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Commit 69380046 authored by Valentina Galata's avatar Valentina Galata
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config: updated rumen

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......@@ -2,10 +2,9 @@
# STEPS
# Steps to be done
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
steps: ["preprocessing", "assembly", "mapping"]
steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "cov"]
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", "cov"] # excluded: mummer
steps_taxonomy: ["kraken2", "kaiju"]
############################################################
......
......@@ -79,11 +79,11 @@ mapping_bwa_idx_asm:
mapping_bwa_mem_asm_sr:
time: "00-02:00:00"
partition: "batch"
partition: "bigmem"
mapping_bwa_mem_asm_lr:
time: "00-08:00:00"
partition: "batch"
partition: "bigmem"
mapping_bwa_mem_asm_hy:
time: "00-02:00:00"
......@@ -99,72 +99,72 @@ annotation_rgi:
partition: "batch"
annotation_minced:
time: "00-00:05:00"
time: "00-00:20:00"
partition: "batch"
annotation_plasflow:
time: "00-00:10:00"
time: "00-00:30:00"
partition: "bigmem"
annotation_barrnap:
time: "00-00:10:00"
time: "00-00:20:00"
partition: "batch"
annotation_hmm_kegg:
time: "00-08:00:00"
partition: "batch"
partition: "bigmem"
# Analysis
analysis_quast:
time: "00-00:05:00"
time: "00-00:10:00"
partition: "batch"
analysis_mash_sketch_sr:
time: "00-00:15:00"
time: "00-00:40:00"
partition: "batch"
analysis_mash_sketch_lr:
time: "00-00:15:00"
time: "00-00:40:00"
partition: "batch"
analysis_mash_reads:
time: "00-00:05:00"
time: "00-00:10:00"
partition: "batch"
analysis_mash_sketch_asm:
time: "00-00:05:00"
time: "00-00:10:00"
partition: "batch"
analysis_mash_asm:
time: "00-00:05:00"
time: "00-00:10:00"
partition: "batch"
analysis_mashmap_one2one:
time: "00-00:30:00"
time: "00-01:00:00"
partition: "batch"
analysis_fastani_one2one:
time: "00-00:20:00"
time: "00-01:00:00"
partition: "batch"
analysis_mummer_dnadiff:
time: "00-01:00:00"
partition: "batch"
time: "00-02:00:00"
partition: "bigmem"
analysis_cdhit:
time: "00-00:05:00"
time: "00-01:00:00"
partition: "batch"
analysis_diamond:
time: "00-00:10:00"
time: "00-01:00:00"
partition: "batch"
analysis_diamond_db:
time: "00-02:00:00"
time: "00-06:00:00"
partition: "batch"
analysis_genomecov_pergene:
time: "00-02:00:00"
time: "00-12:00:00"
partition: "batch"
analysis_genomecov_segmentation:
......
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