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@grst
grst committed Mar 7, 2024
1 parent 9460011 commit c78f4bb
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Showing 5 changed files with 84 additions and 160 deletions.
27 changes: 6 additions & 21 deletions assets/schema_input.json
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Expand Up @@ -11,9 +11,7 @@
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sample name must be provided and cannot contain spaces",
"meta": [
"id"
]
"meta": ["id"]
},
"fastq_1": {
"type": "string",
Expand All @@ -32,31 +30,18 @@
"expected_cells": {
"type": "integer",
"errorMessage": "Expected cells must be an Integer",
"meta": [
"expected_cells"
]
"meta": ["expected_cells"]
},
"seq_center": {
"type": "string",
"meta": [
"seq_center"
]
"meta": ["seq_center"]
},
"sample_type": {
"type": "string",
"enum": [
"atac",
"gex"
],
"meta": [
"sample_type"
]
"enum": ["atac", "gex"],
"meta": ["sample_type"]
}
},
"required": [
"sample",
"fastq_1",
"fastq_2"
]
"required": ["sample", "fastq_1", "fastq_2"]
}
}
76 changes: 19 additions & 57 deletions modules.json
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Expand Up @@ -8,114 +8,82 @@
"cellranger/count": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"cellranger/mkgtf": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"cellranger/mkref": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"cellrangerarc/count": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"cellrangerarc/mkgtf": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"cellrangerarc/mkref": {
"branch": "master",
"git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"gffread": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"kallistobustools/count": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"kallistobustools/ref": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"universc": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"unzip": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
}
}
},
Expand All @@ -124,23 +92,17 @@
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
}
}
}
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78 changes: 39 additions & 39 deletions modules/nf-core/universc/CITATION.cff
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37 changes: 5 additions & 32 deletions nextflow_schema.json
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Expand Up @@ -10,10 +10,7 @@
"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 Down Expand Up @@ -64,14 +61,7 @@
"default": "alevin",
"help_text": "The workflow can handle three types of methods:\n\n- Kallisto/Bustools\n- Salmon Alevin + AlevinQC\n- STARsolo\n\nTo choose which one to use, please specify either `alevin`, `star` or `kallisto` as a parameter option for `--aligner`. By default, the pipeline runs the `alevin` option. Note that specifying another aligner option also requires choosing appropriate parameters (see below) for the selected option.",
"fa_icon": "fas fa-align-center",
"enum": [
"kallisto",
"star",
"alevin",
"cellranger",
"cellrangerarc",
"universc"
]
"enum": ["kallisto", "star", "alevin", "cellranger", "cellrangerarc", "universc"]
},
"protocol": {
"type": "string",
Expand Down Expand Up @@ -212,11 +202,7 @@
"star_feature": {
"type": "string",
"default": "Gene",
"enum": [
"Gene",
"GeneFull",
"Gene Velocyto"
],
"enum": ["Gene", "GeneFull", "Gene Velocyto"],
"description": "Quantification type of different transcriptomic feature. Use `GeneFull` on pre-mRNA count for single-nucleus RNA-seq reads. Use `Gene Velocyto` to generate RNA velocity matrix.",
"fa_icon": "fas fa-asterisk"
}
Expand Down Expand Up @@ -247,13 +233,7 @@
"default": "standard",
"description": "Type of workflow. Use `lamanno` for RNA velocity based on La Manno et al. 2018 logic. Use `nucleus` for RNA velocity on single-nucleus RNA-seq reads. Use `kite` for feature barcoding. Use `kite: 10xFB` for 10x Genomics Feature Barcoding technology. (default: standard)",
"fa_icon": "fas fa-fish",
"enum": [
"standard",
"lamanno",
"nucleus",
"kite",
"kite: 10xFB"
]
"enum": ["standard", "lamanno", "nucleus", "kite", "kite: 10xFB"]
}
}
},
Expand Down Expand Up @@ -413,14 +393,7 @@
"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"],
"hidden": true
},
"email_on_fail": {
Expand Down
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