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authorArun Isaac2021-03-17 23:58:08 +0530
committerArun Isaac2021-03-17 23:58:08 +0530
commit82336f79f04ccf37849f7ef1814f60fb85f3a738 (patch)
treee2424c201f46de84dac2027cbf09be8c73dd23c4 /scripts/fastq2fasta.scm
parentf8a9462c56b481d34af5d142fb746974c7d7bc5c (diff)
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Use default output of pipelinegenerate-cwl
Diffstat (limited to 'scripts/fastq2fasta.scm')
-rw-r--r--scripts/fastq2fasta.scm18
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")