Use mpox PCR sequence reference file

OpenOmics · Apr 3, 2024 · b5d50b5 · b5d50b5
1 parent f1d698f
commit b5d50b5
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Showing 3 changed files with 5 additions and 6 deletions.
diff --git a/config/genome.json b/config/genome.json
@@ -1,5 +1,6 @@
 {
     "references": {
-        "mpox_ref_genome": "/data/OpenOmics/references/mpox-seek/mpox_NC_003310_1.fa"
+        "mpox_ref_genome":   "/data/OpenOmics/references/mpox-seek/mpox_NC_003310_1.fa",
+        "mpox_pcr_sequence": "/data/OpenOmics/references/mpox-seek/mpox_NC_003310_1_pcr_sequence.fa"
     }
 }
diff --git a/workflow/rules/map.smk b/workflow/rules/map.smk
@@ -14,7 +14,7 @@ rule minimap2:
         sam  = join(workpath, "{name}", "bams", "{name}.sam"),
     params:
         rname  = 'minimap2',
-        ref_fa  = config['references']['mpox_ref_genome'],
+        ref_fa  = config['references']['mpox_pcr_sequence'],
     conda: depending(conda_yaml_or_named_env, use_conda)
     container: depending(config['images']['mpox-seek'], use_singularity)
     shell: 
@@ -48,7 +48,7 @@ rule consensus:
         fixed = join(workpath, "{name}", "consensus", "{name}_consensus_seqid.fa"),
     params:
         rname  = 'consensus',
-        ref_fa  = config['references']['mpox_ref_genome'],
+        ref_fa  = config['references']['mpox_pcr_sequence'],
     conda: depending(conda_yaml_or_named_env, use_conda)
     container: depending(config['images']['mpox-seek'], use_singularity)
     shell: 
@@ -85,7 +85,7 @@ rule concat:
         fa  = join(workpath, "project", "consensus.fa"),
     params:
         rname  = 'premafft',
-        ref_fa  = config['references']['mpox_ref_genome'],
+        ref_fa  = config['references']['mpox_pcr_sequence'],
     conda: depending(conda_yaml_or_named_env, use_conda)
     container: depending(config['images']['mpox-seek'], use_singularity)
     shell: 
@@ -113,7 +113,6 @@ rule mafft:
         msa = join(workpath, "project", "msa.fa"),
     params:
         rname  = 'msa',
-        ref_fa  = config['references']['mpox_ref_genome'],
     conda: depending(conda_yaml_or_named_env, use_conda)
     container: depending(config['images']['mpox-seek'], use_singularity)
     shell: 

diff --git a/workflow/rules/tree.smk b/workflow/rules/tree.smk
@@ -17,7 +17,6 @@ rule tree:
         nw  = join(workpath, "project", "mpox_phylogeny.raxml.bestTree"),
     params:
         rname  = 'tree',
-        ref_fa = config['references']['mpox_ref_genome'],
         prefix = join(workpath, "project", "mpox_phylogeny"),
     conda: depending(conda_yaml_or_named_env, use_conda)
     container: depending(config['images']['mpox-seek'], use_singularity)