From 83655854e690d6a6d9ace9f4ce1488eec5b1f971 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Steffen=20M=C3=B6ller?= Date: Thu, 20 Jul 2023 12:05:05 +0200 Subject: [PATCH 1/5] Update README.md - aded ref to nf-core/rnaseq and Affymetrix --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2cb1013d..82dfd0bd 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ ## Introduction -**nf-core/differentialabundance** is a bioinformatics pipeline that can be used to analyse data represented as matrices, comparing groups of observations to generate differential statistics and downstream analyses. The initial feature set is built around RNA-seq, but we anticipate rapid expansion to include other platforms. +**nf-core/differentialabundance** is an advanced bioinformatics pipeline that can be used to analyse data represented as matrices, comparing groups of observations to generate differential statistics and downstream analyses. The pipeline already supports RNA-seq data, as demonstrated in the nf-core [rnaseq workflow](https://github.com/nf-core/rnaseq), and Affymetrix/ThermoFisher .CEL files. However, our team is actively working on expanding its capabilities to encompass a broader range of platforms and maintain an effective tool to explore gene expression with ease and accuracy. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! From a98ca1256eebf8c397abec35b3c3a2897fc1eac1 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 25 Jul 2023 11:14:56 +0100 Subject: [PATCH 2/5] Update README.md to be more precise on modalities --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 82dfd0bd..19afbaad 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ ## Introduction -**nf-core/differentialabundance** is an advanced bioinformatics pipeline that can be used to analyse data represented as matrices, comparing groups of observations to generate differential statistics and downstream analyses. The pipeline already supports RNA-seq data, as demonstrated in the nf-core [rnaseq workflow](https://github.com/nf-core/rnaseq), and Affymetrix/ThermoFisher .CEL files. However, our team is actively working on expanding its capabilities to encompass a broader range of platforms and maintain an effective tool to explore gene expression with ease and accuracy. +**nf-core/differentialabundance** is a bioinformatics pipeline that can be used to analyse data represented as matrices, comparing groups of observations to generate differential statistics and downstream analyses. The pipeline supports RNA-seq data such as that generated by the nf-core [rnaseq workflow](https://github.com/nf-core/rnaseq), and Affymetrix arrays via .CEL files. Other types of matrix may also work with appropriate changes to parameters, and PRs to support additional specific modalities are welcomed. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! From ddcf6cb485213c729d31c62b9a600f506fc19cbf Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 25 Jul 2023 10:17:39 +0000 Subject: [PATCH 3/5] [automated] Fix linting with Prettier --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 19afbaad..de269d7d 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ ## Introduction -**nf-core/differentialabundance** is a bioinformatics pipeline that can be used to analyse data represented as matrices, comparing groups of observations to generate differential statistics and downstream analyses. The pipeline supports RNA-seq data such as that generated by the nf-core [rnaseq workflow](https://github.com/nf-core/rnaseq), and Affymetrix arrays via .CEL files. Other types of matrix may also work with appropriate changes to parameters, and PRs to support additional specific modalities are welcomed. +**nf-core/differentialabundance** is a bioinformatics pipeline that can be used to analyse data represented as matrices, comparing groups of observations to generate differential statistics and downstream analyses. The pipeline supports RNA-seq data such as that generated by the nf-core [rnaseq workflow](https://github.com/nf-core/rnaseq), and Affymetrix arrays via .CEL files. Other types of matrix may also work with appropriate changes to parameters, and PRs to support additional specific modalities are welcomed. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! From 2207e5d9c2e6256cf40f317c4f6caa4d0045d575 Mon Sep 17 00:00:00 2001 From: Steffen Moeller Date: Tue, 25 Jul 2023 13:18:09 +0200 Subject: [PATCH 4/5] CHANGELOG: Added ref to PR #149 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5ce69e42..1c7311c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#105](https://github.com/nf-core/differentialabundance/pull/105)] - Enabled multiple GMT/GMX files for GSEA ([@WackerO](https://github.com/WackerO), reported by [@grst](https://github.com/grst), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#108](https://github.com/nf-core/differentialabundance/issues/108)] - Add shiny app generation (starting feature set) ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) - [[#110](https://github.com/nf-core/differentialabundance/pull/110)] - Add shiny app outputs to tower.yml ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO), [@maxulysse](https://github.com/maxulysse)) +- [[#149]](https://github.com/nf-core/differentialabundance/pull/149) - Update README.md - add ref to nf-core/rnaseq and Affymetrix ([@smoe](https://github.com/smoe), review by [@pinin4fjordas](https://github.com/pinin4fjords)) ### `Fixed` From 6c2582a223f3eadb487d655bee1666ef64e3e590 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 25 Jul 2023 13:58:39 +0100 Subject: [PATCH 5/5] fix my name --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1c7311c8..b0ed354a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#105](https://github.com/nf-core/differentialabundance/pull/105)] - Enabled multiple GMT/GMX files for GSEA ([@WackerO](https://github.com/WackerO), reported by [@grst](https://github.com/grst), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#108](https://github.com/nf-core/differentialabundance/issues/108)] - Add shiny app generation (starting feature set) ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) - [[#110](https://github.com/nf-core/differentialabundance/pull/110)] - Add shiny app outputs to tower.yml ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO), [@maxulysse](https://github.com/maxulysse)) -- [[#149]](https://github.com/nf-core/differentialabundance/pull/149) - Update README.md - add ref to nf-core/rnaseq and Affymetrix ([@smoe](https://github.com/smoe), review by [@pinin4fjordas](https://github.com/pinin4fjords)) +- [[#149]](https://github.com/nf-core/differentialabundance/pull/149) - Update README.md - add ref to nf-core/rnaseq and Affymetrix ([@smoe](https://github.com/smoe), review by [@pinin4fjords](https://github.com/pinin4fjords)) ### `Fixed`