Commit 9177187f authored by Valentina Galata's avatar Valentina Galata
Browse files

configs: removed not required steps (issue #127)

parent e47143ef
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
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