Update the 'upgrading' documentation to reflect the v1.4.0 release, and warn

[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 dcce3754393d660ed8dc6835eb7f65960475fe5b..3b39403488ff3651e732a5d77358f7239f4b5c45 100644 (file)
--- a/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
+++ b/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
@@ -1,65 +1,78 @@
+{% 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": {
-    "bwa-mem": {
-      "script": "run-command",
-      "script_version": "master",
-      "repository": "arvados",
-      "script_parameters": {
-        "command": [
-          "bwa",
-          "mem",
-          "-t",
-          "$(node.cores)",
-          "-R",
-          "@RG\\tID:group_id\\tPL:illumina\\tSM:sample_id",
-          "$(glob $(dir $(reference_collection))/*.fasta)",
-          "$(glob $(dir $(sample))/*_1.fastq)",
-          "$(glob $(dir $(sample))/*_2.fastq)"
-        ],
-        "reference_collection": {
-          "required": true,
-          "dataclass": "Collection"
+    "name": "Tutorial align using bwa mem and SortSam",
+    "components": {
+        "bwa-mem": {
+            "script": "run-command",
+            "script_version": "master",
+            "repository": "arvados",
+            "script_parameters": {
+                "command": [
+                    "$(dir $(bwa_collection))/bwa",
+                    "mem",
+                    "-t",
+                    "$(node.cores)",
+                    "-R",
+                    "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
+                    "$(glob $(dir $(reference_collection))/*.fasta)",
+                    "$(glob $(dir $(sample))/*_1.fastq)",
+                    "$(glob $(dir $(sample))/*_2.fastq)"
+                ],
+                "reference_collection": {
+                    "required": true,
+                    "dataclass": "Collection"
+                },
+                "bwa_collection": {
+                    "required": true,
+                    "dataclass": "Collection",
+                    "default": "39c6f22d40001074f4200a72559ae7eb+5745"
+                },
+                "sample": {
+                    "required": true,
+                    "dataclass": "Collection"
+                },
+                "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
+            },
+            "runtime_constraints": {
+                "docker_image": "bcosc/arv-base-java",
+                "arvados_sdk_version": "master"
+            }
         },
-        "sample": {
-          "required": true,
-          "dataclass": "Collection"
-        },
-        "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
-      },
-      "runtime_constraints": {
-        "docker_image": "arvados/jobs-java-bwa-samtools"
-      }
-    }
-  },
-  "SortSam": {
-      "script": "run-command",
-      "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
-      "repository": "arvados",
-      "script_parameters": {
-        "command": [
-          "java",
-          "-Xmx4g",
-          "-Djava.io.tmpdir=$(tmpdir)",
-          "-jar",
-          "$(dir $(picard))/SortSam.jar",
-          "CREATE_INDEX=True",
-          "SORT_ORDER=coordinate",
-          "VALIDATION_STRINGENCY=LENIENT",
-          "INPUT=$(glob $(dir $(input))/*.sam)",
-          "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
-        ],
-        "input": {
-          "output_of": "bwa-mem"
-        },
-        "picard": {
-          "required": true,
-          "dataclass": "Collection",
-          "default": "88447c464574ad7f79e551070043f9a9+1970"
+        "SortSam": {
+            "script": "run-command",
+            "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
+            "repository": "arvados",
+            "script_parameters": {
+                "command": [
+                    "java",
+                    "-Xmx4g",
+                    "-Djava.io.tmpdir=$(tmpdir)",
+                    "-jar",
+                    "$(dir $(picard))/SortSam.jar",
+                    "CREATE_INDEX=True",
+                    "SORT_ORDER=coordinate",
+                    "VALIDATION_STRINGENCY=LENIENT",
+                    "INPUT=$(glob $(dir $(input))/*.sam)",
+                    "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
+                ],
+                "input": {
+                    "output_of": "bwa-mem"
+                },
+                "picard": {
+                    "required": true,
+                    "dataclass": "Collection",
+                    "default": "88447c464574ad7f79e551070043f9a9+1970"
+                }
+            },
+            "runtime_constraints": {
+                "docker_image": "bcosc/arv-base-java",
+                "arvados_sdk_version": "master"
+            }
         }
-      },
-      "runtime_constraints": {
-        "docker_image": "arvados/jobs-java-bwa-samtools"
-      }
     }
-}
\ No newline at end of file
+}