diff options
| -rw-r--r-- | scripts/fastq2fasta.scm | 5 | ||||
| -rw-r--r-- | scripts/variant-calling-bowtie-bwa-mem.scm | 8 |
2 files changed, 1 insertions, 12 deletions
diff --git a/scripts/fastq2fasta.scm b/scripts/fastq2fasta.scm index 6fa985c..590a535 100644 --- a/scripts/fastq2fasta.scm +++ b/scripts/fastq2fasta.scm @@ -53,12 +53,10 @@ "-f" ref-fasta "--threads" threads "-") #:other '((stdout . "normalized.bcf")))) (list (output "normalized" - #:type 'File #:source "bcftools_norm/stdout"))) (command "bcftools_index_after_normalization" (list "bcftools" "index" (input "normalized")) #:outputs (list (output "index_after_normalization" - #:type 'File #:binding '((glob . "$(inputs.normalized.basename)")) #:other '((secondary-files . #(".csi"))))) #:other `((hints (Initial-work-dir-requirement @@ -74,7 +72,6 @@ (command "bcftools_index_after_qc" (list "bcftools" "index" (input "bcftools_view_qc_output_vcf")) #:outputs (list (output "index_after_qc" - #:type 'File #:binding '((glob . "$(inputs.bcftools_view_qc_output_vcf.basename)")) #:other '((secondary-files . #(".csi"))))) #:other `((hints (Initial-work-dir-requirement @@ -90,10 +87,8 @@ (list "sed" "s/^>.*/>$(inputs.sample_id)/g") #:additional-inputs (list sample-id))) (list (output "out_fasta" - #:type 'File #:source "set_sample_id/stdout")))) (list (output "out_fasta" - #:type 'File #:source "consensus/out_fasta")))) (write-cwl fastq2fasta "workflows/fastq2fasta/fastq2fasta.cwl") diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm index 598754b..88498f6 100644 --- a/scripts/variant-calling-bowtie-bwa-mem.scm +++ b/scripts/variant-calling-bowtie-bwa-mem.scm @@ -37,13 +37,11 @@ (list "samtools" "markdup" "-" "-") #:other '((stdout . "dedup.bam")))) (list (output "dedup_bam" - #:type 'File #:source "samtools_markdup/stdout"))) (command "samtools_index" (list "samtools" "index" (input "dedup_bam")) #:outputs (list (output "indexed_dedup_bam" - #:type 'File #:binding '((glob . "$(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 |