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Merge pull request #1156 from nf-core/dev
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Dev -> master for 3.14.0 release
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drpatelh authored Jan 8, 2024
2 parents a10f41a + eb5392a commit b89fac3
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3 changes: 3 additions & 0 deletions .github/CONTRIBUTING.md
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Expand Up @@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from

## Tests

You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

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1 change: 1 addition & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
- [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -28,7 +28,7 @@ jobs:
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
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43 changes: 24 additions & 19 deletions .github/workflows/cloud_tests_full.yml
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Expand Up @@ -23,70 +23,75 @@ jobs:
matrix:
aligner: ["star_salmon", "star_rsem"]
steps:
- 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: ${{ secrets.TOWER_CE_AWS_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
run_name: "aws_rnaseq_full_${{ matrix.aligner }}"
revision: ${{ github.sha }}
profiles: test_full_aws
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"aligner": "${{ matrix.aligner }}",
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
run-full-tests-on-gcp:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}

run-full-tests-on-azure:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
runs-on: ubuntu-latest
strategy:
matrix:
aligner: ["star_salmon", "star_rsem"]
steps:
- 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: ${{ secrets.TOWER_CE_GCP_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
run_name: "gcp_rnaseq_full_${{ matrix.aligner }}"
profiles: test_full_gcp
compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
run_name: "azure_rnaseq_full_${{ matrix.aligner }}"
revision: ${{ github.sha }}
profiles: test_full_azure
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"aligner": "${{ matrix.aligner }}",
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/",
"igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
run-full-tests-on-azure:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}

run-full-tests-on-gcp:
if: ${{ github.event.inputs.platform == 'gcp' || !github.event.inputs }}
runs-on: ubuntu-latest
strategy:
matrix:
aligner: ["star_salmon", "star_rsem"]
steps:
- 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: ${{ secrets.TOWER_CE_AZURE_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
run_name: "azure_rnaseq_full_${{ matrix.aligner }}"
profiles: test_full_azure
compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
run_name: "gcp_rnaseq_full_${{ matrix.aligner }}"
revision: ${{ github.sha }}
profiles: test_full_gcp
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"aligner": "${{ matrix.aligner }}",
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
"igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
}
- uses: actions/upload-artifact@v3
with:
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37 changes: 21 additions & 16 deletions .github/workflows/cloud_tests_small.yml
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Expand Up @@ -18,57 +18,62 @@ jobs:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
runs-on: ubuntu-latest
steps:
- 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: ${{ secrets.TOWER_CE_AWS_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
run_name: "aws_rnaseq_small"
revision: ${{ github.sha }}
profiles: test
parameters: |
{
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}"
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}/"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
run-small-tests-on-gcp:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}

run-small-tests-on-azure:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
runs-on: ubuntu-latest
steps:
- 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: ${{ secrets.TOWER_CE_GCP_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
run_name: "gcp_rnaseq_small"
compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
run_name: "azure_rnaseq_small"
revision: ${{ github.sha }}
profiles: test
parameters: |
{
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}"
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}/"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
run-small-tests-on-azure:
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}

run-small-tests-on-gcp:
if: ${{ github.event.inputs.platform == 'gcp' }}
runs-on: ubuntu-latest
steps:
- 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: ${{ secrets.TOWER_CE_AZURE_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
run_name: "azure_rnaseq_small"
compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
run_name: "gcp_rnaseq_small"
revision: ${{ github.sha }}
profiles: test
parameters: |
{
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}"
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}/"
}
- uses: actions/upload-artifact@v3
with:
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4 changes: 2 additions & 2 deletions .github/workflows/fix-linting.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
token: ${{ secrets.nf_core_bot_auth_token }}

Expand All @@ -24,7 +24,7 @@ jobs:
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install Prettier
run: npm install -g prettier @prettier/plugin-php
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12 changes: 6 additions & 6 deletions .github/workflows/linting.yml
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Expand Up @@ -14,9 +14,9 @@ jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
Expand All @@ -27,9 +27,9 @@ jobs:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install Prettier
run: npm install -g prettier
Expand All @@ -40,7 +40,7 @@ jobs:
PythonBlack:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- name: Check code lints with Black
uses: psf/black@stable
Expand Down Expand Up @@ -71,7 +71,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
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File renamed without changes.
4 changes: 3 additions & 1 deletion .gitpod.yml
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Expand Up @@ -4,7 +4,9 @@ tasks:
command: |
pre-commit install --install-hooks
nextflow self-update
- name: unset JAVA_TOOL_OPTIONS
command: |
unset JAVA_TOOL_OPTIONS
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
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54 changes: 54 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,60 @@
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).

## [[3.14.0](https://github.com/nf-core/rnaseq/releases/tag/3.14.0)] - 2024-01-08

### Credits

Special thanks to the following for their contributions to the release:

- [Adam Talbot](https://github.com/adamrtalbot)
- [Jonathan Manning](https://github.com/pinin4fjords)
- [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)
- [Matthias Zepper](https://github.com/MatthiasZepper)
- [Maxime Garcia](https://github.com/maxulysse)
- [Phil Ewels](https://github.com/ewels)
- [Vlad Savelyev](https://github.com/vladsavelyev)

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

### Enhancements & fixes

- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling
- [PR #1141](https://github.com/nf-core/rnaseq/pull/1141) - Important! Template update for nf-core/tools v2.11
- [PR #1143](https://github.com/nf-core/rnaseq/pull/1143) - Move fasta check back to Groovy ([#1142](https://github.com/nf-core/rnaseq/issues/1142))
- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners ([#1111](https://github.com/nf-core/rnaseq/issues/1111))
- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
- [PR #1150](https://github.com/nf-core/rnaseq/pull/1150) - Be more flexible on attribute values in GTFs ([#1132](https://github.com/nf-core/rnaseq/issues/1132))
- [PR #1151](https://github.com/nf-core/rnaseq/pull/1151) - fix to #1150: reinstate conditional
- [PR #1152](https://github.com/nf-core/rnaseq/pull/1152) - Bump container versions for tools using Docker V1 manifest ([#1140](https://github.com/nf-core/rnaseq/issues/1140))
- [PR #1154](https://github.com/nf-core/rnaseq/pull/1154) - Prerelease 3.14.0 fixes ([#1111](https://github.com/nf-core/rnaseq/issues/1111), [#1153](https://github.com/nf-core/rnaseq/issues/1153))
- [PR #1157](https://github.com/nf-core/rnaseq/pull/1157) - Add slash to `--outdir` for cloud tests to fix Azure validation issue
- [PR #1159](https://github.com/nf-core/rnaseq/pull/1159) - Issues loading MultiQC report ([#1158](https://github.com/nf-core/rnaseq/issues/1158))

### Parameters

| Old parameter | New parameter |
| ------------- | ---------------------------- |
| | `--pseudo_aligner_kmer_size` |

> **NB:** Parameter has been **updated** if both old and new parameter information is present.
> **NB:** Parameter has been **added** if just the new parameter information is present.
> **NB:** Parameter has been **removed** if new parameter information isn't present.
### Software dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `multiqc` | 1.17 | 1.19 |
| `qualimap` | 2.2.2d | 2.3 |
| `rseqc` | 3.0.1 | 5.0.3 |

> **NB:** Dependency has been **updated** if both old and new version information is present.
>
> **NB:** Dependency has been **added** if just the new version information is present.
>
> **NB:** Dependency has been **removed** if new version information isn't present.
## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21

### Credits
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15 changes: 5 additions & 10 deletions README.md
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Expand Up @@ -50,11 +50,8 @@
## Usage

:::note
If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
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.
:::
> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how 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.
First, prepare a samplesheet with your input data that looks as follows:

Expand Down Expand Up @@ -84,11 +81,9 @@ nextflow run nf-core/rnaseq \
-profile <docker/singularity/.../institute>
```

:::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).
:::
> [!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 and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).

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5 changes: 2 additions & 3 deletions assets/multiqc_config.yml
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@@ -1,7 +1,5 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.13.0" target="_blank">nf-core/rnaseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/rnaseq/3.13.0/docs/output" target="_blank">documentation</a>.
This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.14.0" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.14.0/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-rnaseq-methods-description":
order: -1000
Expand All @@ -11,6 +9,7 @@ report_section_order:
order: -1002

export_plots: true
disable_version_detection: true

# Run only these modules
run_modules:
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1 change: 1 addition & 0 deletions bin/dupradar.r
Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,7 @@ curve_y <- curve_y[seq(1, length(curve_y), 10)]
curve_x = 10^curve_x
# Write to file
line="#id: dupradar
#plot_type: 'linegraph'
#section_name: 'DupRadar'
#section_href: 'bioconductor.org/packages/release/bioc/html/dupRadar.html'
#description: \"provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication.
Expand Down
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