Skip to content
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.

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

Added a 'target' parameter #18

Merged
merged 1 commit into from
Apr 17, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
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
3 changes: 2 additions & 1 deletion nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,9 @@
params {

// TODO nf-core: Specify your pipeline's command line flags
// Input options
// Mandatory options
input = null
target = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
Expand Down
22 changes: 20 additions & 2 deletions nextflow_schema.json
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,11 @@
"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",
"target"
],
"properties": {
"input": {
"type": "string",
Expand All @@ -23,6 +27,13 @@
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/pairalign/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"target": {
"type": "string",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"format": "file-path",
"description": "Path to FASTA genome file for the target genome.",
"fa_icon": "far fa-file-code"
},
"outdir": {
"type": "string",
"format": "directory-path",
Expand Down Expand Up @@ -182,7 +193,14 @@
"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
Loading