refactoring of aln2taxaffi. use of new_taxdump and prot.accession2taxid.FULL

modules/assign_taxonomy.nf

@@ -4,7 +4,7 @@ process ASSIGN_TAXONOMY {
   label 'PYTHON'
 
   input:
-    tuple path(accession2taxid), path(taxdump)
+    tuple path(accession2taxid), path(new_taxdump)
     tuple val(sampleId), path(m8), path(sam_coverage), path(prot_len)
 
   output:
@@ -23,7 +23,9 @@ process ASSIGN_TAXONOMY {
 
   script:
     """
-    aln2taxaffi.py -a ${accession2taxid} --taxonomy ${taxdump} -o ${sampleId} ${m8} ${prot_len}
+    aln2taxaffi.py -a ${accession2taxid} --taxonomy ${new_taxdump} \
+                  -o ${sampleId} -b ${m8} --keep_only_best_aln  \
+                  --query_length_file ${prot_len} -v
     merge_contig_quantif_perlineage.py -c ${sampleId}.percontig.tsv -s ${sam_coverage} -o ${sampleId}_quantif_percontig
     """
 }

subworkflows/00_databases.nf

@@ -69,9 +69,9 @@ workflow DATABASES {
             }
             else if( params.taxonomy_dir ) {
                 ch_accession2taxid = Channel
-                    .fromPath(params.taxonomy_dir + '/prot.accession2taxid', checkIfExists: true)
+                    .fromPath(params.taxonomy_dir + '/prot.accession2taxid.FULL', checkIfExists: true)
                 ch_taxdump = Channel
-                    .fromPath(params.taxonomy_dir + '/taxdump', checkIfExists: true)
+                    .fromPath(params.taxonomy_dir + '/new_taxdump', checkIfExists: true)
                 ch_taxonomy = ch_accession2taxid.combine(ch_taxdump)
             }
             else {