use subset reference genome as test data

.github/workflows/test_action.yml

@@ -1,8 +1,7 @@
 name: hadge test workflow
-on: 
-  push
+on: push
 jobs:
-  test: 
+  test:
     name: Run pipeline with test data
     runs-on: ubuntu-latest
     steps:
@@ -15,9 +14,7 @@ jobs:
         with:
           singularity-version: 3.8.3
       - name: Download test dataset
-        run:  bash ${GITHUB_WORKSPACE}/test_data/download_data.sh
+        run: bash ${GITHUB_WORKSPACE}/test_data/download_data.sh
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,conda_singularity
-
-      

test.config

@@ -10,16 +10,16 @@ params {
   bam = "$projectDir/test_data/jurkat_293t_downsampled_n500_full_bam.bam"
   bai = "$projectDir/test_data/jurkat_293t_downsampled_n500_full_bam.bam.bai"
   barcodes = "$projectDir/test_data/barcodes.tsv"
-  fasta = "$projectDir/test_data/refdata-cellranger-hg19-3.0.0/fasta/genome.fa"
-  fasta_index = "$projectDir/test_data/refdata-cellranger-hg19-3.0.0/fasta/genome.fa.fai"
+  fasta = "$projectDir/test_data/refdata-cellranger-hg19-3.0.0/fasta/genome_chr1.fa"
+  fasta_index = "$projectDir/test_data/refdata-cellranger-hg19-3.0.0/fasta/genome_chr1.fa.fai"
   nsample = 2
   common_variants_scSplit = "$projectDir/test_data/common_variants_hg19_list.vcf"
   common_variants_souporcell =  "$projectDir/test_data/common_variants_hg19.vcf"
   common_variants_freemuxlet = "$projectDir/test_data/jurkat_293t_exons_only.vcf.withAF.vcf.gz"
   common_variants_cellsnp  = "$projectDir/test_data/genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz"
   vcf_donor = "$projectDir/test_data/jurkat_293t_exons_only.vcf.withAF.vcf"
   // Call freebayes on chr 1 and chr 2 only to speed up run time
-  region = "1;2"
+  region = "1"
   // donor genotype file provided by popscle doesnt work on souporcell
   use_known_genotype = "False"
   ignore = "True"

test_data/download_data.sh

@@ -12,10 +12,14 @@ unzip final_res.zip
 rm final_res.zip
 mv final_res/jurkat_293t_demuxlet.best .
 rm -rf final_res
+# To run souporcell, unzip VCF file
+gzip -dk jurkat_293t_exons_only.vcf.withAF.vcf.gz
+
+# Download subset reference genome
+wget --no-check-certificate https://figshare.com/ndownloader/files/43102459 -O genome_chr1.fa
+wget --no-check-certificate https://figshare.com/ndownloader/files/43102453 -O genome_chr1.fa.fai
+# source: http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-hg19-3.0.0.tar.gz
 
-# Download reference genome
-wget http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-hg19-3.0.0.tar.gz
-tar -xzvf refdata-cellranger-hg19-3.0.0.tar.gz
 # Download common variants
 wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1lw4T6d7uXsm9dt39ZtEwpuB2VTY3wK1y' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1lw4T6d7uXsm9dt39ZtEwpuB2VTY3wK1y" -O common_variants_hg19.vcf && rm -rf /tmp/cookies.txt
 wget https://master.dl.sourceforge.net/project/cellsnp/SNPlist/genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz
@@ -36,5 +40,3 @@ unzip rna.zip
 rm hto.zip
 rm rna.zip
 
-# To run souporcell, unzip VCF file
-gzip -dk test_data/jurkat_293t_exons_only.vcf.withAF.vcf.gz