diff options
Diffstat (limited to 'scripts/variant-calling-bowtie-bwa-mem.scm')
| -rw-r--r-- | scripts/variant-calling-bowtie-bwa-mem.scm | 8 |
1 files changed, 1 insertions, 7 deletions
diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm index 598754b..88498f6 100644 --- a/scripts/variant-calling-bowtie-bwa-mem.scm +++ b/scripts/variant-calling-bowtie-bwa-mem.scm @@ -37,13 +37,11 @@ (list "samtools" "markdup" "-" "-") #:other '((stdout . "dedup.bam")))) (list (output "dedup_bam" - #:type 'File #:source "samtools_markdup/stdout"))) (command "samtools_index" (list "samtools" "index" (input "dedup_bam")) #:outputs (list (output "indexed_dedup_bam" - #:type 'File #:binding '((glob . "$(inputs.dedup_bam.basename)")) #:other '((secondary-files . #(".bai"))))) #:other `((hints (Initial-work-dir-requirement @@ -60,17 +58,15 @@ "-Oz") #:other `((stdout . ,(string-append prefix "_output.vcf.gz"))))) (list (output "vcf" - #:type 'File #:source "bcftools_view/stdout"))) (command "tabix" - #:outputs (list (output "indexed_vcf" #:type 'File (list "tabix" (input "vcf")) + #:outputs (list (output "indexed_vcf" #:binding '((glob . "$(inputs.vcf.basename)")) #:other '((secondary-files . #(".tbi"))))) #:other `((hints (Initial-work-dir-requirement (listing . #("$(inputs.vcf)"))))))) (list (output (string-append prefix "_output") - #:type 'File #:source "tabix/indexed_vcf")))) (define variant-calling @@ -88,10 +84,8 @@ #:outputs (list (output "bwa_mem_input" #:type 'stdout))) (bam2vcf "bwa_mem")) (list (output "bowtie_output" - #:type 'File #:source "bowtie_bam2vcf/bowtie_output") (output "bwa_mem_output" - #:type 'File #:source "bwa_mem_bam2vcf/bwa_mem_output")))) (write-cwl variant-calling |