example_variant_calling.nf: fix input channel

src/example_variant_calling.nf

@@ -8,22 +8,29 @@ include {
   mapping;
 } from "./nf_modules/bwa/main.nf"
 
+include {
+  sort_bam;
+} from "./nf_modules/samtools/main.nf"
+
 include {
   germline_cohort_data_variant_calling;
 } from "./nf_modules/gatk4/main.nf" addParams(
   variant_calling_out: "vcf/",
 )
 
+params.fastq = ""
+params.fasta = ""
+
 channel
   .fromFilePairs( params.fastq, size: -1)
   .set { fastq_files }
 channel
   .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
   .map { it -> [it.simpleName, it]}
   .set { fasta_files }
 
 workflow {
   mapping(fasta_files, fastq_files)
-  germline_cohort_data_variant_calling(mapping.out.bam, fasta_files)
+  sort_bam(mapping.out.bam)
+  germline_cohort_data_variant_calling(sort_bam.out.bam, fasta_files)
 }