modify input tests - enable running on a cluster

needlestack.nf

@@ -102,10 +102,10 @@ assert params.all_SNVs in [true,false] : "do not assign a value to --all_SNVs"
 assert params.no_plots in [true,false] : "do not assign a value to --no_plots"
 assert params.no_indels in [true,false] : "do not assign a value to --no_indels"
 assert params.use_file_name in [true,false] : "do not assign a value to --use_file_name"
-assert fasta_ref.exists() : "input fasta reference does not exist"
-assert fasta_ref_fai.exists() : "input fasta reference does not seem to have a .fai index (use samtools faidx)"
-assert bed.exists() : "input bed file does not exist"
-assert file(params.bam_folder).exists() : "input bam folder does not exist"
+try { assert fasta_ref.exists() : "\n WARNING : fasta reference not located in execution directory. Make sure reference index is in the same folder as fasta reference" } catch (AssertionError e) { println e.getMessage() }
+if (fasta_ref.exists()) {assert fasta_ref_fai.exists() : "input fasta reference does not seem to have a .fai index (use samtools faidx)"}
+try { assert bed.exists() : "\n WARNING : bed file not located in execution directory" } catch (AssertionError e) { println e.getMessage() }
+try { assert file(params.bam_folder).exists() : "\n WARNING : input BAM folder not located in execution directory" } catch (AssertionError e) { println e.getMessage() }
 assert (params.min_dp > 0) : "minimum coverage must be higher than 0 (--min_dp)"
 assert (params.max_DP > 1) : "maximum coverage before downsampling must be higher than 1 (--max_DP)"
 assert (params.min_ao > 0) : "minimum alternative reads must be higher than 0 (--min_ao)"
@@ -122,6 +122,7 @@ if(params.use_file_name == true){
 
 /* Software information */
 
+log.info ''
 log.info '--------------------------------------------------'
 log.info 'NEEDLESTACK: A MULTI-SAMPLE SOMATIC VARIANT CALLER'
 log.info '--------------------------------------------------'