prettier

ssjunnebo · Jan 17, 2024 · 8ea4523 · 8ea4523
1 parent 267fe25
commit 8ea4523
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Showing 16 changed files with 536 additions and 518 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -11,9 +11,7 @@
     "features": {},
     "customizations": {
         "vscode": {
-            "extensions": [
-                "ms-python.python",
-            ]
+            "extensions": ["ms-python.python"]
         }
     },
     // Features to add to the dev container. More info: https://containers.dev/features.
@@ -28,4 +26,4 @@
     "mounts": [
         "source=${localEnv:HOME}/repos/flowcell_parser,target=/workspaces/flowcell_parser,type=bind,consistency=cached"
     ]
-}
+}
diff --git a/.github/pr_labels.yml b/.github/pr_labels.yml
@@ -1,4 +1,4 @@
-version: '1'
+version: "1"
 invalidStatus: "pending"
 labelRule:
   values:

diff --git a/.travis.yml b/.travis.yml
@@ -1,19 +1,19 @@
 language: python
 
 python:
-    - "2.7"
-    - "3.8"
+  - "2.7"
+  - "3.8"
 
 install:
-    - python setup.py install
-    - mkdir ~/.taca && cp tests/data/taca_test_cfg.yaml ~/.taca/taca.yaml
-    - pip install codecov
+  - python setup.py install
+  - mkdir ~/.taca && cp tests/data/taca_test_cfg.yaml ~/.taca/taca.yaml
+  - pip install codecov
 
 script:
-    - cd tests && nosetests --with-coverage -v -s
+  - cd tests && nosetests --with-coverage -v -s
 
 after_success:
-    - codecov
+  - codecov
 
 notifications:
-    email: false
+  email: false
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -2,13 +2,14 @@
 
 When contribution to this package please have the following things in mind:
 
-__NOTE__: _Please make sure that there are no exisiting [issues]((https://github.com/SciLifeLab/TACA/issues)) relating to whatever you want to report._
+**NOTE**: _Please make sure that there are no exisiting [issues](<(https://github.com/SciLifeLab/TACA/issues)>) relating to whatever you want to report._
 
 ####To contribute:
+
 1. Create an issue describing the bug / suggestion / improvement / ... [here](https://github.com/SciLifeLab/TACA/issues).
 2. Fork this repository to your GitHub account
 3. Make the necessary changes / additions to your forked TACA repository
-4. Please *make sure* that you've documented your code and changes using [sphinx](http://sphinx.readthedocs.org/en/latest/tutorial.html) syntax, as the documentation will be automatically generated using this engine, and published to [ReadTheDocs](http://project-management.readthedocs.org/)
+4. Please _make sure_ that you've documented your code and changes using [sphinx](http://sphinx.readthedocs.org/en/latest/tutorial.html) syntax, as the documentation will be automatically generated using this engine, and published to [ReadTheDocs](http://project-management.readthedocs.org/)
 5. Update the version number in `TACA/__init__.py`
 6. Pull Request and wait for the responsible reviewer to review and merge the code
 

diff --git a/README.md b/README.md
@@ -101,7 +101,6 @@ When a non-invasive tool is used to tidy up a lot of code, it is useful to supre
 
 To do this, add the hash of the commit containing the changes to `.git-blame-ignore-revs`, headed by an explanatory comment.
 
-
 ### Deliver command
 
 There is also a [plugin for the deliver command](https://github.com/SciLifeLab/taca-ngi-pipeline). To install this in the same development environment:

diff --git a/VERSIONLOG.md b/VERSIONLOG.md
@@ -21,9 +21,11 @@ Version 1.0.0
 Fix bug with rsync permission issue cont.
 
 ## 20231031.1
+
 Improve run_folder transfer
 
 ## 20231026.1
+
 Fix bug with rsync permission issue
 
 ## 20231024.1
@@ -46,7 +48,6 @@ Fix bug that NovaSeqXPlus date format cause error in writing pdc_archived timest
 
 Remove the temp change of creating links
 
-
 ## 20230920.1
 
 Supplement last PR, primary purpose is to differentiate user runs from QC runs in the instrument transfer script rather than the installed TACA.

diff --git a/tests/data/Stats.json b/tests/data/Stats.json
@@ -1,75 +1,75 @@
 {
-   "RunNumber":131,
-   "Flowcell":"FCIDXX",
-   "RunId":"141124_ST-COMPLEX1_01_AFCIDXX",
-   "ConversionResults":[
-      {
-         "LaneNumber":1,
-         "DemuxResults":[
-            {
-               "SampleId":"Sample_P12345_1001",
-               "SampleName":"P12345_1001",
-               "NumberReads":494288265,
-               "Yield":58820303535,
-               "ReadMetrics":[
-                  {
-                     "ReadNumber":1,
-                     "Yield":13840071420,
-                     "YieldQ30":13329609381,
-                     "QualityScoreSum":503672520160,
-                     "TrimmedBases":0
-                  }
-               ]
+    "RunNumber": 131,
+    "Flowcell": "FCIDXX",
+    "RunId": "141124_ST-COMPLEX1_01_AFCIDXX",
+    "ConversionResults": [
+        {
+            "LaneNumber": 1,
+            "DemuxResults": [
+                {
+                    "SampleId": "Sample_P12345_1001",
+                    "SampleName": "P12345_1001",
+                    "NumberReads": 494288265,
+                    "Yield": 58820303535,
+                    "ReadMetrics": [
+                        {
+                            "ReadNumber": 1,
+                            "Yield": 13840071420,
+                            "YieldQ30": 13329609381,
+                            "QualityScoreSum": 503672520160,
+                            "TrimmedBases": 0
+                        }
+                    ]
+                }
+            ],
+            "Undetermined": {
+                "NumberReads": 17709745,
+                "Yield": 2036620675,
+                "ReadMetrics": [
+                    {
+                        "ReadNumber": 1,
+                        "Yield": 885487250,
+                        "YieldQ30": 680049984,
+                        "QualityScoreSum": 28815661398,
+                        "TrimmedBases": 0
+                    },
+                    {
+                        "ReadNumber": 2,
+                        "Yield": 283355920,
+                        "YieldQ30": 179655904,
+                        "QualityScoreSum": 8324058259,
+                        "TrimmedBases": 0
+                    }
+                ]
             }
-         ],
-         "Undetermined":{
-            "NumberReads":17709745,
-            "Yield":2036620675,
-            "ReadMetrics":[
-               {
-                  "ReadNumber":1,
-                  "Yield":885487250,
-                  "YieldQ30":680049984,
-                  "QualityScoreSum":28815661398,
-                  "TrimmedBases":0
-               },
-               {
-                  "ReadNumber":2,
-                  "Yield":283355920,
-                  "YieldQ30":179655904,
-                  "QualityScoreSum":8324058259,
-                  "TrimmedBases":0
-               }
+        }
+    ],
+    "ReadInfosForLanes": [
+        {
+            "LaneNumber": 1,
+            "ReadInfos": [
+                {
+                    "Number": 1,
+                    "NumCycles": 28,
+                    "IsIndexedRead": "false"
+                }
             ]
-         }
-      }
-   ],
-   "ReadInfosForLanes":[
-      {
-         "LaneNumber":1,
-         "ReadInfos":[
-            {
-               "Number":1,
-               "NumCycles":28,
-               "IsIndexedRead":"false"
+        }
+    ],
+    "UnknownBarcodes": [
+        {
+            "Lane": 1,
+            "Barcodes": {
+                "GGGGGGGG": 3203920,
+                "CCCTAACA": 290420
             }
-         ]
-      }
-   ],
-   "UnknownBarcodes":[
-      {
-         "Lane":1,
-         "Barcodes":{
-            "GGGGGGGG":3203920,
-            "CCCTAACA":290420
-         }
-      },
-      {
-         "Lane":2,
-         "Barcodes":{
-            "GGGGGGGG":3075440,
-            "CCCTAACA":296260
-         }
-      }
-   ]
+        },
+        {
+            "Lane": 2,
+            "Barcodes": {
+                "GGGGGGGG": 3075440,
+                "CCCTAACA": 296260
+            }
+        }
+    ]
 }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -101,7 +101,6 @@ When a non-invasive tool is used to tidy up a lot of code, it is useful to supre

		To do this, add the hash of the commit containing the changes to `.git-blame-ignore-revs`, headed by an explanatory comment.


		### Deliver command

		There is also a [plugin for the deliver command](https://github.com/SciLifeLab/taca-ngi-pipeline). To install this in the same development environment:
Expand Down