Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add parameter freyja_depthcutoff #412

Merged
merged 4 commits into from
Jan 25, 2024
Merged

Add parameter freyja_depthcutoff #412

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
24b0952
Add depthcutoff parameter of FREYJA_BOOT and FREYJA_DEMIX modules as …
Joon-Klaps Jan 17, 2024
788fe2e
bad closure
Joon-Klaps Jan 17, 2024
b86f0e7
[automated] Fix linting with Prettier
nf-core-bot Jan 17, 2024
66d2cf1
Update parameters in CHANGELOG.md
Joon-Klaps Jan 25, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions .devcontainer/devcontainer.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,11 @@
"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"
"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"]
}
}
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
},
},
}
16 changes: 9 additions & 7 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,16 +20,18 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [[PR #387](https://github.com/nf-core/viralrecon/pull/387)] - Software closes gracefully when encountering an error
- [[PR #395](https://github.com/nf-core/viralrecon/pull/395)] - Remove minia from default assemblers because it is unreliable
- [[PR #393](https://github.com/nf-core/viralrecon/pull/393)] - Changed primer set to params
- [[PR [#405](https://github.com/nf-core/viralrecon/issues/405)]] - Including parameter `depthcutoff` to freyja demix and boot

### Parameters

| Old parameter | New parameter |
| ------------------- | ------------- |
| `--skip_freyja` | |
| `--freyja_repeats` | |
| `--freyja_db_name` | |
| `--freyja_barcodes` | |
| `--freyja_lineages` | |
| Old parameter | New parameter |
| ---------------------- | ------------- |
| `--skip_freyja` | |
| `--freyja_repeats` | |
| `--freyja_db_name` | |
| `--freyja_barcodes` | |
| `--freyja_lineages` | |
| `--freyja_depthcutoff` | |
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think --freyja_depthcutoff should go in the new parameter column?

Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I thought so too 😅 but given that the previous PR, introducing freyja had its variables in the old column I putted it there.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Okay then everything looks good to me!


> **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.
Expand Down
9 changes: 8 additions & 1 deletion conf/modules_illumina.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -194,21 +194,28 @@ if (!params.skip_variants) {
if (!params.skip_freyja) {
process {
withName: 'FREYJA_VARIANTS' {
ext.args = {}
publishDir = [
path: { "${params.outdir}/variants/freyja/variants" },
mode: params.publish_dir_mode,
pattern: "*.{tsv,csv}"
]
}
withName: 'FREYJA_DEMIX' {
ext.args = [
params.freyja_depthcutoff ? "--depthcutoff ${params.freyja_depthcutoff}" : '',
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/variants/freyja/demix" },
mode: params.publish_dir_mode,
pattern: "*.{tsv,csv}"
]
}
withName: 'FREYJA_BOOT' {
ext.args = '--boxplot pdf'
ext.args = [
params.freyja_depthcutoff ? "--depthcutoff ${params.freyja_depthcutoff}" : '',
'--boxplot pdf',
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/variants/freyja/bootstrap" },
mode: params.publish_dir_mode,
Expand Down
12 changes: 9 additions & 3 deletions conf/modules_nanopore.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -240,17 +240,23 @@ if (!params.skip_freyja) {
}

withName: 'FREYJA_DEMIX' {
ext.args = [
params.freyja_depthcutoff ? "--depthcutoff ${params.freyja_depthcutoff}" : '',
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/${params.artic_minion_caller}/freyja/demix" },
path: { "${params.outdir}/variants/freyja/demix" },
mode: params.publish_dir_mode,
pattern: "*.{tsv,csv}"
]
}

withName: 'FREYJA_BOOT' {
ext.args = '--boxplot pdf'
ext.args = [
params.freyja_depthcutoff ? "--depthcutoff ${params.freyja_depthcutoff}" : '',
'--boxplot pdf',
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/${params.artic_minion_caller}/freyja/bootstrap" },
path: { "${params.outdir}/variants/freyja/bootstrap" },
mode: params.publish_dir_mode,
pattern: "*.{tsv,csv,pdf}"
]
Expand Down
1 change: 1 addition & 0 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ params {
max_multiqc_email_size = '25.MB'
skip_freyja = false
freyja_repeats = 100
freyja_depthcutoff = null
freyja_db_name = 'freyja_db'
freyja_barcodes = null
freyja_lineages = null
Expand Down
8 changes: 7 additions & 1 deletion nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -253,7 +253,7 @@
},
"skip_freyja": {
"type": "boolean",
"fa_icon": "fas fast-forward",
"fa_icon": "fas fa-forward",
"description": "Skip freyja deep SARS-CoV-2 variant analysis using a depth weighted approach."
},
"freyja_db_name": {
Expand All @@ -262,6 +262,12 @@
"fa_icon": "fas fa-folder-open",
"description": "Specify the name where to store UShER database (default: 'freyja_db')."
},
"freyja_depthcutoff": {
"type": "number",
"description": "Specify a coverage depth minimum which excludes sites with coverage less than the specified value",
"fa_icon": "fas fa-hand-paper",
"help_text": "Using the `depthcutoff` option may result in some distinct lineages now having identical barcodes, which are grouped into the format `[lineage]-like(num)` (based on their shared phylogeny) in the output."
},
"freyja_repeats": {
"type": "integer",
"default": 100,
Expand Down
Loading