From c43a223cf50b6aa88bbeb335f995ac96606482f7 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Wed, 17 Mar 2021 17:06:36 +0530
Subject: Do not specify inputs to be of File type.

---
 scripts/fastq2fasta.scm                    |  8 ++------
 scripts/variant-calling-bowtie-bwa-mem.scm | 14 +++++---------
 2 files changed, 7 insertions(+), 15 deletions(-)

diff --git a/scripts/fastq2fasta.scm b/scripts/fastq2fasta.scm
index ef4682c..6fa985c 100644
--- a/scripts/fastq2fasta.scm
+++ b/scripts/fastq2fasta.scm
@@ -12,7 +12,6 @@
 
 (define ref-fasta
   (input "ref_fasta"
-         #:type 'File
          #:other '((secondary-files . #(".amb" ".ann" ".bwt" ".pac" ".sa")))))
 
 (define output-sam
@@ -23,7 +22,6 @@
 
 (define fastq-forward
   (input "fastq_forward"
-         #:type 'File
          #:label "input fastq file to map (single-end or forward for pair-end)"))
 
 (define fastq-reverse
@@ -58,7 +56,7 @@
                                           #:type 'File
                                           #:source "bcftools_norm/stdout")))
                   (command "bcftools_index_after_normalization"
-                           (list "bcftools" "index" (input "normalized" #:type 'File))
+                           (list "bcftools" "index" (input "normalized"))
                            #:outputs (list (output "index_after_normalization"
                                                    #:type 'File
                                                    #:binding '((glob . "$(inputs.normalized.basename)"))
@@ -70,12 +68,11 @@
                                  "-i" "'QUAL > 10 && GT=\"a\"'"
                                  "-Oz" "--threads" threads
                                  (input "index_after_normalization"
-                                        #:type 'File
                                         #:other '((secondary-files . #(".csi")))))
                            #:outputs (list (output "bcftools_view_qc_output_vcf" #:type 'stdout))
                            #:other '((stdout . "bcftools_view_output.vcf.gz")))
                   (command "bcftools_index_after_qc"
-                           (list "bcftools" "index" (input "bcftools_view_qc_output_vcf" #:type 'File))
+                           (list "bcftools" "index" (input "bcftools_view_qc_output_vcf"))
                            #:outputs (list (output "index_after_qc"
                                                    #:type 'File
                                                    #:binding '((glob . "$(inputs.bcftools_view_qc_output_vcf.basename)"))
@@ -88,7 +85,6 @@
                                                  "-i" "'QUAL > 10 && GT=\"a\"'"
                                                  "-Hla" "-f" ref-fasta
                                                  (input "index_after_qc"
-                                                        #:type 'File
                                                         #:other '((secondary-files . #(".csi"))))))
                                   (command "set_sample_id"
                                            (list "sed" "s/^>.*/>$(inputs.sample_id)/g")
diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm
index 59c1337..598754b 100644
--- a/scripts/variant-calling-bowtie-bwa-mem.scm
+++ b/scripts/variant-calling-bowtie-bwa-mem.scm
@@ -3,25 +3,22 @@
 (use-modules (ccwl ccwl))
 
 (define fastq-1
-  (input "fastq_1" #:type 'File))
+  (input "fastq_1"))
 
 (define fastq-2
-  (input "fastq_2" #:type 'File))
+  (input "fastq_2"))
 
 (define bowtie2-index
   (input "bowtie2_index"
-         #:type 'File
          #:other '((secondary-files . #(".1.bt2" ".2.bt2" ".3.bt2" ".4.bt2"
                                         ".rev.1.bt2" ".rev.2.bt2")))))
 
 (define bwa-mem-index
   (input "bwa_mem_index"
-         #:type 'File
          #:other '((secondary-files . #(".amb" ".ann" ".bwt" ".pac" ".sa")))))
 
 (define reference
   (input "reference"
-         #:type 'File
          #:other '((secondary-files . #(".fai")))))
 
 (define (bam2vcf prefix)
@@ -29,7 +26,7 @@
             (list (pipeline "samtools"
                             (list (command "samtools_view"
                                            (list "samtools" "view" "-h" "-b" "-F" "4"
-                                                 (input (string-append prefix "_input") #:type 'File)))
+                                                 (input (string-append prefix "_input"))))
                                   (command "samtools_sort"
                                            (list "samtools" "sort" "-n"))
                                   (command "samtools_fixmate"
@@ -44,7 +41,7 @@
                                           #:source "samtools_markdup/stdout")))
                   (command "samtools_index"
                            (list "samtools" "index"
-                                 (input "dedup_bam" #:type 'File))
+                                 (input "dedup_bam"))
                            #:outputs (list (output "indexed_dedup_bam"
                                                    #:type 'File
                                                    #:binding '((glob . "$(inputs.dedup_bam.basename)"))
@@ -55,7 +52,6 @@
                             (list (command "freebayes"
                                            (list "freebayes" "--ploidy" "1"
                                                  "--bam" (input "indexed_dedup_bam"
-                                                                #:type 'File
                                                                 #:other '((secondary-files . #("bai"))))
                                                  "-f" reference))
                                   (command "bcftools_view"
@@ -67,8 +63,8 @@
                                           #:type 'File
                                           #:source "bcftools_view/stdout")))
                   (command "tabix"
-                           (list "tabix" (input "vcf" #:type 'File))
                            #:outputs (list (output "indexed_vcf" #:type 'File
+                           (list "tabix" (input "vcf"))
                                                    #:binding '((glob . "$(inputs.vcf.basename)"))
                                                    #:other '((secondary-files . #(".tbi")))))
                            #:other `((hints (Initial-work-dir-requirement
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