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annotation.wdl
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annotation.wdl
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version 1.0
import "structural-annotation.wdl" as sa
import "functional-annotation.wdl" as fa
workflow annotation {
input {
String cmzscore
File imgap_input_fasta
String imgap_project_id="GaXXXXXXX_contigs.fna"
String database_location="/refdata/img/"
String imgap_project_type="metagenome"
Int additional_threads=16
Int? fa_approx_num_proteins
String? gm_license
}
call sa.s_annotate {
input:
imgap_input_fasta = imgap_input_fasta,
imgap_project_id = imgap_project_id,
additional_threads = additional_threads,
imgap_project_type = imgap_project_type,
cmzscore = cmzscore,
database_location = database_location,
gm_license = gm_license
}
call fa.f_annotate {
input:
imgap_project_id = imgap_project_id,
imgap_project_type = imgap_project_type,
additional_threads = additional_threads,
input_fasta = s_annotate.proteins,
approx_num_proteins = fa_approx_num_proteins,
database_location = database_location,
sa_gff = s_annotate.gff
}
output{
File sa_gff = s_annotate.gff
File? crt_gff = s_annotate.crt_gff
File? crisprs = s_annotate.crisprs
File? crt_out = s_annotate.crt_out
File? genemark_gff = s_annotate.genemark_gff
File? genemark_genes = s_annotate.genemark_genes
File? genemark_proteins = s_annotate.genemark_proteins
File? prodigal_gff = s_annotate.prodigal_gff
File? prodigal_genes = s_annotate.prodigal_genes
File? prodigal_proteins = s_annotate.prodigal_proteins
File? cds_gff = s_annotate.cds_gff
File? cds_proteins = s_annotate.cds_proteins
File? cds_genes = s_annotate.cds_genes
File? trna_gff = s_annotate.trna_gff
File? trna_bacterial_out = s_annotate.trna_bacterial_out
File? trna_archaeal_out = s_annotate.trna_archaeal_out
File? rfam_gff = s_annotate.rfam_gff
File? rfam_tbl = s_annotate.rfam_tbl
File? proteins = s_annotate.proteins
File? genes = s_annotate.genes
File product_name_gff = f_annotate.gff
File product_name_tsv = f_annotate.product_name_tsv
File ko_tsv = f_annotate.ko_tsv
File ec_tsv = f_annotate.ec_tsv
File phylo_tsv = f_annotate.phylo_tsv
File ko_ec_gff = f_annotate.ko_ec_gff
File last_blasttab = f_annotate.last_blasttab
File lineage_tsv = f_annotate.lineage_tsv
File cog_gff = f_annotate.cog_gff
File pfam_gff = f_annotate.pfam_gff
File tigrfam_gff = f_annotate.tigrfam_gff
File supfam_gff = f_annotate.supfam_gff
File smart_gff = f_annotate.smart_gff
File cath_funfam_gff = f_annotate.cath_funfam_gff
File cog_domtblout = f_annotate.cog_domtblout
File pfam_domtblout = f_annotate.pfam_domtblout
File tigrfam_domtblout = f_annotate.tigrfam_domtblout
File supfam_domtblout = f_annotate.supfam_domtblout
File smart_domtblout = f_annotate.smart_domtblout
File cath_funfam_domtblout = f_annotate.cath_funfam_domtblout
}
}