Commit cd6dd688 authored by Jean Mainguy's avatar Jean Mainguy
Browse files

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

parent f81cd2d3
This diff is collapsed.
...@@ -4,7 +4,7 @@ process ASSIGN_TAXONOMY { ...@@ -4,7 +4,7 @@ process ASSIGN_TAXONOMY {
label 'PYTHON' label 'PYTHON'
input: input:
tuple path(accession2taxid), path(taxdump) tuple path(accession2taxid), path(new_taxdump)
tuple val(sampleId), path(m8), path(sam_coverage), path(prot_len) tuple val(sampleId), path(m8), path(sam_coverage), path(prot_len)
output: output:
...@@ -23,7 +23,9 @@ process ASSIGN_TAXONOMY { ...@@ -23,7 +23,9 @@ process ASSIGN_TAXONOMY {
script: 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 merge_contig_quantif_perlineage.py -c ${sampleId}.percontig.tsv -s ${sam_coverage} -o ${sampleId}_quantif_percontig
""" """
} }
...@@ -69,9 +69,9 @@ workflow DATABASES { ...@@ -69,9 +69,9 @@ workflow DATABASES {
} }
else if( params.taxonomy_dir ) { else if( params.taxonomy_dir ) {
ch_accession2taxid = Channel ch_accession2taxid = Channel
.fromPath(params.taxonomy_dir + '/prot.accession2taxid', checkIfExists: true) .fromPath(params.taxonomy_dir + '/prot.accession2taxid.FULL', checkIfExists: true)
ch_taxdump = Channel 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) ch_taxonomy = ch_accession2taxid.combine(ch_taxdump)
} }
else { else {
......
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