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Merge pull request #499 from nf-core/dev
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1.1.8 Patch Release
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jfy133 authored Jun 20, 2024
2 parents f1e6153 + e21b3ed commit 5d3ee55
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6 changes: 1 addition & 5 deletions .editorconfig
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Expand Up @@ -28,10 +28,6 @@ indent_style = unset
[/assets/email*]
indent_size = unset

# ignore Readme
[README.md]
indent_style = unset

# ignore python
# ignore python and markdown
[*.{py,md}]
indent_style = unset
2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/taxp
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/taxprofiler/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/taxprofiler _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 (`nf-test test main.nf.test -profile test,docker`).
- [ ] 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.
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10 changes: 5 additions & 5 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -8,12 +8,12 @@ on:
types: [published]
workflow_dispatch:
jobs:
run-tower:
run-platform:
name: Run AWS full tests
if: github.repository == 'nf-core/taxprofiler'
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
Expand All @@ -30,7 +30,7 @@ jobs:

- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
name: Seqera Platform debug log file
path: |
tower_action_*.log
tower_action_*.json
seqera_platform_action_*.log
seqera_platform_action_*.json
12 changes: 6 additions & 6 deletions .github/workflows/awstest.yml
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Expand Up @@ -5,13 +5,13 @@ name: nf-core AWS test
on:
workflow_dispatch:
jobs:
run-tower:
run-platform:
name: Run AWS tests
if: github.repository == 'nf-core/taxprofiler'
runs-on: ubuntu-latest
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
# Launch workflow using Seqera Platform CLI tool action
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
Expand All @@ -27,7 +27,7 @@ jobs:

- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
name: Seqera Platform debug log file
path: |
tower_action_*.log
tower_action_*.json
seqera_platform_action_*.log
seqera_platform_action_*.json
4 changes: 2 additions & 2 deletions .github/workflows/ci.yml
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Expand Up @@ -42,10 +42,10 @@ jobs:

steps:
- name: Check out pipeline code
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"

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18 changes: 15 additions & 3 deletions .github/workflows/download_pipeline.yml
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Expand Up @@ -32,7 +32,10 @@ jobs:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.12"
architecture: "x64"
Expand Down Expand Up @@ -67,8 +70,17 @@ jobs:
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}

- name: Run the downloaded pipeline
- name: Run the downloaded pipeline (stub)
id: stub_run_pipeline
continue-on-error: true
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test_nothing,singularity --outdir ./results
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
6 changes: 3 additions & 3 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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
with:
token: ${{ secrets.nf_core_bot_auth_token }}

Expand All @@ -32,9 +32,9 @@ jobs:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

# Install and run pre-commit
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: 3.11
python-version: "3.12"

- name: Install pre-commit
run: pip install pre-commit
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19 changes: 9 additions & 10 deletions .github/workflows/linting.yml
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Expand Up @@ -14,13 +14,12 @@ jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Set up Python 3.11
uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- name: Set up Python 3.12
uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: 3.11
cache: "pip"
python-version: "3.12"

- name: Install pre-commit
run: pip install pre-commit
Expand All @@ -32,14 +31,14 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.11"
python-version: "3.12"
architecture: "x64"

- name: Install dependencies
Expand All @@ -60,7 +59,7 @@ jobs:

- name: Upload linting log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
with:
name: linting-logs
path: |
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2 changes: 1 addition & 1 deletion .github/workflows/linting_comment.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Download lint results
uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
with:
workflow: linting.yml
workflow_conclusion: completed
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6 changes: 3 additions & 3 deletions .github/workflows/release-announcements.yml
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Expand Up @@ -12,7 +12,7 @@ jobs:
- name: get topics and convert to hashtags
id: get_topics
run: |
curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT
- uses: rzr/fediverse-action@master
with:
Expand All @@ -25,13 +25,13 @@ jobs:
Please see the changelog: ${{ github.event.release.html_url }}
${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
send-tweet:
runs-on: ubuntu-latest

steps:
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.10"
- name: Install dependencies
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1 change: 1 addition & 0 deletions .nf-core.yml
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@@ -1 +1,2 @@
repository_type: pipeline
nf_core_version: "2.14.1"
3 changes: 3 additions & 0 deletions .pre-commit-config.yaml
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Expand Up @@ -3,6 +3,9 @@ repos:
rev: "v3.1.0"
hooks:
- id: prettier
additional_dependencies:
- [email protected]

- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
rev: "2.7.3"
hooks:
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24 changes: 24 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,30 @@
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).

## v1.1.8 - Augmented Akita Patch [2024-06-20]

### `Added`

- [#487](https://github.com/nf-core/taxprofiler/pull/487) Updated to nf-core pipeline template v2.14.1 (added by @jfy133)

### `Fixed`

- [#484](https://github.com/nf-core/taxprofiler/pull/484) Improved input validation to immediately fail if run accession IDs within a given sample ID are not unique (❤️ to @sofstam for reporting, fixed by @jfy133)
- [#491](https://github.com/nf-core/taxprofiler/pull/491) Added flag to publish intermediate bracken files (❤️ to @ewissel for reporting, fixed by @sofstam and @jfy133)
- [#489](https://github.com/nf-core/taxprofiler/pull/489) Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133)
- [#495](https://github.com/nf-core/taxprofiler/pull/495) Stop TAXPASTA failures when profiles do not have exact compositionality (fixes by @Midnighter, @jfy133)

### `Dependencies`

| Tool | Previous version | New version |
| -------- | ---------------- | ----------- |
| KMCP | 0.9.1 | 0.9.4 |
| TAXPASTA | 0.6.1 | 0.7.0 |

### `Deprecated`

- [#492](https://github.com/nf-core/taxprofiler/pull/492) Removed `--kmcp_mode` parameter from KMCP to allow per database specification by setting in db_params in database sheet (fixed by @jfy133)

## v1.1.7 - Augmented Akita Patch [2024-04-25]

### `Added`
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -13,7 +13,7 @@
[![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/)
[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/taxprofiler)
[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/taxprofiler)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)

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5 changes: 3 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,7 +1,8 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/1.1.7" target="_blank">nf-core/taxprofiler</a>
This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/1.1.8" target="_blank">nf-core/taxprofiler</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/taxprofiler/1.1.7/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/taxprofiler/1.1.8/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-taxprofiler-methods-description":
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1 change: 1 addition & 0 deletions assets/schema_input.json
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Expand Up @@ -14,6 +14,7 @@
},
"run_accession": {
"type": "string",
"unique": ["sample"],
"errorMessage": "Run accession must be provided and cannot contain spaces."
},
"instrument_platform": {
Expand Down
23 changes: 12 additions & 11 deletions conf/modules.config
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Expand Up @@ -467,7 +467,8 @@ process {
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt,fastq.gz}'
pattern: '*.{txt,fastq.gz}',
saveAs: { !params.bracken_save_intermediatekraken2 && meta.tool == "bracken" ? null : it }
]
}

Expand Down Expand Up @@ -517,7 +518,7 @@ process {
publishDir = [
path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt,fasta.gz}'
pattern: '*.{txt,fastq.gz,fasta.gz}'
]
}

Expand Down Expand Up @@ -753,15 +754,14 @@ process {

withName: TAXPASTA_MERGE {
tag = { "${meta.tool}|${meta.id}" }
ext.prefix = { "${meta.tool}_${meta.id}" }
ext.args = {
[
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.taxpasta_add_name ? "--add-name" : "",
params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "",
params.taxpasta_add_idlineage ? "--add-id-lineage" : "",
params.taxpasta_add_ranklineage ? "--add-rank-lineage" : "",
params.taxpasta_ignore_errors ? "--ignore-errors" : ""
].join(' ').trim()
}
publishDir = [
Expand All @@ -773,14 +773,15 @@ process {

withName: TAXPASTA_STANDARDISE {
tag = { "${meta.tool}|${meta.id}" }
ext.prefix = { "${meta.tool}_${meta.id}" }
ext.args = {
[
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.taxpasta_add_name ? "--add-name" : "",
params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "",
params.taxpasta_add_idlineage ? "--add-id-lineage" : ""
].join(' ').trim()
[
params.taxpasta_add_name ? "--add-name" : "",
params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "",
params.taxpasta_add_idlineage ? "--add-id-lineage" : "",
params.taxpasta_add_ranklineage ? "--add-rank-lineage" : ""
].join(' ').trim()
}
publishDir = [
path: { "${params.outdir}/taxpasta/" },
Expand Down
9 changes: 4 additions & 5 deletions conf/test.config
Original file line number Diff line number Diff line change
Expand Up @@ -20,16 +20,16 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_v1.1.csv'
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_mergepairs = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_bracken = true
Expand All @@ -42,8 +42,7 @@ params {
run_ganon = true
run_krona = true
run_kmcp = true
kmcp_mode = 0
krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
krona_taxonomy_directory = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
malt_save_reads = true
kraken2_save_reads = true
centrifuge_save_reads = true
Expand Down
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