kfukuta/wf-transcriptomes-v202
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Merge branch 'schema_split' into 'dev'

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Seperated out the params into logical sections

See merge request epi2melabs/workflow-containers/wf-isoforms!40
This commit is contained in:
Neil Horner 2022-02-23 14:58:39 +00:00
commit 8b1cc95433
2 changed files with 157 additions and 127 deletions
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2
environment.yaml
View File

@ -6,7 +6,7 @@ channels:
- defaults
dependencies:
- python==3.8.*
- aplanat >=0.5.0
- aplanat >=0.6.2
- epi2melabs
- minimap2 ==2.24
- samtools ==1.14

118
nextflow_schema.json
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@ -37,24 +37,29 @@
"description": "Use additional heuristics to identify barcodes from file paths.",
"help_text": "Enabling this option will group together files into samples by the presence of strings of the form `barcodeXXX` present in filenames, rather than simply files grouped into directories (as output by MinKNOW and the Guppy basecaller)."
},
"plot_gffcmp_stats": {
"type": "boolean",
"description": "Create a pdf of plots from showing gffcompare results"
},
"gffcompare_opts": {
"type": "string",
"description": "Extra options for gffcompare -r",
"default": " -R "
},
"ref_genome": {
"type": "string",
"format": "file-path",
"description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]"
"description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow"
},
"ref_annotation": {
"type": "string",
"format": "file-path",
"description": "A reference annotation of gff format"
}
},
"required": [
"fastq"
]
},
"global_options": {
"title": "Global options",
"type": "object",
"description": "Options for both sub-workflows",
"properties": {
"threads": {
"type": "integer",
"default": 4
},
"use_pychopper": {
"type": "boolean",
@ -66,9 +71,40 @@
"description": "Extra pychopper opts",
"default": "-m edlib"
},
"threads": {
"bundle_min_reads": {
"type": "integer",
"default": 8
"description": "Minimum size of bam bundle for parallel processing."
},
"stringtie_opts": {
"type": "string",
"description": "Extra options for stringtie transcript assembly.",
"default": " --conservative "
},
"transcript_table_cov_thresh": {
"type": "integer",
"description": "Minimum coverage for a transcript to appear in the report table",
"default": 50
},
"denovo": {
"type": "boolean",
"description": "Use denovo transcript assembly rather than reference guided",
"default": false
}
}
},
"reference_wf_options": {
"title": "Options for reference-based workflow",
"type": "object",
"description": "Parameters that are used solely for the referenc-guided workflow",
"properties": {
"plot_gffcmp_stats": {
"type": "boolean",
"description": "Create a pdf of plots from showing gffcompare results"
},
"gffcompare_opts": {
"type": "string",
"description": "Extra options for gffcompare -r",
"default": " -R "
},
"minimap_index_opts": {
"type": "string",
@ -94,34 +130,15 @@
"type": "integer",
"description": "Max poly(A) region allowed with poly_context-sized end regions.",
"default": 8
}
}
},
"bundle_min_reads": {
"type": "integer",
"description": "Minimum size of bam bundle for parallel processing."
},
"use_guide_annotation": {
"type": "boolean",
"description": "Use reference annotation in stringtie transcript assembly.",
"default": "true"
},
"stringtie_opts": {
"type": "string",
"description": "Extra options for stringtie transcript assembly.",
"default": " --conservative "
},
"disable_ping": {
"type": "boolean"
},
"transcript_table_cov_thresh": {
"type": "integer",
"description": "Minimum coverage for a transcript to appear in the report table",
"default": 50
},
"denovo": {
"type": "boolean",
"description": "Use denovo transcript assembly rather than reference guided",
"default": false
},
"denovo_wf_options": {
"title": "Options for de novo-based workflow",
"type": "object",
"description": "Parameters that are used solely for the de novo workflow",
"properties": {
"batch_size": {
"type": "integer",
"description": "Maximum sequences per input batch (-1 means no limit)",
@ -197,10 +214,7 @@
"description": "Minimum probability for i consecutive minimizers to be different between read and representative",
"default": 0.2
}
},
"required": [
"fastq"
]
}
},
"meta_data": {
"title": "Meta Data",
@ -212,6 +226,12 @@
"type": "string",
"default": "report",
"description": "Output report filename suffix."
},
"disable_ping": {
"type": "boolean",
"default": false,
"description": "Enable to prevent sending a workflow ping."
}
}
},
@ -231,10 +251,20 @@
}
}
},
"allOf": [
{
"$ref": "#/definitions/basic_input_output_options"
},
{
"$ref": "#/definitions/global_options"
},
{
"$ref": "#/definitions/reference_wf_options"
},
{
"$ref": "#/definitions/denovo_wf_options"
},
{
"$ref": "#/definitions/meta_data"
},
@ -253,7 +283,7 @@
},
"wfversion": {
"type": "string",
"default": "v0.1.0",
"default": "v0.1.1",
"hidden": true
},
"monochrome_logs": {