Providing a NCBI user setting file for tests

phac-nml · Nov 12, 2024 · f025b1b · f025b1b
1 parent 28fa88f
commit f025b1b
Show file tree

Hide file tree

Showing 6 changed files with 18 additions and 11 deletions.
diff --git a/modules.json b/modules.json
@@ -15,9 +15,14 @@
                         "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
                         "installed_by": ["modules"]
                     },
+                    "sratools/fasterqdump": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/sratools/fasterqdump/environment.yml b/modules/local/sratools/fasterqdump/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::sra-tools=3.0.8
+  - bioconda::sra-tools=2.11.0
   - conda-forge::pigz=2.6
diff --git a/tests/data/ncbi_user_settings.mkfg b/tests/data/ncbi_user_settings.mkfg
@@ -0,0 +1,2 @@
+/LIBS/GUID = "5b0d4b7d-88c7-4802-98fd-e3afd06feb32"
+/libs/cloud/report_instance_identity = "true"
diff --git a/tests/modules/fasterqdump/main.nf.test b/tests/modules/fasterqdump/main.nf.test
@@ -12,7 +12,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [irida_id: "SAMPLE1"], file("$baseDir/tests/data/ERR1109373.sra", checkIfExists: true) ])
-                input[1] = []
+                input[1] = file('$baseDir/tests/data/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }

diff --git a/tests/modules/fasterqdump/main.nf.test.snap b/tests/modules/fasterqdump/main.nf.test.snap
@@ -15,7 +15,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ],
                 "reads": [
                     [
@@ -30,14 +30,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-31T11:23:17.630455595"
+        "timestamp": "2024-11-11T20:36:55.563890217"
     }
 }
diff --git a/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap b/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap
@@ -24,8 +24,8 @@
                 ],
                 "1": [
                     "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
-                    "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
-                    "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
+                    "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
+                    "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3"
                 ],
                 "reads": [
                     [
@@ -49,15 +49,15 @@
                 ],
                 "versions": [
                     "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
-                    "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
-                    "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
+                    "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
+                    "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-05T15:53:20.740235848"
+        "timestamp": "2024-11-11T20:52:02.578591475"
     }
 }
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		/LIBS/GUID = "5b0d4b7d-88c7-4802-98fd-e3afd06feb32"
		/libs/cloud/report_instance_identity = "true"