removing files from LFS

LANL-Bioinformatics · Dec 10, 2024 · 76c285d · 76c285d
1 parent 167adfc
commit 76c285d
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Showing 7 changed files with 4 additions and 14 deletions.
diff --git 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
@@ -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
diff --git a/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz b/test_data/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz
diff --git a/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa b/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa
diff --git a/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz b/test_data/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz
diff --git 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
                 }
             }
Original file line number	Diff line number	Diff line change
		@@ -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