Commit 1d96308c authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

Merge branch 'dev' of forgemia.inra.fr:genotoul-bioinfo/metagwgs into dev

parents e30f00a2 0ff60cf3
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......@@ -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
"""
}
......@@ -65,9 +65,9 @@ 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 {
......
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