Merge pull request #11 from RoanKanninga/master

fixing dependency

protocols_compute/run_asterix.sh

@@ -25,7 +25,9 @@ mkdir -p "${cnvOutDir}.target"
 
 bcftools query -l "${imputationOutputDir}/target/range_"*"_CYP2C9.annotated.bar.target.vcf.gz" > "${cnvOutDir}.target_sample_list.txt"
 head -n 1 "${cnvOutDir}.combined_cnv_status.txt" > "${cnvOutDir}.target/cnv_status.txt"
-awk 'NR==FNR { ids[$1]; next } $1 in ids' "${cnvOutDir}.target_sample_list.txt" "${cnvOutDir}.combined_cnv_status.txt" >> "${cnvOutDir}.target/cnv_status.txt"
+awk 'NR==FNR { ids[$1]; next } $1 in ids' \
+"${cnvOutDir}.target_sample_list.txt" \
+"${cnvOutDir}.combined_cnv_status.txt" >> "${cnvOutDir}.target/cnv_status.txt"
 
 mkdir -p "${asterixOutputDir}/star_alleles/"
 mkdir -p "${asterixOutputDir}/pheno_out/"
@@ -40,4 +42,4 @@ java -jar "${EBROOTASTERIX}/asterix-0.10-SNAPSHOT.jar" \
         -pheno_out_dir          "${asterixOutputDir}/pheno_out/" \
         -sample_matrix_out      "${asterixOutputDir}/sample_matrix.csv" \
         -hl7_output_file        "${asterixOutputDir}/hl7_llnext_prelim.json" \
-        -hl7_input_file         "${asterixDefaultJson}"
+        -hl7_input_file         "${asterixDefaultJson}"

workflow_pgx.csv

@@ -4,7 +4,7 @@ s02_create_final_report,protocols_compute/create_final_report.sh,s01_execute_pre
 s03_variant_filtering,protocols_compute/variant_filtering.sh,s01_execute_preprocessing
 s04_concatenate_chromosomes,protocols_compute/concatenate_chromosomes.sh,s03_variant_filtering
 s05_sample_filtering,protocols_compute/sample_filtering.sh,s04_concatenate_chromosomes
-s06_stage_intensities,protocols_compute/stage_intensities.sh,s05_sample_filtering
+s06_stage_intensities,protocols_compute/stage_intensities.sh,s05_sample_filtering;s02_create_final_report
 s07_cnv_calling,protocols_compute/cnv_calling.sh,s06_stage_intensities
 s08_cnv_genotype_call_integration,protocols_compute/cnv_genotype_call_integration.sh,s07_cnv_calling
 s09_imputation_pipeline,protocols_compute/imputation_pipeline.sh,s08_cnv_genotype_call_integration