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Merge pull request #234 from nf-core/dev
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Dev -> Master for 2.2.0 release
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robsyme authored Apr 26, 2023
2 parents 27514c4 + 7d0d94f commit 5ce052d
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27 changes: 27 additions & 0 deletions .devcontainer/devcontainer.json
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{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",

// Configure tool-specific properties.
"customizations": {
// Configure properties specific to VS Code.
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
"python.formatting.yapfPath": "/opt/conda/bin/yapf",
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
}
1 change: 1 addition & 0 deletions .gitattributes
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@@ -1,3 +1,4 @@
*.config linguist-language=nextflow
*.nf.test linguist-language=nextflow
modules/nf-core/** linguist-generated
subworkflows/nf-core/** linguist-generated
16 changes: 16 additions & 0 deletions .github/CONTRIBUTING.md
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Expand Up @@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
### Images and figures

For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

## GitHub Codespaces

This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.

To get started:

- Open the repo in [Codespaces](https://github.com/nf-core/smrnaseq/codespaces)
- Tools installed
- nf-core
- Nextflow

Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
- [Dockerfile](.devcontainer/Dockerfile)
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -42,7 +42,7 @@ body:
attributes:
label: System information
description: |
* Nextflow version _(eg. 21.10.3)_
* Nextflow version _(eg. 22.10.1)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
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8 changes: 6 additions & 2 deletions .github/workflows/ci.yml
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Expand Up @@ -11,6 +11,10 @@ on:
env:
NXF_ANSI_LOG: false

concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true

jobs:
test:
name: Run pipeline with test data
Expand All @@ -20,14 +24,14 @@ jobs:
strategy:
matrix:
NXF_VER:
- "21.10.3"
- "22.10.1"
- "latest-everything"
profile:
- "test"
- "test_no_genome"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
uses: actions/checkout@v3

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
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6 changes: 3 additions & 3 deletions .github/workflows/fix-linting.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

- uses: actions/setup-node@v2
- uses: actions/setup-node@v3

- name: Install Prettier
run: npm install -g prettier @prettier/plugin-php
Expand All @@ -34,9 +34,9 @@ jobs:
id: prettier_status
run: |
if prettier --check ${GITHUB_WORKSPACE}; then
echo "::set-output name=result::pass"
echo "result=pass" >> $GITHUB_OUTPUT
else
echo "::set-output name=result::fail"
echo "result=fail" >> $GITHUB_OUTPUT
fi
- name: Run 'prettier --write'
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18 changes: 10 additions & 8 deletions .github/workflows/linting.yml
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Expand Up @@ -4,6 +4,8 @@ name: nf-core linting
# that the code meets the nf-core guidelines.
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
Expand All @@ -12,9 +14,9 @@ jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: actions/setup-node@v2
- uses: actions/setup-node@v3

- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
Expand All @@ -25,9 +27,9 @@ jobs:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: actions/setup-node@v2
- uses: actions/setup-node@v3

- name: Install Prettier
run: npm install -g prettier
Expand All @@ -38,7 +40,7 @@ jobs:
PythonBlack:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- name: Check code lints with Black
uses: psf/black@stable
Expand Down Expand Up @@ -69,12 +71,12 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
uses: actions/checkout@v3

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1

- uses: actions/setup-python@v3
- uses: actions/setup-python@v4
with:
python-version: "3.7"
architecture: "x64"
Expand All @@ -97,7 +99,7 @@ jobs:

- name: Upload linting log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v3
with:
name: linting-logs
path: |
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2 changes: 1 addition & 1 deletion .github/workflows/linting_comment.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:

- name: Get PR number
id: pr_number
run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT

- name: Post PR comment
uses: marocchino/sticky-pull-request-comment@v2
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2 changes: 2 additions & 0 deletions .prettierignore
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@@ -1,5 +1,6 @@
email_template.html
adaptivecard.json
slackreport.json
.nextflow*
work/
data/
Expand All @@ -8,3 +9,4 @@ results/
testing/
testing*
*.pyc
bin/
13 changes: 12 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,18 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-25 Maroon Tin Dalmatian
## [v2.2.0](https://github.com/nf-core/smrnaseq/releases/tag/2.2.0) - 2023-04-26

- [[#220](https://github.com/nf-core/smrnaseq/issues/220)] - Fixed an issue where miRTrace reports fastq basename instead of sample ID
- [[#208](https://github.com/nf-core/smrnaseq/issues/208)] - Fixed usability of `--skip_qc` parameter
- Updated FASTP module to allow direct addition of adapter_fasta file to it
- [[#205](https://github.com/nf-core/smrnaseq/issues/205)] - Fix mirTrace Report to be a single report again instead of per sample reports
- [[#206](https://github.com/nf-core/smrnaseq/issues/206)] - Use % as separator in sed commands to enable conda working properly on OSX and Linux
- [[#207](https://github.com/nf-core/smrnaseq/issues/224)] - Fix Samplesheet print error
- Group samples by adapter sequence before running mirtrace
- Remove `--skip_qc` parameter

## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian

### Enhancements & fixes

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56 changes: 0 additions & 56 deletions CITATION.cff

This file was deleted.

2 changes: 1 addition & 1 deletion LICENSE
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@@ -1,6 +1,6 @@
MIT License

Copyright (c) P. Ewels, C. Wang, R. Hammarén, L. Pantano
Copyright (c) P. Ewels, C. Wang, R. Hammarén, L. Pantano, A. Peltzer

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -2,7 +2,7 @@

[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3456879-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3456879)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
Expand Down Expand Up @@ -52,7 +52,7 @@ You can find numerous talks on the nf-core events page from various topics inclu

## Quick Start

1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)

2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.

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2 changes: 0 additions & 2 deletions assets/methods_description_template.yml
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Expand Up @@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
section_name: "nf-core/smrnaseq Methods Description"
section_href: "https://github.com/nf-core/smrnaseq"
plot_type: "html"
## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
## You inject any metadata in the Nextflow '${workflow}' object
data: |
<h4>Methods</h4>
<p>Data was processed using nf-core/smrnaseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
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34 changes: 34 additions & 0 deletions assets/slackreport.json
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@@ -0,0 +1,34 @@
{
"attachments": [
{
"fallback": "Plain-text summary of the attachment.",
"color": "<% if (success) { %>good<% } else { %>danger<%} %>",
"author_name": "sanger-tol/readmapping v${version} - ${runName}",
"author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
"fields": [
{
"title": "Command used to launch the workflow",
"value": "```${commandLine}```",
"short": false
}
<%
if (!success) { %>
,
{
"title": "Full error message",
"value": "```${errorReport}```",
"short": false
},
{
"title": "Pipeline configuration",
"value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
"short": false
}
<% }
%>
],
"footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
}
]
}
3 changes: 1 addition & 2 deletions bin/check_samplesheet.py
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Expand Up @@ -50,14 +50,13 @@ def check_samplesheet(file_in, file_out):

sample_mapping_dict = {}
with open(file_in, "r") as fin:

## Check header
MIN_COLS = 2
HEADER = ["sample", "fastq_1"]
header = [x.strip('"') for x in fin.readline().strip().split(",")]
if any([item not in header for item in HEADER]):
missing = [item for item in HEADER if item not in header]
eprint("ERROR: Please check samplesheet header. Missing columns: '{}'".format(",".join(missing)))
print_error("ERROR: Please check samplesheet header. Missing columns: '{}'".format(",".join(missing)))
sys.exit(1)

## Check sample entries
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2 changes: 1 addition & 1 deletion bin/edgeR_miRBase.r
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Expand Up @@ -43,7 +43,7 @@ for (i in 1:2) {
# Only subset if at least one sample is remaining
nr_keep <- sum(row_sub)
if (nr_keep > 0){
data<-data[!row_sub,]
data<-data[!row_sub,, drop=FALSE]
}
#Also check for colSums > 0, otherwise DGEList will fail if samples have entirely colSum == 0 #Fixes #134
drop_colsum_zero <- (colSums(data, na.rm=T) != 0) # T if colSum is not 0, F otherwise
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5 changes: 2 additions & 3 deletions conf/modules.config
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Expand Up @@ -87,7 +87,7 @@ process {
}
}

if (!(params.skip_fastqc || params.skip_qc)) {
if (!(params.skip_fastqc)) {
process {
withName: '.*:FASTQC_FASTP:FASTQC_.*' {
ext.args = '--quiet'
Expand All @@ -104,8 +104,7 @@ if (!params.skip_fastp) {
params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
params.fastp_min_length > 0 ? "-l ${params.fastp_min_length}" : "",
params.fastp_max_length > 0 ? "--max_len1 ${params.fastp_max_length}" : "",
params.three_prime_adapter == null ? '' : "--adapter_sequence ${params.three_prime_adapter}",
params.fastp_known_mirna_adapters == null ? '' : "--adapter_fasta ${params.fastp_known_mirna_adapters}"
params.three_prime_adapter == null ? '' : "--adapter_sequence ${params.three_prime_adapter}"
].join(" ").trim()
publishDir = [
[
Expand Down
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