refactor: change test files location

CCBR · Aug 15, 2024 · 6dc37fa · 6dc37fa
1 parent 750dbf5
commit 6dc37fa
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Showing 9 changed files with 20 additions and 20 deletions.
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -23,63 +23,63 @@ jobs:
         run: |
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/WES_NC_N_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_N_1_sub.R2.fastq.gz \
-          /opt2/.tests/WES_NC_T_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_T_1_sub.R2.fastq.gz \
+          /opt2/tests/data/WES_NC_N_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_N_1_sub.R2.fastq.gz \
+          /opt2/tests/data/WES_NC_T_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_T_1_sub.R2.fastq.gz \
           --output /opt2/output_tn_fqs --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \
-          --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init
+          --pairs /opt2/tests/data/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init
 
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/WES_NC_N_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_N_1_sub.R2.fastq.gz \
-          /opt2/.tests/WES_NC_T_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_T_1_sub.R2.fastq.gz \
+          /opt2/tests/data/WES_NC_N_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_N_1_sub.R2.fastq.gz \
+          /opt2/tests/data/WES_NC_T_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_T_1_sub.R2.fastq.gz \
           --output /opt2/output_tn_fqs --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \
-          --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun
+          --pairs /opt2/tests/data/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun
 
       - name: Tumor-only FastQ Dry Run
         run: |
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/WES_NC_N_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_N_1_sub.R2.fastq.gz \
-          /opt2/.tests/WES_NC_T_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_T_1_sub.R2.fastq.gz \
+          /opt2/tests/data/WES_NC_N_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_N_1_sub.R2.fastq.gz \
+          /opt2/tests/data/WES_NC_T_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_T_1_sub.R2.fastq.gz \
           --output /opt2/output_tonly_fqs --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \
           --genome hg38 --mode local --ffpe --runmode init
 
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/WES_NC_N_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_N_1_sub.R2.fastq.gz \
-          /opt2/.tests/WES_NC_T_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_T_1_sub.R2.fastq.gz \
+          /opt2/tests/data/WES_NC_N_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_N_1_sub.R2.fastq.gz \
+          /opt2/tests/data/WES_NC_T_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_T_1_sub.R2.fastq.gz \
           --output /opt2/output_tonly_fqs --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \
           --genome hg38 --mode local --ffpe --runmode dryrun
 
       - name: Tumor-normal BAM Dry Run
         run: |
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/WES_NC_N_1_sub.bam \
-          /opt2/.tests/WES_NC_T_1_sub.bam  \
+          /opt2/tests/data/WES_NC_N_1_sub.bam \
+          /opt2/tests/data/WES_NC_T_1_sub.bam  \
           --output /opt2/output_tn_bams --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \
-          --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init
+          --pairs /opt2/tests/data/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init
 
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/WES_NC_N_1_sub.bam \
-          /opt2/.tests/WES_NC_T_1_sub.bam  \
+          /opt2/tests/data/WES_NC_N_1_sub.bam \
+          /opt2/tests/data/WES_NC_T_1_sub.bam  \
           --output /opt2/output_tn_bams --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \
-          --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun
+          --pairs /opt2/tests/data/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun
 
       - name: Tumor-only BAM Dry Run
         run: |
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/WES_NC_N_1_sub.bam \
-          /opt2/.tests/WES_NC_T_1_sub.bam  \
+          /opt2/tests/data/WES_NC_N_1_sub.bam \
+          /opt2/tests/data/WES_NC_T_1_sub.bam  \
           --output /opt2/output_tonly_bams --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \
           --genome hg38 --mode local --ffpe --runmode init
 
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/WES_NC_N_1_sub.bam \
-          /opt2/.tests/WES_NC_T_1_sub.bam  \
+          /opt2/tests/data/WES_NC_N_1_sub.bam \
+          /opt2/tests/data/WES_NC_T_1_sub.bam  \
           --output /opt2/output_tonly_bams --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \
           --genome hg38 --mode local --ffpe --runmode dryrun
 

diff --git a/.tests/README.md → tests/data/README.md b/.tests/README.md → tests/data/README.md
diff --git a/.tests/WES_NC_N_1_sub.R1.fastq.gz → tests/data/WES_NC_N_1_sub.R1.fastq.gz b/.tests/WES_NC_N_1_sub.R1.fastq.gz → tests/data/WES_NC_N_1_sub.R1.fastq.gz
diff --git a/.tests/WES_NC_N_1_sub.R2.fastq.gz → tests/data/WES_NC_N_1_sub.R2.fastq.gz b/.tests/WES_NC_N_1_sub.R2.fastq.gz → tests/data/WES_NC_N_1_sub.R2.fastq.gz
diff --git a/.tests/WES_NC_N_1_sub.bam → tests/data/WES_NC_N_1_sub.bam b/.tests/WES_NC_N_1_sub.bam → tests/data/WES_NC_N_1_sub.bam
diff --git a/.tests/WES_NC_T_1_sub.R1.fastq.gz → tests/data/WES_NC_T_1_sub.R1.fastq.gz b/.tests/WES_NC_T_1_sub.R1.fastq.gz → tests/data/WES_NC_T_1_sub.R1.fastq.gz
diff --git a/.tests/WES_NC_T_1_sub.R2.fastq.gz → tests/data/WES_NC_T_1_sub.R2.fastq.gz b/.tests/WES_NC_T_1_sub.R2.fastq.gz → tests/data/WES_NC_T_1_sub.R2.fastq.gz
diff --git a/.tests/WES_NC_T_1_sub.bam → tests/data/WES_NC_T_1_sub.bam b/.tests/WES_NC_T_1_sub.bam → tests/data/WES_NC_T_1_sub.bam
diff --git a/.tests/pairs.tsv → tests/data/pairs.tsv b/.tests/pairs.tsv → tests/data/pairs.tsv