diff --git a/snakefile b/snakefile index bf15de5b5e2a4d28b8cc0639932686c0efe4e5b7..a3185198d5be43b3a1382e0cf992a65d67ec0627 100644 --- a/snakefile +++ b/snakefile @@ -6,6 +6,7 @@ log_dir = f"{output_dir}LOGS/" script_dir = config["DATA"]["SCRIPTS"] gff_dir = config["DATA"]["GFF"] dbcan_db = config["DATA"]["DBCAN_DB"] +phibase_db = config["DATA"]["BDD_PHIBASE"] PROTEIN, = glob_wildcards(fasta_prot_dir+"{samples}.fasta", followlinks=True) @@ -33,14 +34,14 @@ def get_threads(rule, default): rule finale: input: - domain_prot=expand(f"{output_dir}3_HMMER_PFAM/{{samples}}_secreted.tbl",samples=PROTEIN), - effector_contig=expand(f"{output_dir}5_FINAL_RESULT/EFFECTOR/{{samples}}/{{samples}}_effector_per_contig.txt",samples=PROTEIN), - cazyme_counts_list=expand(f"{output_dir}6_CAZYMES/dbcan_{{samples}}/{{samples}}_cazyme_count.csv",samples=PROTEIN), - orthogroups_sequences=expand(f"{output_dir}7_ORTHOFINDER/Results_orthofinder/sequences_specific/prot_specific_{{samples}}.fasta",samples=PROTEIN), - csv_orthogroups=expand(f"{output_dir}7_ORTHOFINDER/Results_orthofinder/sequences_specific/OG_specific_{{samples}}.csv",samples=PROTEIN), - dbcan_list=expand(f"{output_dir}6_CAZYMES/dbcan_{{samples}}/overview.txt",samples=PROTEIN), - interpro_gff_list=expand(f"{output_dir}8_INTERPROSCAN/{{samples}}/{{samples}}.fasta.gff3",samples=PROTEIN), - blast_phibase=expand(f"{output_dir}9_PHIBASE/{{samples}}/{{samples}}_blast_phibase.out",samples=PROTEIN) + domain_prot = expand(f"{output_dir}3_HMMER_PFAM/{{samples}}_secreted.tbl", samples = PROTEIN), + effector_contig = expand(f"{output_dir}5_FINAL_RESULT/EFFECTOR/{{samples}}/{{samples}}_effector_per_contig.txt", samples = PROTEIN), + cazyme_counts_list = expand(f"{output_dir}6_CAZYMES/dbcan_{{samples}}/{{samples}}_cazyme_count.csv",samples=PROTEIN), + orthogroups_sequences = expand(f"{output_dir}7_ORTHOFINDER/Results_orthofinder/sequences_specific/prot_specific_{{samples}}.fasta",samples=PROTEIN), + csv_orthogroups = expand(f"{output_dir}7_ORTHOFINDER/Results_orthofinder/sequences_specific/OG_specific_{{samples}}.csv",samples=PROTEIN), + dbcan_list = expand(f"{output_dir}6_CAZYMES/dbcan_{{samples}}/overview.txt", samples = PROTEIN), + interpro_gff_list = expand(f"{output_dir}8_INTERPROSCAN/{{samples}}/{{samples}}.fasta.gff3", samples = PROTEIN), + blast_phibase = expand(f"{output_dir}9_PHIBASE/{{samples}}/{{samples}}_blast_phibase.out", samples = PROTEIN) #gff_cazymes_list = expand(f"{output_dir}GFF_with_cazymes/{{samples}}_gff.csv",samples=PROTEIN) @@ -850,4 +851,5 @@ rule phibase: envmodules: "blast" shell: - "blastp -db {input.phibase_database} -query {input.fasta_effectors} -outfmt 6 -out {output.blast_result}" \ No newline at end of file + "blastp -db {input.phibase_database} -query {input.fasta_effectors} -out {output.blast_result} -outfmt '6 qacc sacc length evalue score title' -evalue 0.001" +