Initial Commit Help Pages

VERSION

@@ -0,0 +1 @@
+'0.3.0'

eval.nf

@@ -1,3 +1,10 @@
+//load in help function
+File helppages_class_file = new File("./src/Helppages.groovy");
+Class HelppagesClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(helppages_class_file);
+GroovyObject help = (GroovyObject) HelppagesClass.newInstance();
+
+if (params.help) { exit 0, help.helpEval(workflow.manifest.version, params) }
+
 // 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 helppages_class_file = new File("./src/Helppages.groovy");
+Class HelppagesClass = new GroovyClassLoader(getClass().getClassLoader()).parseClass(helppages_class_file);
+GroovyObject help = (GroovyObject) HelppagesClass.newInstance();
+
+if (params.help) { exit 0, help.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/Helppages.groovy

@@ -0,0 +1,81 @@
+class Helper {
+    def helpEval(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 """
+        ____________________________________________________________________________________________
+
+        ${c_blue}Robert Koch Institute, Genome Competence Center${c_reset}
+
+        Workflow: cievad (${version}) - evaluation of callsets
+
+        ${c_yellow}Minimal Usage Examples:${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>
+
+        ${c_yellow}Input parameter (required):${c_reset}
+
+        ${c_green} --callsets_dir ${c_reset} Directory containing variant callsets for evaluation (files of format: callset_<X>.vcf[.gz]), where <X> is the index of the corresponding truthset.
+        OR
+        ${c_green} --sample_sheet ${c_reset} Sample sheet (.csv) with the header "index,truthset,callset". Every following line contains an index and matching truth- and callset.
+
+        ${c_yellow}Other workflow parameter:${c_reset}
+
+        ${c_green} --outdir ${c_reset} directory to save results in [default: ${params.outdir}]
+        """
+    }
+
+    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 """
+        ____________________________________________________________________________________________
+
+        ${c_blue}Robert Koch Institute, Genome Competence Center${c_reset}
+
+        Workflow: cievad (${version}) - haplotype generation
+
+        ${c_yellow}Minimal Usage Example:${c_reset}
+
+        nextflow run hap.nf -profile local,conda --reference <cievad/path/to/ref>
+
+        ${c_yellow}Input parameter (required):${c_reset}
+
+        ${c_green} --reference ${c_reset} reference genome (.fasta) used for the generation of synthetic sequencing data
+
+        ${c_yellow}Other workflow parameter:${c_reset}
+
+        ${c_green} --n ${c_reset} number of synthetic samples to be generated [default: ${params.n}]
+        ${c_green} --read_type ${c_reset} type of synthetic reads to be generated (options: ngs, ont) [default: ${params.read_type}]
+        ${c_green} --outdir ${c_reset} directory to save results in [default: ${params.outdir}]
+
+        ${c_yellow}Next Generation Sequencing parameter, optional if [--read_type ngs] is 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 parameter, optional if [--read_type ont] is supplied ${c_reset}
+
+        ${c_green} --dna_type ${c_reset} used DNA type (options: linear, circular) [default: ${params.dna_type}]
+        ${c_green} --model_prefix ${c_reset} path and prefix of a NanoSim model [default: ${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 synthetic reads [default: ${params.median_length}]
+        ${c_green} --sd_length ${c_reset} standard deviation of the synthetic read lengths [default: ${params.sd_length}]
+        ${c_green} --nb_reads ${c_reset} number of synthetic reads per sample [default: ${params.nb_reads}]
+        """
+    }
+}