Patch read indicator

.github/workflows/ci-lint-validate-convert.yml

@@ -32,21 +32,29 @@ jobs:
     name: Validate CSV
     if: always()
     runs-on: ubuntu-latest
+
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
+
       - name: Install IPython
         run: |
           pip install ipython==8.18.1    
+
       - name: Install Schematic
+        shell: bash
         run: |
           pip install schematicpy==$SCHEMATIC_VERSION
+
       - name: Convert CSV schema
+        shell: bash
         run: |
           schematic schema convert .github/CSV.model.csv
+
       - name: Validate data model CSV
+        shell: bash
         run: |
           schematic model -c .github/CSV_schematic_config.yml validate -mp HTAN.model.csv -dt "DataModel" |
             grep "Your manifest has been validated successfully. There are no errors in your manifest, and it can be submitted without any modifications."
@@ -57,36 +65,37 @@ jobs:
       - lint
       - validate
     runs-on: ubuntu-latest
+
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
+
       - name: Install IPython
         run: |
           pip install ipython==8.18.1
+
       - name: Install Schematic
+        shell: bash
         run: |
           pip install schematicpy==$SCHEMATIC_VERSION
+
       - name: Convert .csv to .jsonld
+        shell: bash
         run: |
           schematic schema convert HTAN.model.csv
-      - name: Set up Git user
-        run: |
-          git config --local user.name "github-actions[bot]"
-          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
-      - name: Fetch PR details
-        if: github.event_name == 'pull_request'
-        uses: r-lib/actions/pr-fetch@v2
+
+      - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Commit the changes
         run: |
           git add HTAN.model.jsonld
           git commit -m "GitHub Action: convert *.model.csv to *.model.jsonld" || echo "No changes to commit"
-      - name: Push changes back to PR
-        if: github.event_name == 'pull_request'
-        uses: r-lib/actions/pr-push@v2
+
+      - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 

HTAN.model.csv

@@ -311,7 +311,7 @@ Median Fraction of Reads in Annotated cis DNA Elements,Median fraction of reads
 Median Passing Read Percentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,,,,TRUE,scATAC-seq Level 1,,,
 Median Percentage of Mitochondrial Reads per Nucleus,Contamination from mitochondrial sequences,,,,TRUE,scATAC-seq Level 1,,,
 Peaks Calling Software,Generic name of peaks calling tool,,,,TRUE,scATAC-seq Level 1,,,
-Read Indicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other","R1, R2, R1&R2, I1, Other",,,TRUE,Sequencing,,,
+Read Indicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other","R1, R2, R1&R2, I1, I2, Other",,,TRUE,Sequencing,,,
 Read1,Read 1 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Level 1,,,
 Read2,Read 2 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Level 1,,,
 cDNA,"Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase",,"cDNA Offset, cDNA Length",,FALSE,Sequencing,,,
@@ -1070,4 +1070,4 @@ Days to Vital Status Reference,Number of days between the date used for index an
 Precancer Case,Yes/No indicator to designate the participant for whom precancerous lesion(s) was identified (premalignancy only).,"Yes - Precancer Case, No, Not Reported, unknown",,,TRUE,Patient,,,
 Yes - Precancer Case,Indicates that the participant is a precancer case,,"Precancerous Condition Type, Days to Precancer Case Designation, WHO Precursor Lesion Code",,FALSE,Patient,,,
 Days to Precancer Case Designation,Number of days between the date used for index and the reference date for designation of precancer status.,,,,FALSE,Patient,,,int
-WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$
+WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$