From b12a6036163921b507c38e780a9f4d8cb4631d18 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 24 Oct 2022 12:47:35 +0000 Subject: [PATCH 1/2] Add online video as per Joses suggestion :-) --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index e1054a4c..b0cecd05 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool 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/smrnaseq/results). +## Online videos + +A short talk about the history, current status and functionality on offer in this pipeline was given by Lorena Pantano (@lpantano) on [9th November 2021](https://youtu.be/4YLQ2VwpCJE) as part of the nf-core/bytesize series. + +You can find numerous talks on the nf-core events page from various topics including writing pipelines/modules in Nextflow DSL2, using nf-core tooling, running nf-core pipelines as well as more generic content like contributing to Github. Please check them out! + ## Pipeline summary 1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) From 5aa27a312b2ec39c80e90455ae5b90f42e0d3875 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 24 Oct 2022 12:53:43 +0000 Subject: [PATCH 2/2] Added url for mirgenedb --- docs/usage.md | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 3e3a3960..901084fc 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -20,7 +20,7 @@ This option indicates the experimental protocol used for the sample preparation. ### `mirtrace_species` or `mirgenedb_species` -It should point to the 3-letter species name used by [miRBase](https://www.mirbase.org/help/genome_summary.shtml) or MirGeneDB. Note the difference in case for the two databases. +It should point to the 3-letter species name used by [miRBase](https://www.mirbase.org/help/genome_summary.shtml) or [MirGeneDB](https://www.mirgenedb.org/browse). Note the difference in case for the two databases. ### miRNA related files diff --git a/nextflow_schema.json b/nextflow_schema.json index b5c52a3e..77b04352 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -76,7 +76,7 @@ "mirgenedb_species": { "type": "string", "description": "Species of MirGeneDB.", - "help_text": "This replaces the value of `--mirtrace_species` if `--mirgenedb` is used. \n Note the difference in case for species names used in MirGeneDB and miRBase." + "help_text": "This replaces the value of `--mirtrace_species` if `--mirgenedb` is used. \n Note the difference in case for species names used in MirGeneDB and miRBase. See https://www.mirgenedb.org/browse for more information." }, "fasta": { "type": "string",