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Krferrier main #109

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merged 3 commits into from
Dec 20, 2024
Merged

Krferrier main #109

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12e470c
emit step 1 logs in regenie.nf
krferrier Dec 18, 2024
b60314c
report step 1 logs in single_variant_tests.nf
krferrier Dec 18, 2024
1c2e440
Update java version for tests
seppinho Dec 20, 2024
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6 changes: 3 additions & 3 deletions .github/workflows/ci-tests.yml
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Expand Up @@ -15,10 +15,10 @@ jobs:
- name: Checkout
uses: actions/checkout@v2

- name: Set up JDK 11
- name: Set up JDK 17
uses: actions/setup-java@v2
with:
java-version: '11'
java-version: '17'
distribution: 'adopt'

- name: Setup Nextflow
Expand All @@ -28,7 +28,7 @@ jobs:

- name: Install nf-test
run: |
wget -qO- get.nf-test.com | bash -s 0.9.0-rc2
wget -qO- get.nf-test.com | bash
sudo mv nf-test /usr/local/bin/

- name: Set up Docker Buildx
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4 changes: 3 additions & 1 deletion workflows/regenie/regenie.nf
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Expand Up @@ -61,7 +61,9 @@ workflow REGENIE {
regenie_step2_out = REGENIE_STEP2_GENE_TESTS.out.regenie_step2_by_phenotype
regenie_step2_parsed_logs = REGENIE_STEP2_GENE_TESTS.out.regenie_step2_parsed_logs
}
emit:
emit:
regenie_step1_out_ch
regenie_step1_parsed_logs_ch
regenie_step2_out
regenie_step2_parsed_logs
}
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5 changes: 3 additions & 2 deletions workflows/single_variant_tests.nf
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Expand Up @@ -88,8 +88,9 @@ workflow SINGLE_VARIANT_TESTS {

regenie_step2_out = REGENIE.out.regenie_step2_out
regenie_step2_parsed_logs = REGENIE.out.regenie_step2_parsed_logs
//TODO return logs from step1
regenie_step1_parsed_logs_ch = Channel.empty()
//return logs from step1
regenie_step1_parsed_logs_ch = REGENIE.out.regenie_step1_parsed_logs_ch
regenie_step1_out_ch = REGENIE.out.regenie_step1_out_ch

if (!run_interaction_tests) {

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