diff options
Diffstat (limited to 'scripts/fastq2fasta.scm')
| -rw-r--r-- | scripts/fastq2fasta.scm | 18 |
1 files changed, 7 insertions, 11 deletions
diff --git a/scripts/fastq2fasta.scm b/scripts/fastq2fasta.scm index 590a535..ddb507d 100644 --- a/scripts/fastq2fasta.scm +++ b/scripts/fastq2fasta.scm @@ -34,7 +34,7 @@ (define fastq2fasta (workflow "fastq2fasta" - (list (pipeline "bwa_mem_to_normalized" + (list (pipeline "normalization" (list (command "bwa_mem" (list "bwa" "mem" "-t" threads ref-fasta fastq-forward fastq-reverse)) @@ -51,16 +51,14 @@ (command "bcftools_norm" (list "bcftools" "norm" "-Ob" "-f" ref-fasta "--threads" threads "-") - #:other '((stdout . "normalized.bcf")))) - (list (output "normalized" - #:source "bcftools_norm/stdout"))) + #:other '((stdout . "normalized.bcf"))))) (command "bcftools_index_after_normalization" - (list "bcftools" "index" (input "normalized")) + (list "bcftools" "index" (input "normalization_stdout")) #:outputs (list (output "index_after_normalization" - #:binding '((glob . "$(inputs.normalized.basename)")) + #:binding '((glob . "$(inputs.normalization_stdout.basename)")) #:other '((secondary-files . #(".csi"))))) #:other `((hints (Initial-work-dir-requirement - (listing . #("$(inputs.normalized)")))))) + (listing . #("$(inputs.normalization_stdout)")))))) (command "bcftools_view_qc" (list "bcftools" "view" "-i" "'QUAL > 10 && GT=\"a\"'" @@ -85,10 +83,8 @@ #:other '((secondary-files . #(".csi")))))) (command "set_sample_id" (list "sed" "s/^>.*/>$(inputs.sample_id)/g") - #:additional-inputs (list sample-id))) - (list (output "out_fasta" - #:source "set_sample_id/stdout")))) + #:additional-inputs (list sample-id))))) (list (output "out_fasta" - #:source "consensus/out_fasta")))) + #:source "consensus/consensus_stdout")))) (write-cwl fastq2fasta "workflows/fastq2fasta/fastq2fasta.cwl") |