From 82336f79f04ccf37849f7ef1814f60fb85f3a738 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Wed, 17 Mar 2021 23:58:08 +0530
Subject: Use default output of pipeline

---
 scripts/fastq2fasta.scm | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

(limited to 'scripts/fastq2fasta.scm')

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")
-- 
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