Skip to content

Updating parameters schema and readme #20

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

Open
wants to merge 2 commits into
base: dev
Choose a base branch
from
Open

Updating parameters schema and readme #20

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
a7164bd
Updated schema
reganhayward Jun 24, 2021
ad445ca
Removed params from readme
reganhayward Jun 24, 2021
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: 0 additions & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,6 @@ The nf-core/dualrnaseq pipeline comes with documentation about the pipeline, fou
2. Pipeline configuration
* [Local installation](https://nf-co.re/usage/local_installation)
* [Adding your own system config](https://nf-co.re/usage/adding_own_config)
* [Parameters](docs/parameters.md)
3. [Running the pipeline](docs/usage.md)
4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
Expand Down
70 changes: 30 additions & 40 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -287,12 +287,14 @@
"libtype": {
"type": "string",
"description": "Options for setting the library type. A = automatic detection",
"fa_icon": "fas fa-sliders-h"
"fa_icon": "fas fa-sliders-h",
"default": "A"
},
"incompatPrior": {
"type": "integer",
"type": "string",
Copy link
Member

Choose a reason for hiding this comment

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

Is this meant to be a string?

"description": "By default, this is set to 0.0, to ensure that only mappings or alignments that are compatible with the specified library type are considered by Salmon",
"fa_icon": "fas fa-sliders-h"
"fa_icon": "fas fa-sliders-h",
"default": "0.0"
},
"generate_salmon_uniq_ambig": {
"type": "boolean",
Expand All @@ -309,7 +311,7 @@
"gene_feature_gff_to_create_transcriptome_pathogen": {
"type": "string",
"default": "gene,sRNA,tRNA,rRNA",
"description": "The pipeline uses gene features from the 3rd column of the pathogen annotative fikle (gff3) to extract the coordinates of transcripts to be quantified. By default, the pipeline uses features as `gene`, `sRNA`, `tRNA` and `rRNA` from the `--gff_pathogen` file. Should be a comma-separated string.",
"description": "The pipeline uses gene features from the 3rd column of the pathogen annotative file (gff3) to extract the coordinates of transcripts to be quantified. By default, the pipeline uses features as `gene`, `sRNA`, `tRNA` and `rRNA` from the `--gff_pathogen` file. Should be a comma-separated string.",
"fa_icon": "fas fa-sliders-h"
},
"gene_attribute_gff_to_create_transcriptome_host": {
Expand Down Expand Up @@ -485,7 +487,7 @@
"limitBAMsortRAM": {
"type": "integer",
"description": "Option to limit RAM when sorting BAM file. If 0, will be set to the genome index size, which can be quite large when running on a desktop or laptop",
"default": "0",
"default": 0,
"fa_icon": "fas fa-sliders-h"
},
"winAnchorMultimapNmax": {
Expand All @@ -499,6 +501,28 @@
"default": 100,
"description": "Option to specify the length of the donor/acceptor sequence on each side of the junctions used in constructing the splice junctions database. By default the option is set to 100. However, we recommend setting a value depending on the read length: read/mate length - 1.",
"fa_icon": "fas fa-sliders-h"
},
"outWigType": {
"type": "string",
"default": "None",
"description": "Used to generate signal outputs, such as \"wiggle\" and \"bedGraph\".",
"fa_icon": "fas fa-sliders-h"
},
"outWigStrand": {
"type": "string",
"default": "Stranded",
"description": "Options are Stranded or Unstranded when defining the strandedness of wiggle/bedGraph output",
Copy link
Member

Choose a reason for hiding this comment

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

Please use the enum option in the schema to limit the options that can be entered if there are only specific valid values.

This can be done via the little settings cog on the right hand side in the nf-core schema build GUI.

"fa_icon": "fas fa-sliders-h"
},
"star_index_params": {
"type": "string",
"description": "Set of additional parameters for creating an index with STAR",
"fa_icon": "fas fa-ellipsis-h"
},
"star_alignment_params": {
"type": "string",
"description": "Set of additional parameters for alignment with STAR",
"fa_icon": "fas fa-ellipsis-h"
}
},
"fa_icon": "fas fa-star"
Expand Down Expand Up @@ -528,37 +552,6 @@
},
"fa_icon": "fas fa-star"
},
"star_htseq": {
"title": "STAR - HTseq",
"type": "object",
"description": "Parameters available for STAR - HTSeq",
"default": "",
"properties": {
"outWigType": {
"type": "string",
"default": "None",
"description": "Used to generate signal outputs, such as \"wiggle\" and \"bedGraph\".",
"fa_icon": "fas fa-sliders-h"
},
"outWigStrand": {
"type": "string",
"default": "Stranded",
"description": "Options are Stranded or Unstranded when defining the strandedness of wiggle/bedGraph output",
"fa_icon": "fas fa-sliders-h"
},
"star_index_params": {
"type": "string",
"description": "Set of additional parameters for creating an index with STAR",
"fa_icon": "fas fa-ellipsis-h"
},
"star_alignment_params": {
"type": "string",
"description": "Set of additional parameters for alignment with STAR",
"fa_icon": "fas fa-ellipsis-h"
}
},
"fa_icon": "fas fa-star"
},
"htseq_general": {
"title": "HTSeq - general",
"type": "object",
Expand Down Expand Up @@ -838,9 +831,6 @@
{
"$ref": "#/definitions/star_salmon_alignment_based_mode"
},
{
"$ref": "#/definitions/star_htseq"
},
{
"$ref": "#/definitions/htseq_general"
},
Expand All @@ -857,4 +847,4 @@
"$ref": "#/definitions/institutional_config_options"
}
]
}
}