From d781e42c9adac07253cb928ae66e9b7314710267 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 20 Apr 2020 12:55:18 -0400
Subject: Move workflows into main repo

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 workflows/fastq2fasta/bam2fasta.cwl | 65 +++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 workflows/fastq2fasta/bam2fasta.cwl

(limited to 'workflows/fastq2fasta/bam2fasta.cwl')

diff --git a/workflows/fastq2fasta/bam2fasta.cwl b/workflows/fastq2fasta/bam2fasta.cwl
new file mode 100644
index 0000000..efe580f
--- /dev/null
+++ b/workflows/fastq2fasta/bam2fasta.cwl
@@ -0,0 +1,65 @@
+# Reference:
+#  https://github.com/VGP/vgp-assembly/blob/33cd6236a68a1aee5f282e365dfe6b97e0b4ebb7/pipeline/freebayes-polish/freebayes.sh
+#  https://github.com/VGP/vgp-assembly/blob/33cd6236a68a1aee5f282e365dfe6b97e0b4ebb7/pipeline/freebayes-polish/consensus.sh
+class: Workflow
+cwlVersion: v1.1
+id: bam2fasta
+label: bam2fasta
+requirements: []
+
+inputs:
+  bam:
+    type: File
+  fasta:
+    type: File
+  threads:
+    type: int
+    default: 4
+
+outputs:
+  out_fasta:
+    type: File
+    outputSource: bcftools_consensus/out_fasta
+
+steps:
+  freebayes:
+    in:
+      bam: bam
+      ref_fasta: fasta
+    out: [vcf]
+    run: freebayes.cwl
+  bcftools_view_exclude_ref:
+    in:
+      vcf: freebayes/vcf
+      threads: threads
+    out: [bcf]
+    run: bcftools-view-exclude-ref.cwl
+  bcftools_norm:
+    in:
+      ref_fasta: fasta
+      bcf: bcftools_view_exclude_ref/bcf
+      threads: threads
+    out: [normalized_bcf]
+    run: bcftools-norm.cwl
+  bcftools_index_after_normalization:
+    in:
+      bcf: bcftools_norm/normalized_bcf
+    out: [indexed]
+    run: bcftools-index.cwl
+  bcftools_view_qc:
+    in:
+      bcf: bcftools_index_after_normalization/indexed
+      threads: threads
+    out: [vcf]
+    run: bcftools-view-qc.cwl
+  bcftools_index_after_qc:
+    in:
+      bcf: bcftools_view_qc/vcf
+    out: [indexed]
+    run: bcftools-index.cwl
+  bcftools_consensus:
+    in:
+      ref_fasta: fasta
+      vcf: bcftools_index_after_qc/indexed
+    out: [out_fasta]
+    run: bcftools-consensus.cwl
-- 
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