From f8a9462c56b481d34af5d142fb746974c7d7bc5c Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Wed, 17 Mar 2021 17:09:35 +0530
Subject: Do not specify outputs to be of File type.

---
 scripts/fastq2fasta.scm                    | 5 -----
 scripts/variant-calling-bowtie-bwa-mem.scm | 8 +-------
 2 files changed, 1 insertion(+), 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
-- 
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