From fa462f7133968b99596073aab0a90136c2b3d296 Mon Sep 17 00:00:00 2001 From: Lee Katz Date: Thu, 29 Jul 2021 14:44:39 -0400 Subject: [PATCH] Kraken1 unit test (#21) * with fixed taxonomy, unit test kraken1 * shortened the minimizer length to 9 * kraken1 query * m * adding a query is $query statement Co-authored-by: Lee Katz - Aspen --- ...en1.yml.bak => unit-testing.Listeria.Kraken1.yml} | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) rename .github/workflows/{unit-testing.Listeria.Kraken1.yml.bak => unit-testing.Listeria.Kraken1.yml} (89%) diff --git a/.github/workflows/unit-testing.Listeria.Kraken1.yml.bak b/.github/workflows/unit-testing.Listeria.Kraken1.yml similarity index 89% rename from .github/workflows/unit-testing.Listeria.Kraken1.yml.bak rename to .github/workflows/unit-testing.Listeria.Kraken1.yml index 9c5d6fc..dbb06cc 100644 --- a/.github/workflows/unit-testing.Listeria.Kraken1.yml.bak +++ b/.github/workflows/unit-testing.Listeria.Kraken1.yml @@ -81,16 +81,24 @@ jobs: cp -vf jellyfish1 $a_bin/jellyfish which kraken-build mkdir -pv kraken - cp -rv Kalamari/src/taxonomy_v3.9 kraken/taxonomy + cp -rv Kalamari/src/taxonomy kraken/taxonomy find ${{ env.OUTDIR }} -name '*.fasta' -exec kraken-build --db kraken --add-to-library {} \; tree kraken # Some super debugging here with -x sed -i.bak 's/set -e/set -e; set -x/' $a_bin/build_kraken_db.sh grep -v '^#' -m 20 -C 2 $a_bin/build_kraken_db.sh echo ".....Building the database....." - kraken-build --rebuild --db kraken --threads 2 --work-on-disk + kraken-build --minimizer-len 9 --rebuild --db kraken --threads 2 --work-on-disk + - name: Kraken1 query + run: | + QUERY=$(find ${{ env.OUTDIR }} -name '*.fasta' | head -n 1) + echo "Query is $QUERY" + kraken --db kraken -output kraken.raw --fasta-input $QUERY - name: Kraken1 view results run: | tree kraken ls -lhSR kraken + echo + head kraken.raw +