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-rw-r--r--scripts/fastq2fasta.scm5
-rw-r--r--scripts/variant-calling-bowtie-bwa-mem.scm8
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