Merge pull request #51 from ZaahidShaik/add_help_option

Add --help flag for displaying usage information to users.

README.md

@@ -63,6 +63,14 @@ nextflow run . -params-file params.yaml
 ```
 NOTE: You need to create `params.yaml` by copying [params.yaml.example](params.yaml.example) file and follow the instruction.
 
+
+For more information on usage and parameters which are open for modification, please use `--help` option as shown below.
+
+```
+nextflow run main.nf --help
+```
+
+
 ## License
 AI-MARRVEL is licensed under GPL-3.0. You are welcomed to use it for research purpose.  
 For business purpose, please contact us for licensing.

docs/source/nf_usage.txt

@@ -0,0 +1,41 @@
+Usage: 
+
+    nextflow run main.nf [All Args] [Options]
+
+Example:  
+
+    nextflow run main.nf --ref_dir   path/to/aim_data_dependencies \
+                         --input_vcf path/to/sample.vcf.gz \
+                         --input_hpo path/to/sample/hpos.txt \
+                         --outdir    path/to/sample/Output \ 
+                         --run_id [Sample ID] \
+                         --ref_ver [hg19/hg38] 
+
+Args:
+  --input_vcf               Path to input VCF file.
+  --input_hpo               Path to input HPO file.
+  --ref_dir                 Path to aim pipeline dependencies directory.
+  --outdir                  Output directory.
+  --run_id                  Unique identifier for this run. (default: 1)
+  --ref_ver                 Reference genome version [hg38 or hg19] (default: hg19)
+
+
+Options:
+  --exome_filter            Enable exonic filter. Addition will filter out variants outside of exonic region  (default: false)
+  --help                    Displays the usage information.
+
+Reference Files:
+  --ref_loc                 Path to reference location file
+  --ref_to_sym              Path to reference to symbol file
+  --ref_sorted_sym          Path to reference sorted symbol file
+  --ref_exonic_filter_bed   Path to exonic filter BED file
+
+VEP Annotation:
+  --vep_dir_cache           Path to VEP cache directory
+  --vep_dir_plugins         Path to VEP plugins directory
+  --vep_custom_gnomad       Path to custom gnomAD file for VEP
+  --vep_custom_clinvar      Path to custom ClinVar file for VEP
+  --vep_custom_hgmd         Path to custom HGMD file for VEP
+
+For detailed information about each process, 
+please refer to the documentation. https://ai-marrvel.readthedocs.io/en/latest/ 

main.nf

@@ -370,8 +370,20 @@ process PREDICTION {
     """
 }
 
+def SHOW_USEAGE() {
+        if (params.help) {
+        def helpFile = file(params.usage_file)  // Specify your Markdown file path here
+        if (helpFile.exists()) {
+            println helpFile.text
+        } else {
+            println "Sorry something went wrong, usage file not found! please vist our website for more info : https://ai-marrvel.readthedocs.io/en/latest/"
+        }
+        exit 0
+    }
+}
 
-workflow { 
+workflow {
+    SHOW_USEAGE()
     INDEX_VCF(params.input_vcf)
     VCF_PRE_PROCESS(INDEX_VCF.out, params.chrmap)
 

nextflow.config

@@ -1,8 +1,12 @@
 params {
     run_id = 1
+    help = false
     ref_ver = "hg19"
     bed_filter = ""
     exome_filter = false
+
+    // Will add exceptions in validations.
+    ref_dir = "NOT_PROVIDED"
 
     ref_assembly = params.ref_ver == "hg19" ? "grch37" : "grch38"
 
@@ -59,6 +63,9 @@ params {
     vep_plugin_dbnsfp = "${ref_dir}/vep/${ref_ver}/${vep_dbnsfp_name}"
     vep_idx = "${ref_dir}/vep/${ref_ver}/*.tbi"
 
+    // Documentation
+    usage_file = "${projectDir}/docs/source/nf_usage.txt"
+
     script_chunking = "${projectDir}/scripts/split_chunks.py"
     script_annot = "${projectDir}/scripts/annotation/*.py"