Commit 1210d2b9 authored by Thomas Van Parys's avatar Thomas Van Parys
Browse files

Disable EF and WGD processes for missing CDS or annotation (#47)

parent ec28c3e1
...@@ -831,7 +831,7 @@ species_name_map ...@@ -831,7 +831,7 @@ species_name_map
species_new_cds_gff3 species_new_cds_gff3
.filter { it.type == 'new' && it.gff3 } .filter { it.type == 'new' && it.cds && it.gff3 }
.map { [it.name, it.cds, it.gff3] } .map { [it.name, it.cds, it.gff3] }
.first() .first()
.set { ef_new_cds_gff3 } .set { ef_new_cds_gff3 }
...@@ -876,6 +876,11 @@ process ef{ ...@@ -876,6 +876,11 @@ process ef{
file species_map from ef_species_map file species_map from ef_species_map
set val(new_name), file(new_cds), file(new_gff3) from ef_new_cds_gff3 set val(new_name), file(new_cds), file(new_gff3) from ef_new_cds_gff3
val species_list from cds_names val species_list from cds_names
when:
//don't run if we don't have any null-species with CDS's
//will not run anyway if no new CDS and GFF3 are supplied
!species_list.isAllWhitespace()
output: output:
file '*' file '*'
...@@ -1033,9 +1038,12 @@ process clime { ...@@ -1033,9 +1038,12 @@ process clime {
""" """
} }
//only use blast hits where species == new //only use blast hits where species is of type new
//also filter out pairs where one of the two does
//not supply a CDS file.
allVsAllProteomeBlasts_wgd allVsAllProteomeBlasts_wgd
.filter { it[1] == newSpeciesId.value } .filter { it[1] == newSpeciesId.value }
.filter { cdsMap[it[1]].value != '' && cdsMap[it[2]].value != '' }
.set { new_species_blasts } .set { new_species_blasts }
......
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