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Merge pull request #72 from genomic-medicine-sweden/develop
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chore: dev to master
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jonca79 authored Mar 13, 2024
2 parents 5fc7ffb + 60c9c46 commit 99a8f35
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Showing 23 changed files with 1,920 additions and 233 deletions.
10 changes: 5 additions & 5 deletions .github/workflows/integration1.yaml
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Expand Up @@ -16,11 +16,6 @@ jobs:
name: integration small data set singularity
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v2
with:
Expand All @@ -34,6 +29,11 @@ jobs:
- name: Set strict channels
run: |
conda config --set channel_priority strict
- uses: actions/checkout@v2
- name: Set up Python 3.8
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: Install requirements.txt
run: |
pip install -r requirements.txt
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3 changes: 0 additions & 3 deletions .github/workflows/lint.yaml
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Expand Up @@ -25,9 +25,6 @@ jobs:
uses: actions/setup-python@v3
with:
python-version: 3.8
- name: Add conda to system path
run: |
echo $CONDA/bin >> $GITHUB_PATH
- name: Install requirements.txt
run: |
pip install -r requirements.txt
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10 changes: 0 additions & 10 deletions .github/workflows/pycodestyl.yaml
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Expand Up @@ -25,16 +25,6 @@ jobs:
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: Add conda to system path
run: |
echo $CONDA/bin >> $GITHUB_PATH
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v2
with:
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: my-env
use-mamba: true
- name: Install requirements.txt
run: |
pip install -r requirements.txt
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5 changes: 4 additions & 1 deletion .tests/integration/config/config.yaml
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Expand Up @@ -78,5 +78,8 @@ reference:
fai: "reference/hg19.chr6.fasta.fai"
dbsnp: "reference/dbsnp_138.sub.vcf.gz"

get_clinical_recommendations:
analysed_variants: "reference/analysed_variants.txt"

generate_pgx_report:
report_template: "reference/report_template.txt"
html_template: "reference/html_template.html"
6 changes: 6 additions & 0 deletions .tests/integration/reference/analysed_variants.txt
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@@ -0,0 +1,6 @@
Analyserade varianter:
DPYD= rs3918290: c.1905+1G>A, splice defect; rs72549303: c.1898delC, p.P633Qfs; rs72549309: c.299delTCAT; rs1801266: c.703C>T, p.R235W; rs1801268: c.2983G>T, p.V995F; rs78060119: c.1156G>T, p.E386X; rs55886062: c.1679T>G, p.I560S; rs75017182: c.1129-5923C>G; rs67376798: c.2846A>T, p.D949V; rs115232898: c.557A>G, p.Y186C. Dessa varianter motsvarar allelerna *2A, *3, *7, *8, *10, *12, *13, HapB3.

TPMT= rs1800462: c.238G>C, p.A80P; rs1142345: c.719A>G, p.Y240C; rs1800460: c.460G>A, p.A154T; rs1800584: c.626-1G>A. Dessa varianter motsvarar allelerna *2, *3A, *3B, *3C, *4.

NUDT15= rs147390019: c.7974G>A, p.R139H; rs186364861: c.52G>A, p.V18I; rs116855232: c. 7973C>T, p.R139C; rs746071566: c.50delGAGTCG, p.del17_18GV / c.55_56insGAGTCG, p.V18_V19insGV. Dessa varianter motsvarar allelerna *2, *3, *4, *5, *6, *9.
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