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Merge branch 'dev' into fix-mirtop-gff
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lpantano committed Oct 20, 2023
2 parents 963b02e + 1aeb518 commit 0113f55
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1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
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"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
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4 changes: 3 additions & 1 deletion .github/CONTRIBUTING.md
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Expand Up @@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
However, don't be put off by this template - other more general issues and suggestions are welcome!
Contributions to the code are even more welcome ;)

> If you need help using or modifying nf-core/smrnaseq then the best place to ask is on the nf-core Slack [#smrnaseq](https://nfcore.slack.com/channels/smrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::info
If you need help using or modifying nf-core/smrnaseq then the best place to ask is on the nf-core Slack [#smrnaseq](https://nfcore.slack.com/channels/smrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::

## Contribution workflow

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3 changes: 3 additions & 0 deletions .github/workflows/awsfulltest.yml
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steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v2
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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2 changes: 1 addition & 1 deletion .github/workflows/linting.yml
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- uses: actions/setup-python@v4
with:
python-version: "3.8"
python-version: "3.11"
architecture: "x64"

- name: Install dependencies
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68 changes: 68 additions & 0 deletions .github/workflows/release-announcments.yml
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name: release-announcements
# Automatic release toot and tweet anouncements
on:
release:
types: [published]
workflow_dispatch:

jobs:
toot:
runs-on: ubuntu-latest
steps:
- uses: rzr/fediverse-action@master
with:
access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
host: "mstdn.science" # custom host if not "mastodon.social" (default)
# GitHub event payload
# https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
message: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
send-tweet:
runs-on: ubuntu-latest

steps:
- uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install dependencies
run: pip install tweepy==4.14.0
- name: Send tweet
shell: python
run: |
import os
import tweepy
client = tweepy.Client(
access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
)
tweet = os.getenv("TWEET")
client.create_tweet(text=tweet)
env:
TWEET: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}

bsky-post:
runs-on: ubuntu-latest
steps:
- uses: zentered/[email protected]
with:
post: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
env:
BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
#
16 changes: 8 additions & 8 deletions CITATIONS.md
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> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
* [trimgalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
- [trimgalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)

* [samtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
- [samtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

> Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PMID: 19505943; PMCID: PMC2723002.
* [mirtop](https://pubmed.ncbi.nlm.nih.gov/31504201/)
- [mirtop](https://pubmed.ncbi.nlm.nih.gov/31504201/)

> Desvignes T, Loher P, Eilbeck K, Ma J, Urgese G, Fromm B, Sydes J, Aparicio-Puerta E, Barrera V, Espín R, Thibord F, Bofill-De Ros X, Londin E, Telonis AG, Ficarra E, Friedländer MR, Postlethwait JH, Rigoutsos I, Hackenberg M, Vlachos IS, Halushka MK, Pantano L. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinformatics. 2020 Feb 1;36(3):698-703. doi: 10.1093/bioinformatics/btz675. PMID: 31504201; PMCID: PMC7566869.
* [seqcluster](https://pubmed.ncbi.nlm.nih.gov/21976421/)
- [seqcluster](https://pubmed.ncbi.nlm.nih.gov/21976421/)

> Pantano L, Estivill X, Martí E. A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5. PMID: 21976421.
* [mirdeep2](https://pubmed.ncbi.nlm.nih.gov/21911355/)
- [mirdeep2](https://pubmed.ncbi.nlm.nih.gov/21911355/)

> Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012 Jan;40(1):37-52. doi: 10.1093/nar/gkr688. Epub 2011 Sep 12. PMID: 21911355; PMCID: PMC3245920.
* [mirtrace](https://pubmed.ncbi.nlm.nih.gov/30514392/)
- [mirtrace](https://pubmed.ncbi.nlm.nih.gov/30514392/)

> Kang W, Eldfjell Y, Fromm B, Estivill X, Biryukova I, Friedländer MR. miRTrace reveals the organismal origins of microRNA sequencing data. Genome Biol. 2018 Dec 4;19(1):213. doi: 10.1186/s13059-018-1588-9. PMID: 30514392; PMCID: PMC6280396.
* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
* [Bioconductor](https://www.bioconductor.org/) and [R](https://cran.r-project.org/)
- [Bioconductor](https://www.bioconductor.org/) and [R](https://cran.r-project.org/)

## Software packaging/containerisation tools

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