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-rw-r--r--scripts/fastq2fasta.scm18
-rw-r--r--scripts/variant-calling-bowtie-bwa-mem.scm21
2 files changed, 15 insertions, 24 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/^>.*/>$(inputs.sample_id)/g")
- #:additional-inputs (list sample-id)))
- (list (output "out_fasta"
- #:source "set_sample_id/stdout"))))
+ #:additional-inputs (list sample-id)))))
(list (output "out_fasta"
- #:source "consensus/out_fasta"))))
+ #:source "consensus/consensus_stdout"))))
(write-cwl fastq2fasta "workflows/fastq2fasta/fastq2fasta.cwl")
diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm
index 88498f6..5ddc1f6 100644
--- a/scripts/variant-calling-bowtie-bwa-mem.scm
+++ b/scripts/variant-calling-bowtie-bwa-mem.scm
@@ -35,17 +35,14 @@
(list "samtools" "sort" "-"))
(command "samtools_markdup"
(list "samtools" "markdup" "-" "-")
- #:other '((stdout . "dedup.bam"))))
- (list (output "dedup_bam"
- #:source "samtools_markdup/stdout")))
+ #:other '((stdout . "dedup.bam")))))
(command "samtools_index"
- (list "samtools" "index"
- (input "dedup_bam"))
+ (list "samtools" "index" (input "samtools_stdout"))
#:outputs (list (output "indexed_dedup_bam"
- #:binding '((glob . "$(inputs.dedup_bam.basename)"))
+ #:binding '((glob . "$(inputs.samtools_stdout.basename)"))
#:other '((secondary-files . #(".bai")))))
#:other `((hints (Initial-work-dir-requirement
- (listing . #("$(inputs.dedup_bam)"))))))
+ (listing . #("$(inputs.samtools_stdout)"))))))
(pipeline "freebayes"
(list (command "freebayes"
(list "freebayes" "--ploidy" "1"
@@ -56,16 +53,14 @@
(list "bcftools" "view"
"-i" "QUAL > 10"
"-Oz")
- #:other `((stdout . ,(string-append prefix "_output.vcf.gz")))))
- (list (output "vcf"
- #:source "bcftools_view/stdout")))
+ #:other `((stdout . ,(string-append prefix "_output.vcf.gz"))))))
(command "tabix"
- (list "tabix" (input "vcf"))
+ (list "tabix" (input "freebayes_stdout"))
#:outputs (list (output "indexed_vcf"
- #:binding '((glob . "$(inputs.vcf.basename)"))
+ #:binding '((glob . "$(inputs.freebayes_stdout.basename)"))
#:other '((secondary-files . #(".tbi")))))
#:other `((hints (Initial-work-dir-requirement
- (listing . #("$(inputs.vcf)")))))))
+ (listing . #("$(inputs.freebayes_stdout)")))))))
(list (output (string-append prefix "_output")
#:source "tabix/indexed_vcf"))))