diff --git a/.gitattributes b/.gitattributes index d13338c..e69de29 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,2 +0,0 @@ -test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa filter=lfs diff=lfs merge=lfs -text -test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa filter=lfs diff=lfs merge=lfs -text diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index c43439f..32d1680 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -12,8 +12,6 @@ jobs: steps: - name: Checkout uses: actions/checkout@v4 - with: - lfs: 'true' - name: Set up JDK 17 uses: actions/setup-java@v2 diff --git a/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa b/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa deleted file mode 100644 index 9df5a63..0000000 --- a/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:69d1b92c83b9390b26e34986e92afb24680cdc2b44866a0cb356b2087f5841c1 -size 253105752 diff --git a/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz b/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz new file mode 100644 index 0000000..fcdf047 Binary files /dev/null and b/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz differ diff --git a/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa b/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa deleted file mode 100644 index c642012..0000000 --- a/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:5890d81dbfcfdda99eac4bfe7a6378b38bed583c101ede6ee0a02b2ec5b51961 -size 246230144 diff --git a/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz b/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz new file mode 100644 index 0000000..4e85f76 Binary files /dev/null and b/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz differ diff --git a/tests/modules/hostRemoval/hostRemoval.nf.test b/tests/modules/hostRemoval/hostRemoval.nf.test index c929856..012254d 100644 --- a/tests/modules/hostRemoval/hostRemoval.nf.test +++ b/tests/modules/hostRemoval/hostRemoval.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { projName = "testHR" } hostRemoval { - host = ["${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa"] + host = ["${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz"] cpus = 4 } @@ -45,7 +45,7 @@ nextflow_workflow { projName = "testHR" } hostRemoval { - host = "${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa" + host = "${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz" cpus = 4 } @@ -77,7 +77,7 @@ nextflow_workflow { projName = "testHR" } hostRemoval { - host = ["${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa", "${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa"] + host = ["${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz", "${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz"] cpus = 4 } } @@ -109,7 +109,7 @@ nextflow_workflow { projName = "testHR" } hostRemoval { - host = ["${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa","${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa"] + host = ["${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz","${projectDir}/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz"] cpus = 4 } }