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Update README.md
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xiaoli-dong authored Nov 14, 2024
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10 changes: 5 additions & 5 deletions README.md
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@@ -98,14 +98,13 @@ You can clone or download the pathogenseq from github to local computer or you c
nextflow run xiaoli-dong/pathogenseq -r revision_number(e.g:8657a20) --help
# download the pipeine and run the program from the local computer
nextflow run main.nf --help
N E X T F L O W ~ version 23.04.1
Launching `main.nf` [spontaneous_kowalevski] DSL2 - revision: 4ef093f544
Launching `main.nf` [focused_goldstine] DSL2 - revision: 4ef093f544
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xiaoli-dong/pathogenseq v1.1.0
xiaoli-dong/pathogenseq v1.1.3
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Typical pipeline command:
@@ -148,15 +147,16 @@ nanopore_options
annotation_options
--bakta_db [string] Path to bakta database. [default: /nfs/APL_Genomics/db/prod/bakta/db]
--checkm2_db [string] Path to checkm2 database. [default: /nfs/APL_Genomics/db/prod/CheckM2_database/uniref100.KO.1.dmnd]
--amrfinderplus_db [string] null
--amrfinderplus_db [string] null [default: /nfs/APL_Genomics/db/prod/AMRFinderPlus/latest]
--skip_checkm2 [boolean] Skip checkm2 step. [default: false]
--skip_bakta [boolean] Skip bakta step. [default: false]
--skip_mlst [boolean] Skip mlst step. [default: false]
--skip_mobsuite [boolean] Skip skip_mobsuite step. [default: false]
--skip_virulome [boolean] Skip virulome step. [default: false]
--skip_multiqc [boolean] null [default: false]
--skip_amr [boolean] Skip amr step. [default: false]
--skip_depth_and_coverage [boolean] Skip assembly depth calculation step. [default: false]
--skip_depth_and_coverage_illumina [boolean] Skip assembly depth calculation step with illumina reads. [default: false]
--skip_depth_and_coverage_nanopore [boolean] Skip assembly depth calculation step with nanopore reads. [default: false]
taxonomic_tool_options
--kraken2_db [string] Specify path to kraken2 database [default: /nfs/APL_Genomics/db/prod/kraken2/k2_standard_08gb_20220926]

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