kfukuta/wf-transcriptomes-v202
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params update defaults

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This commit is contained in:
Sarah Griffiths 2023-09-06 08:00:10 +00:00
parent 68ff1931c5
commit 4065a4d82f
2 changed files with 21 additions and 17 deletions
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4
nextflow.config
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@ -61,10 +61,10 @@ params {
bundle_min_reads = 50000
// Options passed to stringtie:
stringtie_opts = " --conservative "
stringtie_opts = "--conservative"
// Options passed to gffcompare:
gffcompare_opts = " -R "
gffcompare_opts = "-R"
// Plot gffcompare results:
plot_gffcmp_stats = true

34
nextflow_schema.json
View File

@ -29,6 +29,7 @@
"reference-guided",
"denovo"
],
"default": "reference-guided",
"description": "Select how the transcriptome used for analysis should be prepared.",
"help_text": "To analyse only gene fusions and differential expression use of an existing transcriptome may be preferred and so 'precomputed' should be selected. In this case the 'ref_transcriptome' parameter should be specified. To create a reference transcriptome using an existing reference genome, select 'reference guided' and specify the 'ref_genome' parameter. To create a transcriptome from your sequencing data select 'denovo'."
},
@ -57,12 +58,14 @@
},
"direct_rna": {
"type": "boolean",
"default": false,
"title": "direct RNA",
"description": "Set to true for direct RNA sequencing.",
"help_text": " Omits the pychopper step."
},
"analyse_unclassified": {
"type": "boolean",
"default": false,
"title": "Analyse unclassified",
"description": "Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified directory.",
"help_text": "If selected and if the input is a multiplex directory the workflow will also process the unclassified directory."
@ -113,6 +116,7 @@
"properties": {
"plot_gffcmp_stats": {
"type": "boolean",
"default": true,
"title": "Plot gffcompare statistics",
"description": "Create a PDF of plots from showing gffcompare results",
"help_text": "If set to true, a PDF file containing detailed gffcompare reults will be output"
@ -121,7 +125,7 @@
"type": "string",
"title": "Plot gffcompare options",
"description": "Extra command-line options to give to gffcompare -r",
"default": " -R ",
"default": "-R",
"help_text": "For a list of possible options see [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml)."
},
"minimap2_index_opts": {
@ -163,7 +167,7 @@
"type": "string",
"title": "Stringtie options",
"description": "Extra command-line options for stringtie transcript assembly.",
"default": " --conservative ",
"default": "--conservative",
"help_text": "For additional String tie options see [here](https://github.com/gpertea/stringtie#stringtie-options)."
}
}
@ -181,9 +185,9 @@
},
"isOnClust2_sort_options": {
"type": "string",
"default": "--batch-size -1 --kmer-size 11 --window-size 15 --min-shared 5 --min-qual 7.0 --mapped-threshold 0.65 --aligned-threshold 0.2 --min-fraction 0.8 --min-prob-no-hits 0.0 -M -1 -P 500 -g 50 -c 150 -F 2",
"description": "Additional command-line options for isOnClust2 sort.",
"help_text": "isOnClust2 is used for **de novo** transcript assembly. Options for the sort command can be be supplied like so `-opt1 arg -opt2 arg`. Available arguments can be found at [isOnClust2](https://github.com/nanoporetech/isONclust2). It is recommended not to alter this parameter.",
"default": "--kmer-size 11 --window-size 15 --min-shared 5 --min-qual 7.0 --mapped-threshold 0.65 --aligned-threshold 0.2 --min-fraction 0.8 --min-prob-no-hits 0.0 -M -1 -P 500 -g 50 -c 150 -F 2"
"help_text": "isOnClust2 is used for **de novo** transcript assembly. Options for the sort command can be be supplied like so `-opt1 arg -opt2 arg`. Available arguments can be found at [isOnClust2](https://github.com/nanoporetech/isONclust2). It is recommended not to alter this parameter."
}
}
},
@ -230,6 +234,7 @@
"properties": {
"de_analysis": {
"type": "boolean",
"default": false,
"title": "Differential expression analysis",
"description": "Run DE anaylsis",
"help_text": "Running this requires you to provide at least two replicates for a control and treated sample as well as a sample sheet param."
@ -262,11 +267,6 @@
"description": "Transcripts expressed in minimum this many samples",
"help_text": "A transcript must be mapped in at least this this minimum number of samples to be included in the analysis."
}
},
"dependencies": {
"de_analysis": [
"sample_sheet"
]
}
},
"advanced_options": {
@ -276,7 +276,7 @@
"properties": {
"threads": {
"type": "integer",
"default": 2,
"default": 4,
"description": "Number of CPU threads.",
"help_text": "Only provided to processes including alignment and and assembly that benefit from multiple threads."
},
@ -289,6 +289,7 @@
},
"bundle_min_reads": {
"type": "integer",
"default": 50000,
"title": "Bundle minimum reads",
"description": "Minimum size of bam bundle for parallel processing."
},
@ -308,13 +309,21 @@
"properties": {
"help": {
"type": "boolean",
"default": false,
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"disable_ping": {
"type": "boolean",
"default": false,
"description": "Enable to prevent sending a workflow ping."
},
"version": {
"type": "boolean",
"default": false,
"description": "Display version and exit.",
"hidden": true
}
}
}
@ -349,11 +358,6 @@
}
],
"properties": {
"version": {
"type": "boolean",
"description": "Display version and exit.",
"hidden": true
},
"aws_image_prefix": {
"type": "string",
"hidden": true