From 3920d9ddb46602bb9a6256c5ed417f3236f77c47 Mon Sep 17 00:00:00 2001 From: yumisims Date: Mon, 9 Oct 2023 16:15:08 +0100 Subject: [PATCH] add gx database to github test --- .github/workflows/ci.yml | 2 +- assets/github_testing/test.yaml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6639f8b..9506ae9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,7 +46,7 @@ jobs: wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxs -O FCS_gx/test-only.gxs wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.meta.jsonl -O FCS_gx/test-only.meta.jsonl wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.blast_div.tsv.gz -O FCS_gx/test-only.blast_div.tsv.gz - pwd + - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters diff --git a/assets/github_testing/test.yaml b/assets/github_testing/test.yaml index c92eedc..ea4c85a 100755 --- a/assets/github_testing/test.yaml +++ b/assets/github_testing/test.yaml @@ -13,6 +13,7 @@ nt_kraken_db_path: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/n ncbi_taxonomy_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/ ncbi_rankedlineage_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/rankedlineage.dmp busco_lineages_folder: /lustre/scratch123/tol/resources/busco/data/v5/2021-03-14/lineages +fcs_gx_database_path: /home/runner/work/ascc/ascc/FCS_gx/ seqkit: sliding: 6000 window: 100000