added requested changes, updated README

README.md

@@ -69,10 +69,11 @@ The minimal command to evaluate the accordance between a truthset (generated dat
 nextflow run eval.nf -profile local,conda --callsets_dir <path/to/callsets>
 ```
 where `--callsets_dir` is the parameter to specify a folder containing the callset VCF files.
-Currently, a callset within this folder has to follow the naming convention `callset_<X>.vcf[.gz]` where _\<X\>_ is the integer of the corresponding truthset.
-Callsets can optionally be _gzip_ compressed.
-
-🚧 For convenience, the `eval.nf` will get an option to provide a sample sheet as an alternative input format in the future.
+Currently, a callset within this folder has to follow the naming convention `callset_<X>.vcf[.gz]` where _\<X\>_ is the integer of the corresponding truthset. Alternatively, one can provide a sample sheet (","-delimited) with the columns "index", "callset" and truthset", where "index" is an iteration from 1 to n (number of samples) and "callset"/"truthset" are paths to the respectively matching callset VCF files. The command is
+```
+nextflow run eval.nf -profile local,conda --sample_sheet <path/to/sample_sheet>
+```
+Note: Callsets can optionally be _gzip_ compressed.
 
 <details><summary>⚠️ Run commands from the root directory </summary>
 Without further ado, please run the commands from a terminal at the top folder (root directory) of this repository.

eval.nf

@@ -11,13 +11,13 @@ workflow{
     ch_ref      = Channel.value("$baseDir/" + params.reference)
     ch_ref_idx  = SAMTOOLS_FAIDX(ch_ref)
 
-    if (params.callsets_dir != "") {
+    if (params.callsets_dir != "" && params.sample_sheet == "") {
 
         ch_callsets = Channel.fromPath(params.callsets_dir + "/" + "*.{vcf,vcf.gz}")
         ch_callsets
             .map { it -> tuple(it.toString().split('/')[-1].tokenize('_')[1].replaceFirst('.vcf', '').replaceFirst('.gz', '').toInteger(), file(it)) }
             .set {ch_callsets}
-        ch_callsets.view()
+        // ch_callsets.view()
 
         ch_truthsets = Channel.fromPath(params.outdir + "/" + "simulated_hap*.vcf")
         ch_truthsets
@@ -29,17 +29,17 @@ workflow{
             .set {ch_variantsets_map}
         // ch_variantsets_map.view()
 
-    } else if (params.sample_sheet != "") { 
+    } else if (params.sample_sheet != "" && params.callsets_dir == "") { 
 
         ch_variantsets_map = Channel
             .fromPath(params.sample_sheet, checkIfExists: true)
             .splitCsv(header: true, sep: ",")
             .map {row -> [row["index"] as Integer, row["callset"], row["truthset"]]}
-            .view()
+            // .view()
 
     } else {
 
-        exit 1, "ERROR: Either the sample_sheet or callsets_dir parameter has to be provided!\n"
+        exit 1, "ERROR: Data input incorrect - please supply only one of the following parameters: sample_sheet, callsets_dir\n"
 
     }
 

nextflow.config

@@ -11,12 +11,12 @@ manifest {
 params {
     // Individual parameters
     n = 3
-    reference = 'ressources/MN908947.3.fasta'
+    reference = 'reference/Sars-Cov-2/Wuhan-Hu-1/MN908947.3.fasta'
     read_type = 'ngs'
 
     // General parameters
     seed = 479
-    outdir = 'hap_results'
+    outdir = 'results'
 
     // NGS (WGS) - Read simulation parameters
     nb_frag = 3000