From 58a4f8620ae87fa8a30cb2ee145da8789197bef9 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Sat, 7 May 2022 23:30:35 +0200
Subject: [PATCH] [MODIF] prettier
---
nextflow_schema.json | 84 +++++++++++++++-----------------------------
1 file changed, 28 insertions(+), 56 deletions(-)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 37c14f5..ecc9df4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -18,31 +18,26 @@
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
- "description":
- "Path to comma-separated file containing information about the samples in the experiment.",
- "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/hic/usage#samplesheet-input).",
+ "description": "Path to comma-separated file containing information about the samples in the experiment.",
+ "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/hic/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
- "description":
- "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+ "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
- "help_text":
- "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
+ "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
- "description":
- "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
+ "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
@@ -57,8 +52,7 @@
"type": "string",
"description": "Name of iGenomes reference.",
"fa_icon": "fas fa-book",
- "help_text":
- "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
+ "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
},
"fasta": {
"type": "string",
@@ -66,8 +60,7 @@
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?s?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
- "help_text":
- "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
+ "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"fa_icon": "far fa-file-code"
},
"igenomes_base": {
@@ -83,13 +76,11 @@
"description": "Do not load the iGenomes reference config.",
"fa_icon": "fas fa-ban",
"hidden": true,
- "help_text":
- "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+ "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
},
"bwt2_index": {
"type": "string",
- "description":
- "Full path to directory containing Bowtie index including base name. i.e. `/path/to/index/base`.",
+ "description": "Full path to directory containing Bowtie index including base name. i.e. `/path/to/index/base`.",
"fa_icon": "far fa-file-alt"
}
}
@@ -103,26 +94,22 @@
"digestion": {
"type": "string",
"default": null,
- "description":
- "Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)"
+ "description": "Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)"
},
"restriction_site": {
"type": "string",
"default": null,
- "description":
- "Restriction motifs used during digestion. Several motifs (comma separated) can be provided."
+ "description": "Restriction motifs used during digestion. Several motifs (comma separated) can be provided."
},
"ligation_site": {
"type": "string",
"default": null,
- "description":
- "Expected motif after DNA ligation. Several motifs (comma separated) can be provided."
+ "description": "Expected motif after DNA ligation. Several motifs (comma separated) can be provided."
},
"chromosome_size": {
"type": "string",
"format": "file-path",
- "description":
- "Full path to file specifying chromosome sizes (tab separated with chromosome name and size)`.",
+ "description": "Full path to file specifying chromosome sizes (tab separated with chromosome name and size)`.",
"fa_icon": "far fa-file-alt",
"help_text": "If not specified, the pipeline will build this file from the reference genome file"
},
@@ -131,15 +118,12 @@
"format": "file-path",
"description": "Full path to restriction fragment (bed) file.",
"fa_icon": "far fa-file-alt",
- "help_text":
- "This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --restriction_site option"
+ "help_text": "This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --restriction_site option"
},
"save_reference": {
"type": "boolean",
- "description":
- "If generated by the pipeline save the annotation and indexes in the results directory.",
- "help_text":
- "Use this parameter to save all annotations to your results folder. These can then be used for future pipeline runs, reducing processing times.",
+ "description": "If generated by the pipeline save the annotation and indexes in the results directory.",
+ "help_text": "Use this parameter to save all annotations to your results folder. These can then be used for future pipeline runs, reducing processing times.",
"fa_icon": "fas fa-save"
}
}
@@ -156,8 +140,7 @@
},
"min_cis_dist": {
"type": "integer",
- "description":
- "Minimum distance between loci to consider. Useful for --dnase mode to remove spurious ligation products. Only values > 0 are considered"
+ "description": "Minimum distance between loci to consider. Useful for --dnase mode to remove spurious ligation products. Only values > 0 are considered"
}
}
},
@@ -360,8 +343,7 @@
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
- "help_text":
- "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
+ "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
@@ -375,8 +357,7 @@
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
- "help_text":
- "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
+ "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
@@ -409,8 +390,7 @@
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
- "help_text":
- "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
+ "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
@@ -418,8 +398,7 @@
"default": 16,
"fa_icon": "fas fa-microchip",
"hidden": true,
- "help_text":
- "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
+ "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
@@ -428,8 +407,7 @@
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true,
- "help_text":
- "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
+ "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
@@ -438,8 +416,7 @@
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"hidden": true,
- "help_text":
- "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
+ "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
@@ -448,8 +425,7 @@
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
- "help_text":
- "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+ "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"help": {
"type": "boolean",
@@ -461,8 +437,7 @@
"type": "string",
"default": "copy",
"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.",
+ "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"],
"hidden": true
@@ -472,8 +447,7 @@
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
- "help_text":
- "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
+ "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
@@ -521,13 +495,11 @@
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
- "help_text":
- "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
+ "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"enable_conda": {
"type": "boolean",
- "description":
- "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
+ "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
"hidden": true,
"fa_icon": "fas fa-bacon"
}
--
GitLab