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seqeralabs · Oct 21, 2020 · f76f77f · f76f77f
1 parent f7aeab4
commit f76f77f
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Showing 2 changed files with 11 additions and 5 deletions.
diff --git a/modules/samtools/cram_to_bam/cram_to_bam.nf b/modules/samtools/cram_to_bam/cram_to_bam.nf
@@ -18,7 +18,8 @@ process SAMTOOLS_CRAM_TO_BAM {
     maxRetries 3
 
     input:
-    tuple path(ref_fasta), path(ref_fasta_index)
+    path(ref_fasta)
+    path(ref_fasta_index)
     path(ref_dict)
     path(input_cram)
 
@@ -44,10 +45,15 @@ process SAMTOOLS_CRAM_TO_BAM {
 }
 
 workflow test {
-    ref_fasta_ch = Channel.value([Paths.get("./test_data/NC000962_3.fasta"), Paths.get("/test_data/NC000962_3.fasta.fai")])
-    ref_dict_ch = Channel.value(Paths.get("/test_data/NC000962_3.dict"))
+//    ref_fasta_ch = Channel.value([Paths.get("./test_data/NC000962_3.fasta"), Paths.get("/test_data/NC000962_3.fasta.fai")])
+    ref_fasta = "./test_data/NC000962_3.fasta"
+    ref_fasta_fai = "./test_data/NC000962_3.fasta.fai"
+
+//    ref_dict_ch = Channel.value(Paths.get("/test_data/NC000962_3.dict"))
+    ref_dict = "./test_data/NC000962_3.dict"
+
     input_cram_ch = Channel.fromPath("./test_data/*cram")
 
-    SAMTOOLS_CRAM_TO_BAM(ref_fasta_ch, ref_dict_ch, input_cram_ch)
+    SAMTOOLS_CRAM_TO_BAM(ref_fasta, ref_fasta_fai, ref_dict, input_cram_ch)
 
 }
diff --git a/workflows/haplotype_caller.nf b/workflows/haplotype_caller.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl = 2
+nextflow.enable.dsl = 2
 
 include { SAMTOOLS_CRAM_TO_BAM } from "../modules/samtools/cram_to_bam/cram_to_bam"
 include { GATK_HAPLOTYPE_CALLER } from "../modules/gatk/haplotype_caller/haplotype_caller"