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Wait for all accessioning steps before loading accessions #202

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Apr 11, 2024
Merged

Wait for all accessioning steps before loading accessions #202

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6 changes: 3 additions & 3 deletions eva_submission/nextflow/accession_and_load.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,7 @@ workflow {
sort_and_compress_vcf(accession_vcf.out.accession_done)
csi_vcfs = sort_and_compress_vcf.out.compressed_vcf
accessioned_files_to_rm = accession_vcf.out.accessioned_filenames
all_accession_complete = sort_and_compress_vcf.out.compressed_vcf
all_accession_complete = sort_and_compress_vcf.out.compressed_vcf.collect()
}
csi_index_vcf(csi_vcfs)
copy_to_ftp(csi_index_vcf.out.csi_indexed_vcf.toList(), accessioned_files_to_rm.toList())
Expand Down Expand Up @@ -155,8 +155,8 @@ workflow {
.splitCsv(header:true)
.map{row -> tuple(file(row.vcf_file), row.db_name)}
// the vcf_files_dbname give the link between input file and all_accession_complete is to ensure the
// accessioning has been completed
if (all_accession_complete){
// accessioning has been completed for all input files
if (all_accession_complete) {
import_accession(vcf_files_dbname, all_accession_complete, load_variants_vcf.out.variant_load_complete)
}
}
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