From fe4aacfb45c1b9c5096905cc57eb92b5e32f5b26 Mon Sep 17 00:00:00 2001 From: aditigopalan <63365451+aditigopalan@users.noreply.github.com> Date: Wed, 15 Jan 2025 10:11:14 -0500 Subject: [PATCH 1/2] Update HTAN.model.csv --- HTAN.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index 951ebe17..ae41a5e2 100644 --- a/HTAN.model.csv +++ b/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 1 (I1), Index Reads 2 (I2), 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]$ \ No newline at end of file From 18af91def832e095bb54501e819af9a321bf72f5 Mon Sep 17 00:00:00 2001 From: Aditi <63365451+aditigopalan@users.noreply.github.com> Date: Wed, 15 Jan 2025 10:29:41 -0500 Subject: [PATCH 2/2] Update ci-lint-validate-convert.yml --- .github/workflows/ci-lint-validate-convert.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/ci-lint-validate-convert.yml b/.github/workflows/ci-lint-validate-convert.yml index 5eb477f8..fcb0d643 100644 --- a/.github/workflows/ci-lint-validate-convert.yml +++ b/.github/workflows/ci-lint-validate-convert.yml @@ -108,6 +108,7 @@ jobs: uses: actions/checkout@v2 with: fetch-depth: 0 + ref: main - name: Fetch latest changes run: | @@ -176,3 +177,8 @@ jobs: branch: update-attribute-table title: "Update HTAN.dependencies.csv" body: "This PR updates HTAN.dependencies.csv with the latest attribute table." + base: main + committer: GitHub + author: aditigopalan + signoff: false + delete-branch: true