From 76883d02e6073f990ea980dad1f8cf21121255ff Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 22 Jun 2020 18:23:40 +0000
Subject: Adjust QC filter and relabel output sequence with sample_id

---
 workflows/fastq2fasta/bam2fasta.cwl          | 2 ++
 workflows/fastq2fasta/bcftools-consensus.cwl | 9 ++++++++-
 workflows/fastq2fasta/bcftools-view-qc.cwl   | 2 +-
 workflows/fastq2fasta/fastq2fasta.cwl        | 2 ++
 4 files changed, 13 insertions(+), 2 deletions(-)

(limited to 'workflows')

diff --git a/workflows/fastq2fasta/bam2fasta.cwl b/workflows/fastq2fasta/bam2fasta.cwl
index efe580f..dd4020b 100644
--- a/workflows/fastq2fasta/bam2fasta.cwl
+++ b/workflows/fastq2fasta/bam2fasta.cwl
@@ -15,6 +15,7 @@ inputs:
   threads:
     type: int
     default: 4
+  sample_id: string
 
 outputs:
   out_fasta:
@@ -61,5 +62,6 @@ steps:
     in:
       ref_fasta: fasta
       vcf: bcftools_index_after_qc/indexed
+      sample_id: sample_id
     out: [out_fasta]
     run: bcftools-consensus.cwl
diff --git a/workflows/fastq2fasta/bcftools-consensus.cwl b/workflows/fastq2fasta/bcftools-consensus.cwl
index c111792..dffdbe3 100644
--- a/workflows/fastq2fasta/bcftools-consensus.cwl
+++ b/workflows/fastq2fasta/bcftools-consensus.cwl
@@ -4,20 +4,27 @@ cwlVersion: v1.1
 hints:
   DockerRequirement:
     dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+  ShellCommandRequirement: {}
 baseCommand: bcftools
 arguments:
   - consensus
-  - -i'QUAL > 1 && GT="A"'
+  - -i
+  - 'QUAL > 1 && GT="a"'
   - -Hla
   - -f
   - $(inputs.ref_fasta)
   - $(inputs.vcf)
+  - {shellQuote: false, valueFrom: "|"}
+  - sed
+  - "s/^>.*/>$(inputs.sample_id)/g"
 inputs:
   - id: ref_fasta
     type: File
   - id: vcf
     type: File
     secondaryFiles: [.csi]
+  - id: sample_id
+    type: string
 outputs:
   - id: out_fasta
     type: stdout
diff --git a/workflows/fastq2fasta/bcftools-view-qc.cwl b/workflows/fastq2fasta/bcftools-view-qc.cwl
index 477c596..336f455 100644
--- a/workflows/fastq2fasta/bcftools-view-qc.cwl
+++ b/workflows/fastq2fasta/bcftools-view-qc.cwl
@@ -8,7 +8,7 @@ baseCommand: bcftools
 arguments:
   - view
   - -i
-  - 'QUAL>1 && (GT="AA" || GT="Aa")'
+  - 'QUAL > 1 && GT="a"'
   - -Oz
   - --threads=$(inputs.threads)
   - $(inputs.bcf)
diff --git a/workflows/fastq2fasta/fastq2fasta.cwl b/workflows/fastq2fasta/fastq2fasta.cwl
index 0cf5c48..d529d99 100644
--- a/workflows/fastq2fasta/fastq2fasta.cwl
+++ b/workflows/fastq2fasta/fastq2fasta.cwl
@@ -22,6 +22,7 @@ inputs:
     type: int
     default: 4
   metadata: File?
+  sample_id: string
 
 outputs:
   out_fasta:
@@ -57,5 +58,6 @@ steps:
       bam: samtools-sort/sorted_bam
       fasta: ref_fasta
       threads: threads
+      sample_id: sample_id
     out: [out_fasta]
     run: bam2fasta.cwl
-- 
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