Actions workflows and datasets minor changes

.github/workflows/python_lint.yml

@@ -21,8 +21,19 @@ jobs:
         uses: actions/checkout@master
       - name: Install flake8
         run: pip install flake8
+      - name: Check for Python file changes
+        id: file_check
+        uses: tj-actions/changed-files@v44
+        with:
+          sha: ${{ github.event.pull_request.head.sha }}
+          files: |
+             **.py
       - name: Run flake8
+        if: steps.file_check.outputs.any_changed == 'true'
         run: flake8 --ignore E501,W503,E203,W605
+      - name: No Python files changed
+        if: steps.file_check.outputs.any_changed != 'true'
+        run: echo "No Python files have been changed."
 
   black_lint:
     runs-on: ubuntu-latest
@@ -31,5 +42,15 @@ jobs:
           uses: actions/checkout@v2
         - name: Install black in jupyter
           run: pip install black[jupyter]
+        - name: Check for Python file changes
+          id: file_check
+          uses: tj-actions/changed-files@v44
+          with:
+            sha: ${{ github.event.pull_request.head.sha }}
+            files: '**.py'
         - name: Check code lints with Black
+          if: steps.file_check.outputs.any_changed == 'true'
           uses: psf/black@stable
+        - name: No Python files changed
+          if: steps.file_check.outputs.any_changed != 'true'
+          run: echo "No Python files have been changed."

.github/workflows/test_sftp_handle.yml

@@ -2,9 +2,13 @@ name: test_sftp_handle
 
 on:
   pull_request_target:
-    types: [opened, reopened, synchronize, closed]
+    types: [opened, reopened, synchronize]
     branches: "**"
-
+
+concurrency:
+  group: ${{ github.repository }}-test_sftp_handle
+  cancel-in-progress: false
+
 jobs:
   security_check:
     runs-on: ubuntu-latest
@@ -22,21 +26,10 @@ jobs:
         echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}"
         echo "Job originally triggered by ${{ github.actor }}"
         exit 1
-
-  sleep_to_ensure_concurrency:
-    needs: security_check
-    runs-on: ubuntu-latest
-    steps:
-    - name: 
-      run: sleep 10s
-      shell: bash
 
   test_sftp_handle:
-    needs: [security_check, sleep_to_ensure_concurrency]
+    needs: security_check
     if: github.repository_owner == 'BU-ISCIII'
-    concurrency:
-      group: ${{ github.repository }}-test_sftp_handle
-      cancel-in-progress: false
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 1

CHANGELOG.md

@@ -27,10 +27,17 @@ Code contributions to the release:
 
 #### Fixes
 
+- Fixed wrong city name in relecov_tools/conf/laboratory_address.json [#320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
+
 #### Changed
 
 - Renamed and refactored "bioinfo_lab_heading" for "alt_header_equivalences" in configuration.json [#314](https://github.com/BU-ISCIII/relecov-tools/pull/314)
 - Included a few schema fields that were missing or outdated, related to bioinformatics results [#314](https://github.com/BU-ISCIII/relecov-tools/pull/314)
+- Updated metadata excel template, moved to relecov_tools/assets [#320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
+- Now python lint only triggers when PR includes python files [#320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
+- Moved concurrency to whole workflow instead of each step in test_sftp-handle.yml [#320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
+- Updated test_sftp-handle.yml testing datasets [#320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
+
 
 #### Removed
 

relecov_tools/conf/laboratory_address.json

@@ -1424,7 +1424,7 @@
         "collecting_institution_email": "",
         "geo_loc_state": "Pais Vasco",
         "geo_loc_region": "Vizcaya",
-        "geo_loc_city": "Baracaldo",
+        "geo_loc_city": "Barakaldo",
         "geo_loc_country": "Spain",
         "submitting_institution": "Hospital Universitario Cruces",
         "submitting_institution_address": "Plaza Cruces, s/n",

tests/data/sftp_handle/datatest1/md5sum.txt

@@ -1,12 +1,12 @@
-c1551cdf3d5e9849b80a082051907a72  SAMPLE1_R1.fastq.gz
-449407f85d7ed4388b7d8a51e28d97a8  SAMPLE1_R2.fastq.gz
-206ccbe05fff0701bdcf9f899ca3175d  SAMPLE2_R1.fastq.gz
-BADBADe23a1caf88c11678f10666b931  SAMPLE3_R1.fastq.gz
-1be991ce0f9ed442d57c5a359d4c5848  SAMPLE3_R2.fastq.gz
-5d838ce4a93bcf12d3031a5f9ffd4acf  SAMPLE4_R1.fastq.gz
-0a9b0a590b4773e5e4c90c391979a685  SAMPLE4_R2.fastq.gz
-d04d32f14ca56f968d07f61d68598639  SAMPLE5_R1.fastq.gz
-66a057995ac925e3203ff1afdd5770ec  SAMPLE5_R2.fastq.gz
-0d55b49614d1c38582b69ccded1b22c4  SAMPLE6_R1.fastq.gz
-50afab6751cce654b973bb336cf3b3eb  SAMPLE6_R2.fastq.gz
-112d5d2ff3845236576732f7c7dc8b06  Singlesamp.fastq.gz
+bb35d11ae7f99f22eda3db239435d0e3  SAMPLE1_R1.fastq.gz
+ad4883129c29a8e55f102da198b1eb42  SAMPLE1_R2.fastq.gz
+db70941c0c3e72325128b02c4bbe5f28  SAMPLE2_R1.fastq.gz
+BADBAD35deedza0182d5aacae53fe025  SAMPLE3_R1.fastq.gz
+4391785d2fd8a0982d5aacaef3cee057  SAMPLE3_R2.fastq.gz
+57114529183e41b8e8e61dfc84e77b33  SAMPLE4_R1.fastq.gz
+62918f6d284f23e41f19cf740deca660  SAMPLE4_R2.fastq.gz
+87608f9851b25b52d49f6906e5fb23a6  SAMPLE5_R1.fastq.gz
+2f379a4972671c691cd1160c8e5abe00  SAMPLE5_R2.fastq.gz
+bd22843bd5e36a54f9c1ae1f0e7bdbac  SAMPLE6_R1.fastq.gz
+eebd6cc938d962ca54b2cc4f3650e039  SAMPLE6_R2.fastq.gz
+e04c2abf071e931c2d8f2bab52d3f12b  Singlesamp.fastq.gz