Commit 87955f4c authored by Celine Noirot's avatar Celine Noirot
Browse files

rename to merge_contig_quantif_perlineage.py

parent 64bce452
......@@ -1091,19 +1091,19 @@ process diamond_parser {
set replicateId, file("${replicateId}.pergene.tsv") into taxo_pergene_ch
set replicateId, file("${replicateId}.warn.tsv") into taxo_warn_ch
set replicateId, file("graphs") into taxo_graphs_ch
file("${replicateId}_idxstats_percontig.tsv") into idxstats_percontig_ch
file("${replicateId}_idxstats_percontig_by_superkingdom.tsv") into idxstats_percontig_superkingdom_ch
file("${replicateId}_idxstats_percontig_by_phylum.tsv") into idxstats_percontig_phylum_ch
file("${replicateId}_idxstats_percontig_by_order.tsv") into idxstats_percontig_order_ch
file("${replicateId}_idxstats_percontig_by_class.tsv") into idxstats_percontig_class_ch
file("${replicateId}_idxstats_percontig_by_family.tsv") into idxstats_percontig_family_ch
file("${replicateId}_idxstats_percontig_by_genus.tsv") into idxstats_percontig_genus_ch
file("${replicateId}_idxstats_percontig_by_species.tsv") into idxstats_percontig_species_ch
file("${replicateId}_quantif_percontig.tsv") into quantif_percontig_ch
file("${replicateId}_quantif_percontig_by_superkingdom.tsv") into quantif_percontig_superkingdom_ch
file("${replicateId}_quantif_percontig_by_phylum.tsv") into quantif_percontig_phylum_ch
file("${replicateId}_quantif_percontig_by_order.tsv") into quantif_percontig_order_ch
file("${replicateId}_quantif_percontig_by_class.tsv") into quantif_percontig_class_ch
file("${replicateId}_quantif_percontig_by_family.tsv") into quantif_percontig_family_ch
file("${replicateId}_quantif_percontig_by_genus.tsv") into quantif_percontig_genus_ch
file("${replicateId}_quantif_percontig_by_species.tsv") into quantif_percontig_species_ch
script:
"""
aln2taxaffi.py -a ${prot_accession2taxid} --taxonomy ${taxonomy} -o ${replicateId} ${diamond_file} ${contigs_len}
merge_idxstats_percontig_lineage.py -i ${idxstats} -c ${replicateId}.percontig.tsv -o ${replicateId}_idxstats_percontig
merge_contig_quantif_perlineage.py -i ${idxstats} -c ${replicateId}.percontig.tsv -o ${replicateId}_quantif_percontig
"""
}
......@@ -1114,14 +1114,14 @@ process quantif_and_taxonomic_table_contigs {
when: ('07_taxo_affi' in step)
input:
file(files_all) from idxstats_percontig_ch.collect()
file(files_superkingdom) from idxstats_percontig_superkingdom_ch.collect()
file(files_phylum) from idxstats_percontig_phylum_ch.collect()
file(files_order) from idxstats_percontig_order_ch.collect()
file(files_class) from idxstats_percontig_class_ch.collect()
file(files_family) from idxstats_percontig_family_ch.collect()
file(files_genus) from idxstats_percontig_genus_ch.collect()
file(files_species) from idxstats_percontig_species_ch.collect()
file(files_all) from quantif_percontig_ch.collect()
file(files_superkingdom) from quantif_percontig_superkingdom_ch.collect()
file(files_phylum) from quantif_percontig_phylum_ch.collect()
file(files_order) from quantif_percontig_order_ch.collect()
file(files_class) from quantif_percontig_class_ch.collect()
file(files_family) from quantif_percontig_family_ch.collect()
file(files_genus) from quantif_percontig_genus_ch.collect()
file(files_species) from quantif_percontig_species_ch.collect()
output:
file("quantification_by_contig_lineage*.tsv") into quantif_by_lineage_contigs_ch
......
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