Added custom models as submodule, added pipleline for trap species handling (up to alignment). Initial progress on custom model rules

2026-10-03 15:16:36 +01:00
parent 3b93ceaf6e
commit f0cd594148
17 changed files with 270 additions and 21 deletions
@@ -60,13 +60,13 @@ rule download_reference_genome:

 rule concatenate_reference_genomes:
    input:
-        expand("../data/reference_genomes/{species}.fasta",species=config["species_list"])
+        expand("../data/reference_genomes/{species}.fasta",species=config["species_list"]+config["trap_species"])
    output:
        "../data/reference_genomes/full_reference.fasta"
    threads: 1
    shell:
        """
-        cat {input} > {output}
+        cat {input} {config[ont_dcs_fasta]} > {output}
        """

 rule create_minimap_index: