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fix: paths to run wf in main dir #27

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Merged
m-jahn merged 1 commit into from
Dec 12, 2025
Merged

fix: paths to run wf in main dir #27

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2 changes: 1 addition & 1 deletion .github/workflows/deploy_apptainer.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ jobs:
- name: create dockerfile
uses: snakemake/snakemake-github-action@v2
with:
directory: .test
directory: .
snakefile: workflow/Snakefile
install-apptainer: true
args: "--cores 1"
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2 changes: 1 addition & 1 deletion config/config.yml
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@@ -1,4 +1,4 @@
samplesheet: ".test/config/samples.tsv"
samplesheet: "config/samples.tsv"

get_genome:
database: "ncbi"
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2 changes: 2 additions & 0 deletions config/samples.tsv
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@@ -0,0 +1,2 @@
sample description read1 read2
spya20 S. pyogenes A20 .test/data/spy_A20_R1.fastq.gz .test/data/spy_A20_R2.fastq.gz
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