Small formatting changes

DI-435/find_vcfs_to_merge.py

@@ -126,7 +126,6 @@ def find_data(file_name, project_id):
             describe=True
         )
     )
-
     return files
 
 
@@ -265,7 +264,6 @@ def get_qc_files(b38_projects, start=None, end=None):
                 }
                 missing_projects.append(missing_project_info)
             all_qc_files.append(qc_file)
-
     print(len(all_qc_files), "QC files found in total")
     print(len(b37_projects), "b37 projects found in total")
 
@@ -449,6 +447,7 @@ def get_sample_types(projects):
                 non_validation_samples_in_run.append(
                     instrument_id + "-" + sample_id
                 )
+
             else:
                 all_validation_samples.append(
                     {

DI-435/merge_VCF_AF.sh

@@ -81,7 +81,6 @@ while IFS=$'\t' read -r _ field2 field3; do
 
 done < "$input_file"
 
-# Download VCFs in parallel
 echo "Downloading files"
 echo "${project_files[@]}" | tr ' ' '\n' | xargs -n 1 -P "${num_proc}" -I {} dx download --no-progress "{}"
 
@@ -97,7 +96,7 @@ find . -maxdepth 1 -name '*.vcf.gz' -print0 | xargs -0 -P "${num_proc}" -I{} bcf
 # Indexing normalised VCFs
 echo "Indexing normalised VCFs"
 cd norm || exit
-find . -maxdepth 1 -name '*.vcf.gz' -print0 | xargs -0 -P "${num_proc}" -I{} bcftools index -f "{}"
+echo *vcf.gz | tr ' ' '\n' | xargs -n 1 -P "${num_proc}" -I {} bcftools index -f "{}"
 
 # Merging normalised VCFs
 echo "Collating normalised VCFs"