Thread by @nf_core

Super excited to announce the nf-core/rnaseq version 2.0 release! One of our most used pipelines, we have completely re-written it from the ground up using the new and shiny, modular @nextflowio DSL2 language! 🧙‍♂️✨
github.com/nf-core/rnaseq…
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This is the first outing for the new @nf_core DSL2 standards, defined in github.com/nf-core/modules 🏗 This repo has self-contained @nextflowio DSL2 modules, each wrapping a tool. nf-core/modules can be reused by the entire @nextflowio community! It’s all about recycling ♻️
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nf-core/rnaseq v2.0 is also the first @nf_core pipeline that exclusively uses #bioconda and @BioContainers 📦 It uses the one-process : one-container model, that typifies true workflow modularity.
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Working with public datasets? 🤔 The pipeline can now take a list of SRA / ENA / GEO ids and retrieve the metadata, download FastQ files via the ENA FTP, run an md5sum check, and auto-create an input samplesheet for the pipeline! nf-co.re/rnaseq/2.0/par…
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The biggest change for users is that the pipeline now uses an input samplesheet 📋 You can now merge sequencing runs of the same sample! 💥 The #MultiQC report has a PCA plot too 🤞 The pipeline even warns if you have given the wrong strandedness info!
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By using the new @nf_core @jsonschema standard, the pipeline now logs only the parameters that have changed from defaults. It also auto-generates help and usage documentation 📖 This is great for developers - define a new parameter once and forget about it!
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Other features include the addition of a new alignment and quantification route via STAR & RSEM, the creation of bigWig files, the removal of ribosomal RNA, the ability to concatenate spike-ins / other biological sequences to the genome assembly, and much much more…
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With such major changes, we would love for everyone to get involved with trying out the pipeline! Let us know about bugs or feature requests via Slack or GitHub 🐛🪲 We will bring these changes to v2.0 of the @nf_core template soon, and then out to all @nf_core pipelines 🧪
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Massive kudos to our very own @aka_hpatel who has led the charge for @nf_core usage of @nextflowio DSL2 and has been slaving away on this pipeline release for months 🙇‍♂️ Thanks also to all other contributors - there are 1142 commits with 232 files changed in this release!
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