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Merge b77eb9b into 1ca783a
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@jemten
jemten committed Apr 26, 2021
2 parents 1ca783a + b77eb9b commit d8dfd91
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Showing 37 changed files with 88 additions and 14 deletions.
1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/1000g_indels.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_1000g_indels {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/1000g_omni.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_1000g_omni {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/1000g_sites.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_1000g_sites {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/1000g_snps.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_1000g_snps {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Cadd_offline_annotations.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_cadd_offline_annotations {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Cadd_to_vcf_header.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_cadd_to_vcf_header {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Cadd_whole_genome_snvs.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_cadd_whole_genome_snvs {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Chromograph_cytoband.pm
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Expand Up @@ -147,6 +147,7 @@ sub download_chromograph_cytoband {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Clinvar.pm
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Expand Up @@ -152,6 +152,7 @@ sub download_clinvar {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Ctat_resource_lib.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_ctat_resource_lib {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Dbnsfp.pm
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Expand Up @@ -158,6 +158,7 @@ sub download_dbnsfp {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Dbsnp.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_dbsnp {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Delly_exclude.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_delly_exclude {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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20 changes: 10 additions & 10 deletions lib/MIP/Recipes/Download/Expansionhunter.pm
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Expand Up @@ -144,16 +144,16 @@ sub download_expansionhunter {
## Creates recipe directories (info & data & script), recipe script filenames and writes sbatch header
my ( $recipe_file_path, $recipe_info_path ) = setup_script(
{
active_parameter_href => $active_parameter_href,
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
outscript_dir => $reference_dir,
process_time => $recipe{time},
,
active_parameter_href => $active_parameter_href,
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
outscript_dir => $reference_dir,
process_time => $recipe{time},
recipe_data_directory_path => $active_parameter_href->{reference_dir},
recipe_directory => $recipe_name . $UNDERSCORE . $reference_version,
recipe_name => $recipe_name,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Gatk_mitochondrial_ref.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_gatk_mitochondrial_ref {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Genbank_haplogroup.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_genbank_haplogroup {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Gencode_annotation.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_gencode_annotation {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Gencode_transcript.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_gencode_transcript {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Genomic_superdups.pm
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Expand Up @@ -156,6 +156,7 @@ sub download_genomic_superdups {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Giab.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_giab {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Gnomad.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_gnomad {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Gnomad_pli_per_gene.pm
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Expand Up @@ -154,6 +154,7 @@ sub download_gnomad_pli_per_gene {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Hapmap.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_hapmap {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Human_reference.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_human_reference {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $active_parameter_href->{reference_dir},
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Manta_call_regions.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_manta_call_regions {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Mills_and_1000g_indels.pm
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Expand Up @@ -150,6 +150,7 @@ sub download_mills_and_1000g_indels {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Pfam.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_pfam {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Rank_model.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_rank_model {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Reduced_penetrance.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_reduced_penetrance {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Scout_exons.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_scout_exons {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Sv_vcfanno_config.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_sv_vcfanno_config {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Svrank_model.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_svrank_model {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Vcf2cytosure_blacklist_regions.pm
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Expand Up @@ -147,6 +147,7 @@ sub download_vcf2cytosure_blacklist_regions {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Vcfanno_config.pm
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Expand Up @@ -149,6 +149,7 @@ sub download_vcfanno_config {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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1 change: 1 addition & 0 deletions lib/MIP/Recipes/Download/Vcfanno_functions.pm
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Expand Up @@ -148,6 +148,7 @@ sub download_vcfanno_functions {
core_number => $recipe{core_number},
directory_id => q{mip_download},
filehandle => $filehandle,
info_file_id => $genome_version . $UNDERSCORE . $reference_version,
job_id_href => $job_id_href,
memory_allocation => $recipe{memory},
outdata_dir => $reference_dir,
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