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

clonal_threshold accepts multiple values in nextflow_schema.json #293

Merged
merged 5 commits into from
Dec 22, 2023
Merged

clonal_threshold accepts multiple values in nextflow_schema.json #293

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
65a1e89
clonal_threshold validation uses JSON schema format
adamrtalbot Dec 21, 2023
2915e70
cheat linter with extra 'type' entry
adamrtalbot Dec 21, 2023
17470ca
fix docker emulation
ggabernet Dec 22, 2023
adbdd1a
fix schema linting
ggabernet Dec 22, 2023
35463cb
making @maxulysse happy
ggabernet Dec 22, 2023
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
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### `Fixed`

- Removed optional output from FilterQuality to not fail silently
- clonal_threshold is validated to be 'auto' or number greater than zero

### `Dependencies`

Expand Down
63 changes: 53 additions & 10 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,10 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"required": [
"input",
"outdir"
],
"properties": {
"input": {
"type": "string",
Expand All @@ -27,7 +30,10 @@
"type": "string",
"default": "fastq",
"description": "Specify the processing mode for the pipeline. Available options are \"fastq\" and \"assembled\".",
"enum": ["fastq", "assembled"],
"enum": [
"fastq",
"assembled"
],
"fa_icon": "fas fa-terminal"
},
"outdir": {
Expand Down Expand Up @@ -61,7 +67,12 @@
"type": "string",
"fa_icon": "fas fa-flask",
"description": "Protocol used for the V(D)J amplicon sequencing library generation.",
"enum": ["specific_pcr_umi", "specific_pcr", "dt_5p_race", "dt_5p_race_umi"],
"enum": [
"specific_pcr_umi",
"specific_pcr",
"dt_5p_race",
"dt_5p_race_umi"
],
"help_text": "Available protocols are:\n- `specific_pcr_umi`: RT-PCR using transcript-specific primers containing UMIs.\n- `specific_pcr`: RT-PCR using transcript-specific primers.\n- `dt_5p_race_umi`: 5\u2019-RACE PCR using oligo-dT primers and template switch primers containing UMI.\n- `dt_5p_race`: 5\u2019-RACE PCR (i.e. RT is followed by a template switch (TS) step) using oligo-dT primers."
},
"race_linker": {
Expand Down Expand Up @@ -105,7 +116,10 @@
"default": "R1",
"fa_icon": "fas fa-dna",
"description": "Indicate if C region primers are in the R1 or R2 reads.",
"enum": ["R1", "R2"]
"enum": [
"R1",
"R2"
]
},
"primer_revpr": {
"type": "boolean",
Expand All @@ -126,7 +140,10 @@
"default": "R1",
"description": "Indicate if UMI indices are recorded in the R1 (default) or R1 fastq file.",
"help_text": "The pipeline requires UMI barcodes for identifying unique transcripts. These barcodes are typically read from an index file but sometimes can be provided merged with the start of the R1 or R2 reads. If provided in an additional index file, set the `--index_file` parameter, if provided merged with the R1 or R2 reads, set the `--umi_position` parameter to R1 or R2, respectively.",
"enum": ["R1", "R2"],
"enum": [
"R1",
"R2"
],
"fa_icon": "fas fa-barcode"
},
"umi_length": {
Expand Down Expand Up @@ -167,7 +184,6 @@
},
"adapter_fasta": {
"type": "string",
"default": "None",
"fa_icon": "fas fa-file",
"description": "Fasta file with adapter sequences to be trimmed."
},
Expand Down Expand Up @@ -235,7 +251,12 @@
"type": "string",
"default": "cut",
"description": "Masking mode for the pRESTO MaskPrimer step. Available: cut, mask, trim, tag.",
"enum": ["cut", "mask", "trim", "tag"],
"enum": [
"cut",
"mask",
"trim",
"tag"
],
"help_text": "The primer masking modes will perform the following actions:\n\n* `cut`: remove both the primer region and the preceding sequence.\n* `mask`: replace the primer region with Ns and remove the preceding sequence.\n* `trim`: remove the region preceding the primer, but leave the primer region intact.\n* `tag`: leave the input sequence unmodified.",
"fa_icon": "fas fa-mask"
},
Expand Down Expand Up @@ -335,7 +356,22 @@
"default": "",
"properties": {
"clonal_threshold": {
"type": ["string", "number"],
"oneOf": [
{
"type": "string",
"enum": [
"auto"
]
},
{
"type": "number",
"minimum": 0
}
],
"type": [
"string",
"number"
],
"default": "auto",
"fa_icon": "fab fa-pagelines",
"description": "Set the clustering threshold Hamming distance value. Default: 'auto'"
Expand Down Expand Up @@ -559,7 +595,14 @@
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
Copy link
Member

Choose a reason for hiding this comment

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

Suggested change
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
"copy",
"copyNoFollow",
"link",
"move",
"rellink",
"symlink"

Copy link
Member

Choose a reason for hiding this comment

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

This comes from the pipeline template, so best would be to fix it there, as otherwise I'm gonna have conflicts here next time 😄

],
"hidden": true
},
"email_on_fail": {
Expand Down Expand Up @@ -695,4 +738,4 @@
"$ref": "#/definitions/generic_options"
}
]
}
}
Loading