Fix shebang and license

refs #19868

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>

diff --git a/cwl/gvcf2fasta/gvcf2fasta_splitvcf-imputation-wf.cwl b/cwl/gvcf2fasta/gvcf2fasta_splitvcf-imputation-wf.cwl
index 08728ca9a411250b7aa44ff772853fe268cab1bd..f389ba0f04d0c415018da8ed5d256e00909bc3fc 100644 (file)
--- a/cwl/gvcf2fasta/gvcf2fasta_splitvcf-imputation-wf.cwl
+++ b/cwl/gvcf2fasta/gvcf2fasta_splitvcf-imputation-wf.cwl
@@ -2,6 +2,8 @@
 #
 # SPDX-License-Identifier: AGPL-3.0
 
+$namespaces:
+  arv: "http://arvados.org/cwl#"
 cwlVersion: v1.1
 class: Workflow
 label: Impute gVCF and convert to FASTA for gVCF split by chromosome
@@ -11,6 +13,8 @@ requirements:
 hints:
   DockerRequirement:
     dockerPull: vcfutil
+  arv:UsePreemptible:
+    usePreemptible: true
 
 inputs:
   sampleid:

diff --git a/cwl/gvcf2fasta/src/bcftools-consensus.sh b/cwl/gvcf2fasta/src/bcftools-consensus.sh
index 531a7c60567279e49fb3b3d38de5b2253aa5ee57..bac8b1c191eb4042ea2e7ad1a3dbdf6b975d4239 100755 (executable)
--- a/cwl/gvcf2fasta/src/bcftools-consensus.sh
+++ b/cwl/gvcf2fasta/src/bcftools-consensus.sh
@@ -1,9 +1,8 @@
+#!/bin/bash
 # Copyright (C) The Lightning Authors. All rights reserved.
 #
 # SPDX-License-Identifier: AGPL-3.0
 
-#!/bin/bash
-
 set -eo pipefail
 
 sampleid="$1"

diff --git a/cwl/gvcf2fasta/src/concat-get_bed_varonlyvcf.sh b/cwl/gvcf2fasta/src/concat-get_bed_varonlyvcf.sh
index 43f1a9124443e9267da26c94ef490b219dc3f937..13028c92169da55bf4819decef64087d58ae18a3 100755 (executable)
--- a/cwl/gvcf2fasta/src/concat-get_bed_varonlyvcf.sh
+++ b/cwl/gvcf2fasta/src/concat-get_bed_varonlyvcf.sh
@@ -1,9 +1,8 @@
+#!/bin/bash
 # Copyright (C) The Lightning Authors. All rights reserved.
 #
 # SPDX-License-Identifier: AGPL-3.0
 
-#!/bin/bash
-
 set -eo pipefail
 
 sampleid="$1"

diff --git a/cwl/gvcf2fasta/src/fixvcf-get_bed_varonlyvcf.sh b/cwl/gvcf2fasta/src/fixvcf-get_bed_varonlyvcf.sh
index 2ed5369721e2afe75084c8307514e1fd1cb03160..304ef873d90d9ae13bdbf9f68fdbd4c47c24aab2 100755 (executable)
--- a/cwl/gvcf2fasta/src/fixvcf-get_bed_varonlyvcf.sh
+++ b/cwl/gvcf2fasta/src/fixvcf-get_bed_varonlyvcf.sh
@@ -1,9 +1,8 @@
+#!/bin/bash
 # Copyright (C) The Lightning Authors. All rights reserved.
 #
 # SPDX-License-Identifier: AGPL-3.0
 
-#!/bin/bash
-
 set -eo pipefail
 
 sampleid="$1"

diff --git a/cwl/gvcf2fasta/src/untar-concat.sh b/cwl/gvcf2fasta/src/untar-concat.sh
index e10d60782082660a32af3a32d1382b54df4a4b2e..05a6db271f5ad1c58bb127da792826c437c78dc0 100755 (executable)
--- a/cwl/gvcf2fasta/src/untar-concat.sh
+++ b/cwl/gvcf2fasta/src/untar-concat.sh
@@ -1,9 +1,8 @@
+#!/bin/bash
 # Copyright (C) The Lightning Authors. All rights reserved.
 #
 # SPDX-License-Identifier: AGPL-3.0
 
-#!/bin/bash
-
 set -eo pipefail
 
 sampleid="$1"