diff options
Diffstat (limited to 'scripts/fastq2fasta.scm')
| -rw-r--r-- | scripts/fastq2fasta.scm | 5 |
1 files changed, 0 insertions, 5 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") |