From 01fb674a9dbfc455941afadce073aeba08a386c5 Mon Sep 17 00:00:00 2001 From: Thomas Davis Date: Wed, 17 Jan 2024 22:40:50 -0500 Subject: [PATCH 1/2] updating README + name fix --- README.md | 12 ++++++++++++ workflows/epitopeprediction.nf | 4 ++-- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e3b0729..e15f3c5 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,18 @@ **nf-core/epitopeprediction** is a bioinformatics best-practice analysis pipeline for epitope prediction and annotation. The pipeline performs epitope predictions for a given set of variants or peptides directly using state of the art prediction tools. Additionally, resulting prediction results can be annotated with metadata. +Supported prediction tools: + + * `syfpeithi` + * `mhcflurry` + * `mhcnuggets-class-1` + * `mhcnuggets-class-2` + * `netmhcpan-4.0` + * `netmhcpan-4.1` + * `netmhc-4.0` + * `netmhciipan-4.1` + + 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 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! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/epitopeprediction/results). diff --git a/workflows/epitopeprediction.nf b/workflows/epitopeprediction.nf index 00549dd..ca79421 100644 --- a/workflows/epitopeprediction.nf +++ b/workflows/epitopeprediction.nf @@ -180,14 +180,14 @@ workflow EPITOPEPREDICTION { // TODO I guess it would be better to have two subworkflows for the if else parts (CM) if (params.show_supported_models) { - SHOW_SUPPORTED_MODELS( + EPYTOPE_SHOW_SUPPORTED_MODELS( ch_samples_uncompressed .protein .mix(ch_samples_uncompressed.variant, ch_samples_uncompressed.peptide) .combine(ch_prediction_tool_versions) .first() ) - ch_versions = ch_versions.mix(SHOW_SUPPORTED_MODELS.out.versions) + ch_versions = ch_versions.mix(EPYTOPE_SHOW_SUPPORTED_MODELS.out.versions) } else { From 5df6e3b77e020df5db54b241646a263d572bb77f Mon Sep 17 00:00:00 2001 From: Thomas Davis Date: Wed, 17 Jan 2024 22:58:41 -0500 Subject: [PATCH 2/2] reformat --- README.md | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index e15f3c5..1502d0b 100644 --- a/README.md +++ b/README.md @@ -18,15 +18,14 @@ The pipeline performs epitope predictions for a given set of variants or peptide Supported prediction tools: - * `syfpeithi` - * `mhcflurry` - * `mhcnuggets-class-1` - * `mhcnuggets-class-2` - * `netmhcpan-4.0` - * `netmhcpan-4.1` - * `netmhc-4.0` - * `netmhciipan-4.1` - +- `syfpeithi` +- `mhcflurry` +- `mhcnuggets-class-1` +- `mhcnuggets-class-2` +- `netmhcpan-4.0` +- `netmhcpan-4.1` +- `netmhc-4.0` +- `netmhciipan-4.1` 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 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!