From 7fecab2f516792f19db70f0c526005f81e04cea5 Mon Sep 17 00:00:00 2001 From: m-jahn Date: Fri, 12 Dec 2025 09:04:03 +0100 Subject: [PATCH] fix: paths to run wf in main dir --- .github/workflows/deploy_apptainer.yml | 2 +- config/config.yml | 2 +- config/samples.tsv | 2 ++ 3 files changed, 4 insertions(+), 2 deletions(-) create mode 100644 config/samples.tsv diff --git a/.github/workflows/deploy_apptainer.yml b/.github/workflows/deploy_apptainer.yml index ecb016c..e7b8081 100644 --- a/.github/workflows/deploy_apptainer.yml +++ b/.github/workflows/deploy_apptainer.yml @@ -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" diff --git a/config/config.yml b/config/config.yml index db6e714..39cd8fa 100644 --- a/config/config.yml +++ b/config/config.yml @@ -1,4 +1,4 @@ -samplesheet: ".test/config/samples.tsv" +samplesheet: "config/samples.tsv" get_genome: database: "ncbi" diff --git a/config/samples.tsv b/config/samples.tsv new file mode 100644 index 0000000..7531e2a --- /dev/null +++ b/config/samples.tsv @@ -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