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Joses comments resolved for release #198

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merged 2 commits into from
Oct 24, 2022
Merged

Joses comments resolved for release #198

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b12a603
Add online video as per Joses suggestion :-)
apeltzer Oct 24, 2022
5aa27a3
Added url for mirgenedb
apeltzer Oct 24, 2022
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6 changes: 6 additions & 0 deletions README.md
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Expand Up @@ -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/))
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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -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",
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