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Merge branch '12913-secondary-mounts' refs #12913
[arvados.git]
/
doc
/
_includes
/
_tutorial_bwa_sortsam_pipeline.liquid
diff --git
a/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
b/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
index c2be9e281a4c22f65a53c8be6bf9e8aaacbaf22a..3b39403488ff3651e732a5d77358f7239f4b5c45 100644
(file)
--- a/
doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
+++ b/
doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
@@
-1,3
+1,9
@@
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
{
"name": "Tutorial align using bwa mem and SortSam",
"components": {
{
"name": "Tutorial align using bwa mem and SortSam",
"components": {
@@
-7,12
+13,12
@@
"repository": "arvados",
"script_parameters": {
"command": [
"repository": "arvados",
"script_parameters": {
"command": [
- "bwa",
+ "
$(dir $(bwa_collection))/
bwa",
"mem",
"-t",
"$(node.cores)",
"-R",
"mem",
"-t",
"$(node.cores)",
"-R",
- "@RG\\
tID:group_id\\tPL:illumina
\\tSM:sample_id",
+ "@RG\\
\tID:group_id\\\tPL:illumina\
\\tSM:sample_id",
"$(glob $(dir $(reference_collection))/*.fasta)",
"$(glob $(dir $(sample))/*_1.fastq)",
"$(glob $(dir $(sample))/*_2.fastq)"
"$(glob $(dir $(reference_collection))/*.fasta)",
"$(glob $(dir $(sample))/*_1.fastq)",
"$(glob $(dir $(sample))/*_2.fastq)"
@@
-21,14
+27,20
@@
"required": true,
"dataclass": "Collection"
},
"required": true,
"dataclass": "Collection"
},
+ "bwa_collection": {
+ "required": true,
+ "dataclass": "Collection",
+ "default": "39c6f22d40001074f4200a72559ae7eb+5745"
+ },
"sample": {
"required": true,
"dataclass": "Collection"
},
"sample": {
"required": true,
"dataclass": "Collection"
},
- "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
+ "
task.
stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
},
"runtime_constraints": {
},
"runtime_constraints": {
- "docker_image": "arvados/jobs-java-bwa-samtools"
+ "docker_image": "bcosc/arv-base-java",
+ "arvados_sdk_version": "master"
}
},
"SortSam": {
}
},
"SortSam": {
@@
-58,7
+70,8
@@
}
},
"runtime_constraints": {
}
},
"runtime_constraints": {
- "docker_image": "arvados/jobs-java-bwa-samtools"
+ "docker_image": "bcosc/arv-base-java",
+ "arvados_sdk_version": "master"
}
}
}
}
}
}