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Merged
merged 3 commits into from
Mar 25, 2025
Merged

Json schema improvements #453

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bc91f60
update nextflow schema
abartlett004 Mar 24, 2025
0f8d949
update changelog
abartlett004 Mar 24, 2025
932fa1c
[automated] Fix code linting
nf-core-bot Mar 25, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## v4.1.0dev

- Update nextflow_schema.json

## v4.0.0 - 2025-03-10

- Move `txp2gene` to `reference_genome_options` in schema as it is required by `kb_python` and `alevin` ([434](https://github.com/nf-core/scrnaseq/pull/434))
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14 changes: 7 additions & 7 deletions nextflow_schema.json
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Expand Up @@ -32,7 +32,7 @@
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`), then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
Expand Down Expand Up @@ -66,7 +66,7 @@
"protocol": {
"type": "string",
"description": "The protocol that was used to generate the single cell data, e.g. 10x Genomics v2 Chemistry.\n\n Can be 'auto' (cellranger only), '10XV1', '10XV2', '10XV3', '10XV4', or any other protocol string that will get directly passed the respective aligner.",
"help_text": "The default is to auto-detect the protocol when running cellranger. For all other aligners the protocol MUST be manually specified. \n\n The following protocols are recognized by the pipeline and mapped to the corresponding protocol name of the respective aligner: '10XV1', '10XV2', '10XV3', '10XV4'. \n\nAny other protocol value is passed to the aligner in verbatim to support other sequencing platforms. See the [kallisto](https://pachterlab.github.io/kallisto/manual#bus), [simpleaf](https://simpleaf.readthedocs.io/en/latest/quant-command.html#a-note-on-the-chemistry-flag), [starsolo](https://gensoft.pasteur.fr/docs/STAR/2.7.9a/STARsolo.html)",
"help_text": "The default is to auto-detect the protocol when running cellranger. For all other aligners, the protocol MUST be manually specified. \n\n The following protocols are recognized by the pipeline and mapped to the corresponding protocol name of the respective aligner: '10XV1', '10XV2', '10XV3', '10XV4'. \n\nAny other protocol value is passed to the aligner verbatim to support other sequencing platforms. See the [kallisto](https://pachterlab.github.io/kallisto/manual#bus), [simpleaf](https://simpleaf.readthedocs.io/en/latest/quant-command.html#a-note-on-the-chemistry-flag), [starsolo](https://gensoft.pasteur.fr/docs/STAR/2.7.9a/STARsolo.html)",
"default": "auto",
"fa_icon": "fas fa-cogs"
}
Expand All @@ -76,7 +76,7 @@
"skip_tools": {
"title": "Skip Tools",
"type": "object",
"description": "This section can be used to disable certain tools in the pipeline",
"description": "This section can be used to disable certain tools in the pipeline",
"default": "",
"fa_icon": "fas fa-forward",
"properties": {
Expand Down Expand Up @@ -118,7 +118,7 @@
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available, this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"fa_icon": "far fa-file-code"
},
"igenomes_ignore": {
Expand Down Expand Up @@ -334,12 +334,12 @@
"type": "string",
"description": "Provide a panel description for targeted sequencing.",
"format": "file-path",
"exists": "true"
"exists": true
},
"gex_cmo_set": {
"type": "string",
"format": "file-path",
"exists": "true",
"exists": true,
"description": "Provide a Cell Multiplexing Oligo (CMO) description file when working with multiplexed samples. This is only necessary if you with to override Cell Ranger's default CMO-set. Please refer to the [10x documentation](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi#cmo-ref) about CMO references for more details."
},
"fb_reference": {
Expand All @@ -359,7 +359,7 @@
"format": "file-path",
"mimetype": "text/csv",
"exists": true,
"description": "This is only necessary to override Cell Ranger's default cell calling and tag calling steps. In most cases you need to only use the `cellranger_multi_barcodes` parameter. Please refer to the [10x documentation](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi#barcode-asst) for more information about this file."
"description": "This is only necessary to override Cell Ranger's default cell calling and tag calling steps. In most cases, you need to only use the `cellranger_multi_barcodes` parameter. Please refer to the [10x documentation](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi#barcode-asst) for more information about this file."
},
"cellranger_multi_barcodes": {
"type": "string",
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