Initial Commit Help Pages

VERSION

@@ -0,0 +1 @@
+'0.2.0'

eval.nf

@@ -1,3 +1,10 @@
+//load in help function
+File data_class_file = new File("./src/data_class.groovy");
+Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(data_class_file);
+GroovyObject data_class = (GroovyObject) groovyClass.newInstance();
+
+if (params.help) { exit 0, data_class.helpEval(workflow.manifest.version) }
+
 // include modules - here, modules are single processes
 include { SAMTOOLS_FAIDX } from './modules/samtools/faidx/main.nf'
 include { HAPPY } from './modules/happy/main.nf'
@@ -50,3 +57,4 @@ workflow{
 
     SOMPY_SUMMARY(ch_csv.collect())
 }
+

hap.nf

@@ -1,3 +1,10 @@
+//load in help function
+File data_class_file = new File("./src/data_class.groovy");
+Class groovyClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(data_class_file);
+GroovyObject data_class = (GroovyObject) groovyClass.newInstance();
+
+if (params.help) { exit 0, data_class.helpHap(workflow.manifest.version, params) }
+
 // include modules - here, modules are single processes
 //include { AMPLISIM } from './modules/amplisim/main.nf'
 include { MASON_SIMULATOR } from './modules/mason/simulator/main.nf'

nextflow.config

@@ -4,7 +4,7 @@ manifest {
   description = 'A workflow for a simple, streamlined and rapid evaluation of variant callsets ' 
   author = 'Thomas Krannich'
   nextflowVersion = '>=20.04.0'
-  version = '0.2.0'
+  version = new File('./VERSION').text.trim()
 }
 
 // Parameters that are accessible in the pipeline script
@@ -15,6 +15,7 @@ params {
     read_type = 'ngs'
 
     // General parameters
+    help = false
     seed = 479
     outdir = 'results'
 

src/data_class.groovy

@@ -0,0 +1,77 @@
+class Helper {
+    def helpEval(version){
+        String c_green = "\033[0;32m";
+        String c_reset = "\033[0m";
+        String c_yellow = "\033[0;33m";
+        String c_blue = "\033[0;34m";
+        String c_red = "\u001B[31m";
+        String c_dim = "\033[2m";
+        log.info """
+        ____________________________________________________________________________________________
+
+        ${c_blue}Robert Koch Institute, MF1 Bioinformatics${c_reset}
+
+        Workflow: cievad (${version})
+
+        ${c_yellow}Minimal Usage Examples:${c_reset}
+
+        nextflow run eval.nf -profile local,conda --callsets_dir <path/to/callsets>
+        or
+        nextflow run eval.nf -profile local,conda --sample_sheet <path/to/sample_sheet>
+
+        ${c_yellow}Data Input, required:${c_reset}
+
+        ${c_green} --callsets_dir ${c_reset} Directory containing variant callsets for evaluation (naming format: callset_<X>.vcf[.gz]).
+        OR
+        ${c_green} --sample_sheet ${c_reset} Sample sheet (.csv) with the header ("index","truthset","callset"), mapping corresponding truth- and callsets.
+        """
+    }
+
+    def helpHap(version,params){
+        String c_green = "\033[0;32m";
+        String c_reset = "\033[0m";
+        String c_yellow = "\033[0;33m";
+        String c_blue = "\033[0;34m";
+        String c_red = "\u001B[31m";
+        String c_dim = "\033[2m";
+        log.info """
+        ____________________________________________________________________________________________
+
+        ${c_blue}Robert Koch Institute, MF1 Bioinformatics${c_reset}
+
+        Workflow: cievad (${version})
+
+        ${c_yellow}Minimal Usage Example:${c_reset}
+
+        nextflow run hap.nf -profile local,conda
+
+        ${c_yellow}Individual Parameter, required:${c_reset}
+
+        ${c_green} --n ${c_reset} number of synthetic samples to be generated
+        ${c_green} --reference ${c_reset} reference used for the generation of synthetic sequencing data
+        ${c_green} --read_type ${c_reset} type of resulting WGS synthetic reads (options: ngs, ont)
+
+        ${c_yellow}Output Directory, required:${c_reset}
+
+        ${c_green} --outdir ${c_reset} directory to save results in
+
+        ${c_yellow}Next Generation Sequencing (WGS) Parameter, required if [--read_type ngs] supplied ${c_reset}
+
+        ${c_green} --nb_frag ${c_reset} number of fragments per sample [default: ${params.nb_frag}]
+        ${c_green} --fragment_min_size ${c_reset} minimum size of fragments [default: ${params.fragment_min_size}]
+        ${c_green} --fragment_max_size ${c_reset} maximum size of fragments [default: ${params.fragment_max_size}]
+        ${c_green} --fragment_mean_size ${c_reset} mean size of fragments [default: ${params.fragment_mean_size}]
+        ${c_green} --fragment_size_std_dev ${c_reset} standard deviation for fragment size [default: ${params.fragment_size_std_dev}]
+        ${c_green} --illumina_read_length ${c_reset} read length of synthetic illumina reads [default: ${params.illumina_read_length}]
+
+        ${c_yellow}Nanopore Sequencing (WGS) Parameter, required if [--read_type ont] supplied ${c_reset}
+
+        ${c_green} --dna_type ${c_reset} used DNA type [default: ${params.dna_type}]
+        ${c_green} --model_prefix ${c_reset} path and prefix of the used model (e.g.: ${params.model_prefix})
+        ${c_green} --model_caller ${c_reset} algorithm to conduct the basecalling [default: ${params.model_caller}]
+        ${c_green} --median_length ${c_reset} median length of the resulting synthetic reads [default: ${params.median_length}]
+        ${c_green} --sd_length ${c_reset} standard deviation length of the resulting synthetic reads [default: ${params.sd_length}]
+        ${c_green} --nb_reads ${c_reset} number of synthetic reads [default: ${params.nb_reads}]
+        """
+    }
+}