From 68f8201eb21d9acfbf4a6853da19b374b4dec10c Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Sun, 7 Mar 2021 03:55:54 +0530
Subject: Implement bowtie, bwa-mem variant calling in ccwl

---
 scripts/variant-calling-bowtie-bwa-mem.scm | 102 +++++++++++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 scripts/variant-calling-bowtie-bwa-mem.scm

diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm
new file mode 100644
index 0000000..59c1337
--- /dev/null
+++ b/scripts/variant-calling-bowtie-bwa-mem.scm
@@ -0,0 +1,102 @@
+;; fastq sensitive short read SARS-CoV-2 mutation calling
+
+(use-modules (ccwl ccwl))
+
+(define fastq-1
+  (input "fastq_1" #:type 'File))
+
+(define fastq-2
+  (input "fastq_2" #:type 'File))
+
+(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)
+  (workflow (string-append prefix "_bam2vcf")
+            (list (pipeline "samtools"
+                            (list (command "samtools_view"
+                                           (list "samtools" "view" "-h" "-b" "-F" "4"
+                                                 (input (string-append prefix "_input") #:type 'File)))
+                                  (command "samtools_sort"
+                                           (list "samtools" "sort" "-n"))
+                                  (command "samtools_fixmate"
+                                           (list "samtools" "fixmate" "-m" "-" "-"))
+                                  (command "samtools_sort2"
+                                           (list "samtools" "sort" "-"))
+                                  (command "samtools_markdup"
+                                           (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" #:type 'File))
+                           #:outputs (list (output "indexed_dedup_bam"
+                                                   #:type 'File
+                                                   #:binding '((glob . "$(inputs.dedup_bam.basename)"))
+                                                   #:other '((secondary-files . #(".bai")))))
+                           #:other `((hints (Initial-work-dir-requirement
+                                             (listing . #("$(inputs.dedup_bam)"))))))
+                  (pipeline "freebayes"
+                            (list (command "freebayes"
+                                           (list "freebayes" "--ploidy" "1"
+                                                 "--bam" (input "indexed_dedup_bam"
+                                                                #:type 'File
+                                                                #:other '((secondary-files . #("bai"))))
+                                                 "-f" reference))
+                                  (command "bcftools_view"
+                                           (list "bcftools" "view"
+                                                 "-i" "QUAL > 10"
+                                                 "-Oz")
+                                           #:other `((stdout . ,(string-append prefix "_output.vcf.gz")))))
+                            (list (output "vcf"
+                                          #:type 'File
+                                          #:source "bcftools_view/stdout")))
+                  (command "tabix"
+                           (list "tabix" (input "vcf" #:type 'File))
+                           #:outputs (list (output "indexed_vcf" #:type 'File
+                                                   #: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
+  (workflow "variant-calling"
+            (list (command "bowtie"
+                           (list "bowtie2" "-p" "16"
+                                 "-x" bowtie2-index
+                                 "-1" fastq-1
+                                 "-2" fastq-2)
+                           #:outputs (list (output "bowtie_input" #:type 'stdout)))
+                  (bam2vcf "bowtie")
+                  (command "bwa_mem"
+                           (list "bwa" "mem" "-K" "100000000" "-v" "3" "-t" "16"
+                                 "-Y" bwa-mem-index fastq-1 fastq-2)
+                           #: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
+           "workflows/variant-calling-bowtie-bwa-mem.cwl")
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