dumpsoftwareversions/environment.yml | 6 ++++++ modules/nf-core/custom/matrixfilter/environment.yml | 6 ++++++ modules/nf-core/custom/tabulartogseacls/environment.yml | 6 ++++++ modules/nf-core/custom/tabulartogseagct/environment.yml | 6 ++++++ modules/nf-core/deseq2/differential/environment.yml | 6 ++++++ modules/nf-core/geoquery/getgeo/environment.yml | 6 ++++++ modules/nf-core/gsea/gsea/environment.yml | 6 ++++++ modules/nf-core/gunzip/environment.yml | 6 ++++++ modules/nf-core/limma/differential/environment.yml | 6 ++++++ .../nf-core/proteus/readproteingroups/environment.yml | 9 +++++++++ modules/nf-core/rmarkdownnotebook/environment.yml | 8 ++++++++ .../nf-core/shinyngs/staticdifferential/environment.yml | 6 ++++++ .../nf-core/shinyngs/staticexploratory/environment.yml | 6 ++++++ .../shinyngs/validatefomcomponents/environment.yml | 6 ++++++ modules/nf-core/untar/environment.yml | 8 ++++++++ modules/nf-core/zip/environment.yml | 6 ++++++ 18 files changed, 115 insertions(+) create mode 100644 modules/nf-core/affy/justrma/environment.yml create mode 100644 modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml create mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml create mode 100644 modules/nf-core/custom/matrixfilter/environment.yml create mode 100644 modules/nf-core/custom/tabulartogseacls/environment.yml create mode 100644 modules/nf-core/custom/tabulartogseagct/environment.yml create mode 100644 modules/nf-core/deseq2/differential/environment.yml create mode 100644 modules/nf-core/geoquery/getgeo/environment.yml create mode 100644 modules/nf-core/gsea/gsea/environment.yml create mode 100644 modules/nf-core/gunzip/environment.yml create mode 100644 modules/nf-core/limma/differential/environment.yml create mode 100644 modules/nf-core/proteus/readproteingroups/environment.yml create mode 100644 modules/nf-core/rmarkdownnotebook/environment.yml create mode 100644 modules/nf-core/shinyngs/staticdifferential/environment.yml create mode 100644 modules/nf-core/shinyngs/staticexploratory/environment.yml create mode 100644 modules/nf-core/shinyngs/validatefomcomponents/environment.yml create mode 100644 modules/nf-core/untar/environment.yml create mode 100644 modules/nf-core/zip/environment.yml diff --git a/modules/nf-core/affy/justrma/environment.yml b/modules/nf-core/affy/justrma/environment.yml new file mode 100644 index 00000000..587ede1e --- /dev/null +++ b/modules/nf-core/affy/justrma/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bioconductor-affy=1.78.0 diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml new file mode 100644 index 00000000..67ae588e --- /dev/null +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::atlas-gene-annotation-manipulation=1.1.0 diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..7ca22161 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.15 diff --git a/modules/nf-core/custom/matrixfilter/environment.yml b/modules/nf-core/custom/matrixfilter/environment.yml new file mode 100644 index 00000000..383c136b --- /dev/null +++ b/modules/nf-core/custom/matrixfilter/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::r-base=4.2.1 diff --git a/modules/nf-core/custom/tabulartogseacls/environment.yml b/modules/nf-core/custom/tabulartogseacls/environment.yml new file mode 100644 index 00000000..d9675fce --- /dev/null +++ b/modules/nf-core/custom/tabulartogseacls/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::coreutils=9.1 diff --git a/modules/nf-core/custom/tabulartogseagct/environment.yml b/modules/nf-core/custom/tabulartogseagct/environment.yml new file mode 100644 index 00000000..d9675fce --- /dev/null +++ b/modules/nf-core/custom/tabulartogseagct/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::coreutils=9.1 diff --git a/modules/nf-core/deseq2/differential/environment.yml b/modules/nf-core/deseq2/differential/environment.yml new file mode 100644 index 00000000..36e665e6 --- /dev/null +++ b/modules/nf-core/deseq2/differential/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bioconductor-deseq2=1.34.0 diff --git a/modules/nf-core/geoquery/getgeo/environment.yml b/modules/nf-core/geoquery/getgeo/environment.yml new file mode 100644 index 00000000..93ebb27e --- /dev/null +++ b/modules/nf-core/geoquery/getgeo/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bioconductor-geoquery=2.66.0 diff --git a/modules/nf-core/gsea/gsea/environment.yml b/modules/nf-core/gsea/gsea/environment.yml new file mode 100644 index 00000000..3158f736 --- /dev/null +++ b/modules/nf-core/gsea/gsea/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gsea=4.3.2 diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml new file mode 100644 index 00000000..222b301f --- /dev/null +++ b/modules/nf-core/gunzip/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/nf-core/limma/differential/environment.yml b/modules/nf-core/limma/differential/environment.yml new file mode 100644 index 00000000..903fdd04 --- /dev/null +++ b/modules/nf-core/limma/differential/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bioconductor-limma=3.54.0 diff --git a/modules/nf-core/proteus/readproteingroups/environment.yml b/modules/nf-core/proteus/readproteingroups/environment.yml new file mode 100644 index 00000000..bd44f38d --- /dev/null +++ b/modules/nf-core/proteus/readproteingroups/environment.yml @@ -0,0 +1,9 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::r-base=4.2.1 + - bioconda::r-proteus-bartongroup=0.2.16 + - conda-forge::r-plotly=4.10.2 + - bioconda::bioconductor-limma=3.54.0 diff --git a/modules/nf-core/rmarkdownnotebook/environment.yml b/modules/nf-core/rmarkdownnotebook/environment.yml new file mode 100644 index 00000000..996600b5 --- /dev/null +++ b/modules/nf-core/rmarkdownnotebook/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::r-base=4.1.0 + - conda-forge::r-rmarkdown=2.9 + - conda-forge::r-yaml=2.2.1 diff --git a/modules/nf-core/shinyngs/staticdifferential/environment.yml b/modules/nf-core/shinyngs/staticdifferential/environment.yml new file mode 100644 index 00000000..3bf455c0 --- /dev/null +++ b/modules/nf-core/shinyngs/staticdifferential/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::r-shinyngs=1.8.4 diff --git a/modules/nf-core/shinyngs/staticexploratory/environment.yml b/modules/nf-core/shinyngs/staticexploratory/environment.yml new file mode 100644 index 00000000..3bf455c0 --- /dev/null +++ b/modules/nf-core/shinyngs/staticexploratory/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::r-shinyngs=1.8.4 diff --git a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml new file mode 100644 index 00000000..3bf455c0 --- /dev/null +++ b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::r-shinyngs=1.8.4 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml new file mode 100644 index 00000000..2d52ce64 --- /dev/null +++ b/modules/nf-core/untar/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 + - conda-forge::grep=3.11 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/zip/environment.yml b/modules/nf-core/zip/environment.yml new file mode 100644 index 00000000..157fe95c --- /dev/null +++ b/modules/nf-core/zip/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::p7zip=16.02 From e6d1bed3e86e2c32cb7257f641f43acf7def889e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 09:59:45 +0100 Subject: [PATCH 13/15] Fix version --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7e7f2d57..10ef7be9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v1.4.0dev +## v1.3.1 ### `Added` From efd014bc9eac02883d0b289f20549614e28286d3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 10:32:54 +0100 Subject: [PATCH 14/15] Add release date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 10ef7be9..f23cd47b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v1.3.1 +## v1.3.1 - 2023-10-26 ### `Added` From b7e752808d7390d11651a102c3475904b216f012 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 26 Oct 2023 10:33:35 +0100 Subject: [PATCH 15/15] Add release date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f23cd47b..4994335d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#182](https://github.com/nf-core/differentialabundance/pull/182)] - Fixed Jon's employer ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) -## v1.3.0 - 2023-10-25 +## v1.3.0 - 2023-10-24 ### `Added`