From 8d846457862d3ea7adbe4f2c66a2cd17cf8062c6 Mon Sep 17 00:00:00 2001 From: taylorpaisie Date: Wed, 2 Oct 2024 13:22:10 -0400 Subject: [PATCH] updating seqfu tests in dockerfile --- seqfu/1.20.3/Dockerfile | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/seqfu/1.20.3/Dockerfile b/seqfu/1.20.3/Dockerfile index 8fcf217c0..64338ca30 100644 --- a/seqfu/1.20.3/Dockerfile +++ b/seqfu/1.20.3/Dockerfile @@ -71,8 +71,12 @@ WORKDIR /data RUN ls -l /usr/local/bin && \ seqfu --version && seqfu --help +# Running seqfu on test staph-b test dataset +FROM app AS test + RUN mkdir tests && cd tests && \ wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \ wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \ - seqfu check SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz && \ - seqfu count -f SRR13957123_1.fastq.gz -r SRR13957123_2.fastq.gz + seqfu check SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz > seqfu_check_test.txt && \ + seqfu count -f SRR13957123_1.fastq.gz -r SRR13957123_2.fastq.gz > seqfu_count_test.txt +