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skip downstream assets build for NT and NR #324

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Feb 6, 2024
Merged

skip downstream assets build for NT and NR #324

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68 changes: 37 additions & 31 deletions workflows/index-generation/index-generation.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,9 @@ workflow index_generation {
Float nr_compression_similarity_threshold = 0.5

Boolean skip_protein_compression = false
Boolean skip_generate_nr_assets = false
Boolean skip_nuc_compression = false
Boolean skip_generate_nt_assets = false
Boolean logging_enabled = false

File provided_nt = "~{ncbi_server}/blast/db/FASTA/nt.gz"
Expand Down Expand Up @@ -92,37 +94,41 @@ workflow index_generation {
}
File nt_or_compressed = select_first([CompressNT.compressed, unzipped_nt])

call GenerateLocDB as GenerateNTLocDB {
input:
db_fasta = nt_or_compressed,
database_type = "nt",
docker_image_id = docker_image_id
}
if (!skip_generate_nt_assets) {
call GenerateLocDB as GenerateNTLocDB {
input:
db_fasta = nt_or_compressed,
database_type = "nt",
docker_image_id = docker_image_id
}

call GenerateInfoDB as GenerateNTInfoDB {
input:
db_fasta = nt_or_compressed,
database_type = "nt",
docker_image_id = docker_image_id
}
call GenerateInfoDB as GenerateNTInfoDB {
input:
db_fasta = nt_or_compressed,
database_type = "nt",
docker_image_id = docker_image_id
}

call GenerateIndexMinimap2 as GenerateIndexMinimap2 {
input:
nt = nt_or_compressed,
docker_image_id = docker_image_id
call GenerateIndexMinimap2 as GenerateIndexMinimap2 {
input:
nt = nt_or_compressed,
docker_image_id = docker_image_id
}
}

call GenerateLocDB as GenerateNRLocDB {
input:
db_fasta = nr_or_compressed,
database_type = "nr",
docker_image_id = docker_image_id
}
if (!skip_generate_nr_assets) {
call GenerateLocDB as GenerateNRLocDB {
input:
db_fasta = nr_or_compressed,
database_type = "nr",
docker_image_id = docker_image_id
}

call GenerateIndexDiamond as GenerateIndexDiamond {
input:
nr = nr_or_compressed,
docker_image_id = docker_image_id
call GenerateIndexDiamond as GenerateIndexDiamond {
input:
nr = nr_or_compressed,
docker_image_id = docker_image_id
}
}

call GenerateIndexAccessions {
Expand Down Expand Up @@ -153,11 +159,11 @@ workflow index_generation {
File accession2taxid_nucl_gb = unzipped_accession2taxid_nucl_gb
File accession2taxid_pdb = unzipped_accession2taxid_pdb
File accession2taxid_prot = unzipped_accession2taxid_prot
File nt_loc_db = GenerateNTLocDB.loc_db
File nt_info_db = GenerateNTInfoDB.info_db
File nr_loc_db = GenerateNRLocDB.loc_db
Directory minimap2_index = GenerateIndexMinimap2.minimap2_index
Directory diamond_index = GenerateIndexDiamond.diamond_index
File? nt_loc_db = GenerateNTLocDB.loc_db
File? nt_info_db = GenerateNTInfoDB.info_db
File? nr_loc_db = GenerateNRLocDB.loc_db
Directory? minimap2_index = GenerateIndexMinimap2.minimap2_index
Directory? diamond_index = GenerateIndexDiamond.diamond_index
File taxid_lineages_db = GenerateIndexLineages.taxid_lineages_db
File versioned_taxid_lineages_csv = GenerateIndexLineages.versioned_taxid_lineages_csv
File deuterostome_taxids = GenerateIndexLineages.deuterostome_taxids
Expand Down
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