diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index df31904a..30b899dd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -46,6 +46,8 @@ jobs:
steps:
- name: Check out pipeline code
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+ with:
+ fetch-depth: 0
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 13b51e2c..ab06316e 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -34,6 +34,17 @@ jobs:
REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+ steps:
+ - name: Get the repository name and current branch
+ id: get_repo_properties
+ run: |
+ echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+ echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+ echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+
+ download:
+ runs-on: ubuntu-latest
+ needs: configure
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
@@ -56,21 +67,10 @@ jobs:
python -m pip install --upgrade pip
pip install git+https://github.com/nf-core/tools.git@dev
- - name: Get the repository name and current branch set as environment variable
- id: get_repo_properties
- run: |
- echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
- echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
- echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
-
- name: Make a cache directory for the container images
run: |
mkdir -p ./singularity_container_images
- download:
- runs-on: ubuntu-latest
- needs: configure
- steps:
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
@@ -87,6 +87,9 @@ jobs:
- name: Inspect download
run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
+ - name: Inspect container images
+ run: tree ./singularity_container_images | tee ./container_initial
+
- name: Count the downloaded number of container images
id: count_initial
run: |
@@ -123,7 +126,8 @@ jobs:
final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
difference=$((final_count - initial_count))
echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
- tree ./singularity_container_images
+ tree ./singularity_container_images > ./container_afterwards
+ diff ./container_initial ./container_afterwards
exit 1
else
echo "The pipeline can be downloaded successfully!"
diff --git a/.nf-core.yml b/.nf-core.yml
index 3dc43972..f86fe0dc 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,7 @@
lint:
- pipeline_todos: False
- template_strings: False
-nf_core_version: 3.1.1
+ pipeline_todos: false
+ template_strings: false
+nf_core_version: 3.1.2
repository_type: pipeline
template:
author: "Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I.\
diff --git a/CITATIONS.md b/CITATIONS.md
index 153ca3dc..e3ecf3f7 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,7 +12,9 @@
- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+
+- [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.
diff --git a/README.md b/README.md
index dbc8fd9d..e34746ef 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,7 @@ This ensures that the pipeline runs on AWS, has sensible resource allocation def
## 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.
+> 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:
@@ -145,7 +145,9 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
## Citations
-
+
+
+
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
diff --git a/assets/nf-core-pathogensurveillance_logo_light.png b/assets/nf-core-pathogensurveillance_logo_light.png
index 45e276c0..2741d039 100644
Binary files a/assets/nf-core-pathogensurveillance_logo_light.png and b/assets/nf-core-pathogensurveillance_logo_light.png differ
diff --git a/docs/images/nf-core-pathogensurveillance_logo_dark.png b/docs/images/nf-core-pathogensurveillance_logo_dark.png
index b976bead..cf9d2f05 100644
Binary files a/docs/images/nf-core-pathogensurveillance_logo_dark.png and b/docs/images/nf-core-pathogensurveillance_logo_dark.png differ
diff --git a/docs/images/nf-core-pathogensurveillance_logo_light.png b/docs/images/nf-core-pathogensurveillance_logo_light.png
index bdbdca3f..f54396f1 100644
Binary files a/docs/images/nf-core-pathogensurveillance_logo_light.png and b/docs/images/nf-core-pathogensurveillance_logo_light.png differ
diff --git a/nextflow.config b/nextflow.config
index 54d8817a..dc7b3edc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -350,7 +350,7 @@ manifest {
// Nextflow plugins
plugins {
- id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+ id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 910edd43..d447c98b 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
"@id": "./",
"@type": "Dataset",
"creativeWorkStatus": "InProgress",
- "datePublished": "2024-12-20T16:00:22+00:00",
- "description": "
\n \n \n \n \n
[](https://github.com/nf-core/pathogensurveillance/actions/workflows/ci.yml)\n[](https://github.com/nf-core/pathogensurveillance/actions/workflows/linting.yml)[](https://nf-co.re/pathogensurveillance/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pathogensurveillance)\n\n[](https://nfcore.slack.com/channels/pathogensurveillance)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pathogensurveillance** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/pathogensurveillance \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> 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/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pathogensurveillance/usage) and the [parameter documentation](https://nf-co.re/pathogensurveillance/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pathogensurveillance/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pathogensurveillance/output).\n\n## Credits\n\nnf-core/pathogensurveillance was originally written by Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Hung Phan, Je\ufb00 H. Chang, Niklaus J. Gr\u00fcnwald.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pathogensurveillance` channel](https://nfcore.slack.com/channels/pathogensurveillance) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+ "datePublished": "2025-01-20T14:35:27+00:00",
+ "description": "
\n \n \n \n \n
\n\n[](https://github.com/nf-core/pathogensurveillance/actions/workflows/ci.yml)\n[](https://github.com/nf-core/pathogensurveillance/actions/workflows/linting.yml)[](https://nf-co.re/pathogensurveillance/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/pathogensurveillance)\n\n[](https://nfcore.slack.com/channels/pathogensurveillance)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/pathogensurveillance** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/pathogensurveillance \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> 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/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pathogensurveillance/usage) and the [parameter documentation](https://nf-co.re/pathogensurveillance/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pathogensurveillance/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/pathogensurveillance/output).\n\n## Credits\n\nnf-core/pathogensurveillance was originally written by Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Hung Phan, Je\ufb00 H. Chang, Niklaus J. Gr\u00fcnwald.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#pathogensurveillance` channel](https://nfcore.slack.com/channels/pathogensurveillance) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
"hasPart": [
{
"@id": "main.nf"
@@ -99,7 +99,7 @@
},
"mentions": [
{
- "@id": "#3c086e87-1735-4ba8-9f4a-b82d91f439de"
+ "@id": "#44d4b334-952f-4954-874e-9ef29f7f6042"
}
],
"name": "nf-core/pathogensurveillance"
@@ -121,47 +121,31 @@
},
{
"@id": "main.nf",
- "@type": [
- "File",
- "SoftwareSourceCode",
- "ComputationalWorkflow"
- ],
+ "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
"creator": [
{
"@id": "#zacharyfoster1989@gmail.com"
}
],
"dateCreated": "",
- "dateModified": "2024-12-20T17:00:22Z",
+ "dateModified": "2025-01-20T14:35:27Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
- "keywords": [
- "nf-core",
- "nextflow"
- ],
- "license": [
- "MIT"
- ],
+ "keywords": ["nf-core", "nextflow"],
+ "license": ["MIT"],
"maintainer": [
{
"@id": "#zacharyfoster1989@gmail.com"
}
],
- "name": [
- "nf-core/pathogensurveillance"
- ],
+ "name": ["nf-core/pathogensurveillance"],
"programmingLanguage": {
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
},
"sdPublisher": {
"@id": "https://nf-co.re/"
},
- "url": [
- "https://github.com/nf-core/pathogensurveillance",
- "https://nf-co.re/pathogensurveillance/dev/"
- ],
- "version": [
- "1.0dev"
- ]
+ "url": ["https://github.com/nf-core/pathogensurveillance", "https://nf-co.re/pathogensurveillance/dev/"],
+ "version": ["1.0dev"]
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -176,11 +160,11 @@
"version": "!>=24.04.2"
},
{
- "@id": "#3c086e87-1735-4ba8-9f4a-b82d91f439de",
+ "@id": "#44d4b334-952f-4954-874e-9ef29f7f6042",
"@type": "TestSuite",
"instance": [
{
- "@id": "#a78c38d5-b9ce-4292-b46a-c7158d9f3124"
+ "@id": "#ebfe4fd3-7787-4fea-8f08-8ef0e6487044"
}
],
"mainEntity": {
@@ -189,7 +173,7 @@
"name": "Test suite for nf-core/pathogensurveillance"
},
{
- "@id": "#a78c38d5-b9ce-4292-b46a-c7158d9f3124",
+ "@id": "#ebfe4fd3-7787-4fea-8f08-8ef0e6487044",
"@type": "TestInstance",
"name": "GitHub Actions workflow for testing nf-core/pathogensurveillance",
"resource": "repos/nf-core/pathogensurveillance/actions/workflows/ci.yml",
@@ -324,4 +308,4 @@
"name": "Zachary S.L. Foster"
}
]
-}
\ No newline at end of file
+}
![\"nf-core/pathogensurveillance\"](\"docs/images/nf-core-pathogensurveillance_logo_dark.png\"){kind=logo}
\n