configs: removed not required steps (issue #127)

config/gdb/config.yaml

@@ -2,10 +2,14 @@
 # STEPS
 
 # Steps to be done
-steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
-steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
-steps_taxonomy: ["kraken2", "kaiju"]
+# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+# steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
+# steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
+# steps_taxonomy: ["kraken2", "kaiju"]
+steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis"]
+steps_annotation: ["rgi", "barrnap"] # prodigal is run in any case
+steps_analysis: ["quast", "mash", "diamond", "mmseqs2", "cov"]
+steps_taxonomy: []
 
 ############################################################
 # INPUT

config/nwc/config.yaml

@@ -2,10 +2,14 @@
 # STEPS
 
 # Steps to be done
-steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
-steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
-steps_taxonomy: ["kraken2", "kaiju"]
+# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+# steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
+# steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
+# steps_taxonomy: ["kraken2", "kaiju"]
+steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis"]
+steps_annotation: ["rgi", "barrnap"] # prodigal is run in any case
+steps_analysis: ["quast", "mash", "diamond", "mmseqs2", "cov"]
+steps_taxonomy: []
 
 ############################################################
 # INPUT

config/rumen/config.yaml

@@ -2,10 +2,14 @@
 # STEPS
 
 # Steps to be done
-steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps_annotation: ["rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case; excluded: kegg
-steps_analysis: ["quast", "mash", "mashmap", "fastani", "cdhit", "diamond", "mmseqs2", "cov"] # excluded: mummer
-steps_taxonomy: ["kraken2", "kaiju"]
+# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+# steps_annotation: ["rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case; excluded: kegg
+# steps_analysis: ["quast", "mash", "mashmap", "fastani", "cdhit", "diamond", "mmseqs2", "cov"] # excluded: mummer
+# steps_taxonomy: ["kraken2", "kaiju"]
+steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis"]
+steps_annotation: ["rgi", "barrnap"] # prodigal is run in any case
+steps_analysis: ["quast", "mash", "diamond", "mmseqs2", "cov"]
+steps_taxonomy: []
 
 ############################################################
 # INPUT

config/zymo/config.yaml

@@ -2,10 +2,14 @@
 # STEPS
 
 # Steps to be done
-steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
-steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
-steps_taxonomy: ["kraken2", "kaiju"]
+# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+# steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
+# steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "mmseqs2", "cov"]
+# steps_taxonomy: ["kraken2", "kaiju"]
+steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis"]
+steps_annotation: ["rgi", "barrnap"] # prodigal is run in any case
+steps_analysis: ["quast", "mash", "diamond", "mmseqs2", "cov"]
+steps_taxonomy: []
 
 ############################################################
 # INPUT