🔧 update test bams and references files

papaemmelab · Jan 22, 2024 · 4e041a1 · 4e041a1
1 parent 5ddd416
commit 4e041a1
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Showing 25 changed files with 16 additions and 335,180 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -24,8 +24,8 @@ jobs:
         run: |
           nextflow run main.nf -profile cloud \
             --tumor TEST \
-            --tumorBam tests/data/test.bam \
-            --refGenome tests/data/test_reference.fasta \
+            --tumorBam tests/data/tumor.bam \
+            --refGenome tests/data/reference.fasta \
             --outdir /app/results
       - name: Check result
         run: |

diff --git a/tests/README b/tests/README
@@ -2,20 +2,27 @@
 
 ```bash
 # Build test BAM file
-SAMPLE_ID=IID_H208150_T01_01_WG01
-ORIGINAL_BAM=`isabl get-bams $SAMPLE_ID`
-TEST_BAM=test_sample.bam
+TUMOR_ID=IID_H195923_T01_01_WG01
+ORIGINAL_TUMOR_BAM=`isabl get-bams $TUMOR_ID`
+TEST_TUMOR_BAM=tumor.bam
+
+NORMAL_ID=IID_H195923_N01_01_WG01
+ORIGINAL_NORMAL_BAM=`isabl get-bams $NORMAL_ID`
+TEST_NORMAL_BAM=normal.bam
 
 REGION1=1:100000-200000
 REGION2=2:300000-400000
 
-samtools view -b -o $TEST_BAM $ORIGINAL_BAM $REGION1 $REGION2
-samtools index $TEST_BAM
+samtools view -b -o $TEST_TUMOR_BAM $ORIGINAL_TUMOR_BAM $REGION1 $REGION2
+samtools view -b -o $TEST_NORMAL_BAM $ORIGINAL_NORMAL_BAM $REGION1 $REGION2
+
+samtools index $TEST_TUMOR_BAM
+samtools index $TEST_NORMAL_BAM
 
 # Build test Reference file
 ORIGINAL_REF=`isabl get-reference GRCh37`
-LOCAL_REF=reference.fasta
-TEST_REF=test_reference.fasta
+LOCAL_REF=gr37.fasta
+TEST_REF=reference.fasta
 
 cp $ORIGINAL_REF $LOCAL_REF
 cp $ORIGINAL_REF.fai $LOCAL_REF.fai

diff --git a/tests/data/data/normal.bam b/tests/data/data/normal.bam
diff --git a/tests/data/data/normal.bam.bai b/tests/data/data/normal.bam.bai
diff --git a/tests/data/test_reference.fasta → tests/data/data/reference.fasta b/tests/data/test_reference.fasta → tests/data/data/reference.fasta
diff --git a/tests/data/test_reference.fasta.fai → tests/data/data/reference.fasta.fai b/tests/data/test_reference.fasta.fai → tests/data/data/reference.fasta.fai
diff --git a/tests/data/data/tumor.bam b/tests/data/data/tumor.bam
diff --git a/tests/data/data/tumor.bam.bai b/tests/data/data/tumor.bam.bai
diff --git a/tests/data/test.bam b/tests/data/test.bam
diff --git a/tests/data/test.bam.bai b/tests/data/test.bam.bai
diff --git a/tests/dataq/references/reference.access.bed b/tests/dataq/references/reference.access.bed
diff --git a/tests/dataq/references/reference.cnn b/tests/dataq/references/reference.cnn
diff --git a/tests/dataq/references/reference.fasta b/tests/dataq/references/reference.fasta
diff --git a/tests/dataq/references/reference.fasta.amb b/tests/dataq/references/reference.fasta.amb
diff --git a/tests/dataq/references/reference.fasta.ann b/tests/dataq/references/reference.fasta.ann
diff --git a/tests/dataq/references/reference.fasta.bwt b/tests/dataq/references/reference.fasta.bwt
diff --git a/tests/dataq/references/reference.fasta.fai b/tests/dataq/references/reference.fasta.fai
diff --git a/tests/dataq/references/reference.fasta.pac b/tests/dataq/references/reference.fasta.pac
diff --git a/tests/dataq/references/reference.fasta.sa b/tests/dataq/references/reference.fasta.sa