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Release PR for 2.2.2 Patch Release
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apeltzer authored Sep 5, 2023
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1 change: 0 additions & 1 deletion .github/CONTRIBUTING.md
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Expand Up @@ -116,4 +116,3 @@ To get started:
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. 22.10.1)_
* Nextflow version _(eg. 23.04.0)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
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11 changes: 8 additions & 3 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -14,18 +14,23 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v1
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/smrnaseq/work-${{ github.sha }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-${{ github.sha }}"
}
profiles: test_full,public_aws_ecr
profiles: test_full

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
10 changes: 7 additions & 3 deletions .github/workflows/awstest.yml
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Expand Up @@ -12,18 +12,22 @@ jobs:
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v1
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/smrnaseq/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-test-${{ github.sha }}"
}
profiles: test,public_aws_ecr
profiles: test

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "23.04.0"
- "latest-everything"
profile:
- "test"
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5 changes: 5 additions & 0 deletions .gitpod.yml
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@@ -1,4 +1,9 @@
image: nfcore/gitpod:latest
tasks:
- name: Update Nextflow and setup pre-commit
command: |
pre-commit install --install-hooks
nextflow self-update
vscode:
extensions: # based on nf-core.nf-core-extensionpack
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16 changes: 15 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,21 @@
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).

## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-08
## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-09-04

- [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers
- [[#237]](https://github.com/nf-core/smrnaseq/issues/237) - Fix illumina protocol clip parameters to default
- Remove public_aws_ecr profile
- [[#269]](https://github.com/nf-core/smrnaseq/pull/269) - Updated miRBase URLs with new location (old ones were broken)

### Software dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `multiqc` | 1.13 | 1.15 |
| `fastp` | 0.23.2 | 0.23.4 |

## [v2.2.1](https://github.com/nf-core/smrnaseq/releases/tag/2.2.1) - 2023-05-12

### Enhancements & fixes

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5 changes: 5 additions & 0 deletions CITATIONS.md
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Expand Up @@ -12,6 +12,8 @@

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

> 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/)

* [samtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
Expand Down Expand Up @@ -56,5 +58,8 @@
- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
32 changes: 16 additions & 16 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%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.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 @@ -57,46 +57,46 @@ You can find numerous talks on the nf-core events page from various topics inclu
> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
> with `-profile test` before running the workflow on actual data.
<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
Explain what rows and columns represent. For instance (please edit as appropriate):
First, prepare a samplesheet with your input data that looks as follows:

`samplesheet.csv`:

```csv
sample,fastq_1
CONTROL_REP1,AEG588A1_S1_L002_001.fastq.gz
Clone1_N1,s3://ngi-igenomes/test-data/smrnaseq/C1-N1-R1_S4_L001_R1_001.fastq.gz
Clone1_N3,s3://ngi-igenomes/test-data/smrnaseq/C1-N3-R1_S6_L001_R1_001.fastq.gz
Clone9_N1,s3://ngi-igenomes/test-data/smrnaseq/C9-N1-R1_S7_L001_R1_001.fastq.gz
Clone9_N2,s3://ngi-igenomes/test-data/smrnaseq/C9-N2-R1_S8_L001_R1_001.fastq.gz
Clone9_N3,s3://ngi-igenomes/test-data/smrnaseq/C9-N3-R1_S9_L001_R1_001.fastq.gz
Control_N1,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N1-R1_S1_L001_R1_001.fastq.gz
Control_N2,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N2-R1_S2_L001_R1_001.fastq.gz
Control_N3,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N3-R1_S3_L001_R1_001.fastq.gz
```

Each row represents a fastq file (single-end).

-->

Now, you can run the pipeline using:

<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->

```bash
nextflow run nf-core/smrnaseq \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--genome 'GRCh37' \
--mirtrace_species 'hsa' \
--protocol 'illumina' \
--outdir <OUTDIR>
--input samplesheet.csv \
--genome 'GRCh37' \
--mirtrace_species 'hsa' \
--protocol 'illumina' \
--outdir <OUTDIR>
```

> **Warning:**
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
For more details, please refer to the [usage documentation](https://nf-co.re/smrnaseq/usage) and the [parameter documentation](https://nf-co.re/smrnaseq/parameters).
For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/smrnaseq/usage) and the [parameter documentation](https://nf-co.re/smrnaseq/parameters).

## Pipeline output

To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/smrnaseq/results) tab on the nf-core website pipeline page.
To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/smrnaseq/results) tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
[output documentation](https://nf-co.re/smrnaseq/output).

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10 changes: 7 additions & 3 deletions assets/methods_description_template.yml
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Expand Up @@ -5,13 +5,17 @@ section_href: "https://github.com/nf-core/smrnaseq"
plot_type: "html"
data: |
<h4>Methods</h4>
<p>Data was processed using nf-core/smrnaseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
<p>Data was processed using nf-core/smrnaseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
<p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
<pre><code>${workflow.commandLine}</code></pre>
<p>${tool_citations}</p>
<h4>References</h4>
<ul>
<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
<li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
<li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
<li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
<li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
${tool_bibliography}
</ul>
<div class="alert alert-info">
<h5>Notes:</h5>
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/smrnaseq" target="_blank">nf-core/smrnaseq</a>
This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/2.2.2" target="_blank">nf-core/smrnaseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/smrnaseq" target="_blank">documentation</a>.
<a href="https://nf-co.re/smrnaseq/2.2.2/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-smrnaseq-methods-description":
order: -1000
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2 changes: 1 addition & 1 deletion assets/slackreport.json
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{
"fallback": "Plain-text summary of the attachment.",
"color": "<% if (success) { %>good<% } else { %>danger<%} %>",
"author_name": "sanger-tol/readmapping v${version} - ${runName}",
"author_name": "nf-core/smrnaseq v${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": [
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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -207,15 +207,15 @@ process {
}

process {
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_SAMTOOLS:SAMTOOLS_.*' {
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*' {
ext.prefix = { "${meta.id}.sorted" }
publishDir = [
path: { "${params.outdir}/samtools" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
ext.prefix = { "${meta.id}.sorted" }
publishDir = [
path: { "${params.outdir}/samtools/samtools_stats" },
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30 changes: 0 additions & 30 deletions conf/public_aws_ecr.config

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12 changes: 6 additions & 6 deletions docs/usage.md
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Expand Up @@ -26,9 +26,9 @@ It should point to the 3-letter species name used by [miRBase](https://www.mirba

Different parameters can be set for the two supported databases. By default `miRBase` will be used with the parameters below.

- `mirna_gtf`: If not supplied by the user, then `mirna_gtf` will point to the latest GFF3 file in miRbase: `https://mirbase.org/ftp/CURRENT/genomes/${params.mirtrace_species}.gff3`
- `mature`: points to the FASTA file of mature miRNA sequences. `https://mirbase.org/ftp/CURRENT/mature.fa.gz`
- `hairpin`: points to the FASTA file of precursor miRNA sequences. `https://mirbase.org/ftp/CURRENT/hairpin.fa.gz`
- `mirna_gtf`: If not supplied by the user, then `mirna_gtf` will point to the latest GFF3 file in miRbase: `https://mirbase.org/download/CURRENT/genomes/${params.mirtrace_species}.gff3`
- `mature`: points to the FASTA file of mature miRNA sequences. `https://mirbase.org/download/CURRENT/mature.fa`
- `hairpin`: points to the FASTA file of precursor miRNA sequences. `https://mirbase.org/download/CURRENT/hairpin.fa`

If MirGeneDB should be used instead it needs to be specified using `--mirgenedb` and use the parameters below .

Expand Down Expand Up @@ -104,7 +104,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
The typical command for running the pipeline is as follows:

```bash
nextflow run nf-core/smrnaseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile docker
nextflow run nf-core/smrnaseq --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
```

This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
Expand All @@ -123,7 +123,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.

> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
> The above pipeline run specified with a params file in yaml format:
The above pipeline run specified with a params file in yaml format:

```bash
nextflow run nf-core/smrnaseq -profile docker -params-file params.yaml
Expand All @@ -135,7 +136,6 @@ with `params.yaml` containing:
input: './samplesheet.csv'
outdir: './results/'
genome: 'GRCh37'
input: 'data'
<...>
```

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