From 466f99e665e51d6cce7178bf4010792a93d7cbd8 Mon Sep 17 00:00:00 2001
From: Louisa Perelo <louisa.perelo@qbic.uni-tuebingen.de>
Date: Fri, 24 Mar 2023 16:39:58 +0100
Subject: [PATCH] isa. files
---
.gitattributes | 1 +
.gitignore | 388 +++++++++++++
assays/YamMetagenome/README.md | 0
assays/YamMetagenome/dataset/.gitkeep | 0
assays/YamMetagenome/isa.assay.xlsx | Bin 0 -> 16348 bytes
assays/YamMetagenome/protocols/.gitkeep | 0
isa.investigation.xlsx | Bin 4854 -> 4911 bytes
runs/funcscan_yam.sh | 14 +
runs/nfcore_funcscan_yam.yml | 13 +
runs/samplesheet_yam.csv | 6 +
studies/YamDataset/isa.study.xlsx | Bin 3205 -> 16994 bytes
workflows/nfcore_funcscan.cwl | 712 ++++++++++++++++++++++++
12 files changed, 1134 insertions(+)
create mode 100644 .gitattributes
create mode 100644 .gitignore
create mode 100644 assays/YamMetagenome/README.md
create mode 100644 assays/YamMetagenome/dataset/.gitkeep
create mode 100644 assays/YamMetagenome/isa.assay.xlsx
create mode 100644 assays/YamMetagenome/protocols/.gitkeep
create mode 100644 runs/funcscan_yam.sh
create mode 100644 runs/nfcore_funcscan_yam.yml
create mode 100644 runs/samplesheet_yam.csv
create mode 100644 workflows/nfcore_funcscan.cwl
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..2635f9c
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+**/dataset/** filter=lfs diff=lfs merge=lfs -text
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..11819f2
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,388 @@
+## Ignore Visual Studio temporary files, build results, and
+## files generated by popular Visual Studio add-ons.
+##
+## Get latest from https://github.com/github/gitignore/blob/master/VisualStudio.gitignore
+
+# User-specific files
+*.rsuser
+*.suo
+*.user
+*.userosscache
+*.sln.docstates
+
+# User-specific files (MonoDevelop/Xamarin Studio)
+*.userprefs
+
+# Mono auto generated files
+mono_crash.*
+
+# Build results
+[Dd]ebug/
+[Dd]ebugPublic/
+[Rr]elease/
+[Rr]eleases/
+x64/
+x86/
+[Aa][Rr][Mm]/
+[Aa][Rr][Mm]64/
+bld/
+[Bb]in/
+[Oo]bj/
+[Ll]og/
+[Ll]ogs/
+
+# Visual Studio 2015/2017 cache/options directory
+.vs/
+# Uncomment if you have tasks that create the project's static files in wwwroot
+#wwwroot/
+
+# Visual Studio 2017 auto generated files
+Generated\ Files/
+
+# MSTest test Results
+[Tt]est[Rr]esult*/
+[Bb]uild[Ll]og.*
+
+# NUnit
+*.VisualState.xml
+TestResult.xml
+nunit-*.xml
+
+# Build Results of an ATL Project
+[Dd]ebugPS/
+[Rr]eleasePS/
+dlldata.c
+
+# Benchmark Results
+BenchmarkDotNet.Artifacts/
+
+# .NET Core
+project.lock.json
+project.fragment.lock.json
+artifacts/
+
+# StyleCop
+StyleCopReport.xml
+
+# Files built by Visual Studio
+*_i.c
+*_p.c
+*_h.h
+*.ilk
+*.meta
+*.obj
+*.iobj
+*.pch
+*.pdb
+*.ipdb
+*.pgc
+*.pgd
+*.rsp
+*.sbr
+*.tlb
+*.tli
+*.tlh
+*.tmp
+*.tmp_proj
+*_wpftmp.csproj
+*.log
+*.vspscc
+*.vssscc
+.builds
+*.pidb
+*.svclog
+*.scc
+
+# Chutzpah Test files
+_Chutzpah*
+
+# Visual C++ cache files
+ipch/
+*.aps
+*.ncb
+*.opendb
+*.opensdf
+*.sdf
+*.cachefile
+*.VC.db
+*.VC.VC.opendb
+
+# Visual Studio profiler
+*.psess
+*.vsp
+*.vspx
+*.sap
+
+# Visual Studio Trace Files
+*.e2e
+
+# TFS 2012 Local Workspace
+$tf/
+
+# Guidance Automation Toolkit
+*.gpState
+
+# ReSharper is a .NET coding add-in
+_ReSharper*/
+*.[Rr]e[Ss]harper
+*.DotSettings.user
+
+# TeamCity is a build add-in
+_TeamCity*
+
+# DotCover is a Code Coverage Tool
+*.dotCover
+
+# AxoCover is a Code Coverage Tool
+.axoCover/*
+!.axoCover/settings.json
+
+# Visual Studio code coverage results
+*.coverage
+*.coveragexml
+
+# NCrunch
+_NCrunch_*
+.*crunch*.local.xml
+nCrunchTemp_*
+
+# MightyMoose
+*.mm.*
+AutoTest.Net/
+
+# Web workbench (sass)
+.sass-cache/
+
+# Installshield output folder
+[Ee]xpress/
+
+# DocProject is a documentation generator add-in
+DocProject/buildhelp/
+DocProject/Help/*.HxT
+DocProject/Help/*.HxC
+DocProject/Help/*.hhc
+DocProject/Help/*.hhk
+DocProject/Help/*.hhp
+DocProject/Help/Html2
+DocProject/Help/html
+
+# Click-Once directory
+publish/
+
+# Publish Web Output
+*.[Pp]ublish.xml
+*.azurePubxml
+# Note: Comment the next line if you want to checkin your web deploy settings,
+# but database connection strings (with potential passwords) will be unencrypted
+*.pubxml
+*.publishproj
+
+# Microsoft Azure Web App publish settings. Comment the next line if you want to
+# checkin your Azure Web App publish settings, but sensitive information contained
+# in these scripts will be unencrypted
+PublishScripts/
+
+# NuGet Packages
+*.nupkg
+# NuGet Symbol Packages
+*.snupkg
+# The packages folder can be ignored because of Package Restore
+**/[Pp]ackages/*
+# except build/, which is used as an MSBuild target.
+!**/[Pp]ackages/build/
+# Uncomment if necessary however generally it will be regenerated when needed
+#!**/[Pp]ackages/repositories.config
+# NuGet v3's project.json files produces more ignorable files
+*.nuget.props
+*.nuget.targets
+
+# Microsoft Azure Build Output
+csx/
+*.build.csdef
+
+# Microsoft Azure Emulator
+ecf/
+rcf/
+
+# Windows Store app package directories and files
+AppPackages/
+BundleArtifacts/
+Package.StoreAssociation.xml
+_pkginfo.txt
+*.appx
+*.appxbundle
+*.appxupload
+
+# Visual Studio cache files
+# files ending in .cache can be ignored
+*.[Cc]ache
+# but keep track of directories ending in .cache
+!?*.[Cc]ache/
+
+# Others
+ClientBin/
+~$*
+*~
+*.dbmdl
+*.dbproj.schemaview
+*.jfm
+*.pfx
+*.publishsettings
+orleans.codegen.cs
+
+# Including strong name files can present a security risk
+# (https://github.com/github/gitignore/pull/2483#issue-259490424)
+#*.snk
+
+# Since there are multiple workflows, uncomment next line to ignore bower_components
+# (https://github.com/github/gitignore/pull/1529#issuecomment-104372622)
+#bower_components/
+
+# RIA/Silverlight projects
+Generated_Code/
+
+# Backup & report files from converting an old project file
+# to a newer Visual Studio version. Backup files are not needed,
+# because we have git ;-)
+_UpgradeReport_Files/
+Backup*/
+UpgradeLog*.XML
+UpgradeLog*.htm
+ServiceFabricBackup/
+*.rptproj.bak
+
+# SQL Server files
+*.mdf
+*.ldf
+*.ndf
+
+# Business Intelligence projects
+*.rdl.data
+*.bim.layout
+*.bim_*.settings
+*.rptproj.rsuser
+*- [Bb]ackup.rdl
+*- [Bb]ackup ([0-9]).rdl
+*- [Bb]ackup ([0-9][0-9]).rdl
+
+# Microsoft Fakes
+FakesAssemblies/
+
+# GhostDoc plugin setting file
+*.GhostDoc.xml
+
+# Node.js Tools for Visual Studio
+.ntvs_analysis.dat
+node_modules/
+
+# Visual Studio 6 build log
+*.plg
+
+# Visual Studio 6 workspace options file
+*.opt
+
+# Visual Studio 6 auto-generated workspace file (contains which files were open etc.)
+*.vbw
+
+# Visual Studio LightSwitch build output
+**/*.HTMLClient/GeneratedArtifacts
+**/*.DesktopClient/GeneratedArtifacts
+**/*.DesktopClient/ModelManifest.xml
+**/*.Server/GeneratedArtifacts
+**/*.Server/ModelManifest.xml
+_Pvt_Extensions
+
+# Paket dependency manager
+.paket/paket.exe
+paket-files/
+
+# FAKE - F# Make
+.fake/
+
+# CodeRush personal settings
+.cr/personal
+
+# Python Tools for Visual Studio (PTVS)
+__pycache__/
+*.pyc
+
+# Cake - Uncomment if you are using it
+# tools/**
+# !tools/packages.config
+
+# Tabs Studio
+*.tss
+
+# Telerik's JustMock configuration file
+*.jmconfig
+
+# BizTalk build output
+*.btp.cs
+*.btm.cs
+*.odx.cs
+*.xsd.cs
+
+# OpenCover UI analysis results
+OpenCover/
+
+# Azure Stream Analytics local run output
+ASALocalRun/
+
+# MSBuild Binary and Structured Log
+*.binlog
+
+# NVidia Nsight GPU debugger configuration file
+*.nvuser
+
+# MFractors (Xamarin productivity tool) working folder
+.mfractor/
+
+# Local History for Visual Studio
+.localhistory/
+
+# BeatPulse healthcheck temp database
+healthchecksdb
+
+# Backup folder for Package Reference Convert tool in Visual Studio 2017
+MigrationBackup/
+
+# Ionide (cross platform F# VS Code tools) working folder
+.ionide/
+
+
+
+
+## MacOS temporaries
+##
+
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+
+# R temporaries
+.Rhistory
+.RData
diff --git a/assays/YamMetagenome/README.md b/assays/YamMetagenome/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/YamMetagenome/dataset/.gitkeep b/assays/YamMetagenome/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/YamMetagenome/isa.assay.xlsx b/assays/YamMetagenome/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..0e7109e932e2a855b35930a861396a2b2671c934
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diff --git a/assays/YamMetagenome/protocols/.gitkeep b/assays/YamMetagenome/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
index 63cb372c3eb9bdff5b0e0093c6d67e9d475a8660..f0fb31a192cfba576e80a81c28d642b4a8f12556 100644
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diff --git a/runs/funcscan_yam.sh b/runs/funcscan_yam.sh
new file mode 100644
index 0000000..28909b2
--- /dev/null
+++ b/runs/funcscan_yam.sh
@@ -0,0 +1,14 @@
+nextflow run nf-core/funcscan \
+-profile cfc \
+-r 1.0.1 \
+--input './samplesheet.csv' \
+--annotation_tool 'prodigal' \
+--save_annotations true \
+--save_databases true \
+--run_amp_screening true \
+--amp_skip_hmmsearch true \
+--run_arg_screening true \
+--arg_skip_deeparg true \
+--run_bgc_screening true \
+--bgc_skip_hmmsearch true \
+--outdir 'results_sampleARC'
\ No newline at end of file
diff --git a/runs/nfcore_funcscan_yam.yml b/runs/nfcore_funcscan_yam.yml
new file mode 100644
index 0000000..f18d840
--- /dev/null
+++ b/runs/nfcore_funcscan_yam.yml
@@ -0,0 +1,13 @@
+profile: cfc
+r: 1.0.1
+input: './samplesheet_yam.csv'
+annotation_tool: 'prodigal'
+save_annotations: true
+save_databases: true
+run_amp_screening: true
+amp_skip_hmmsearch: true
+run_arg_screening: true
+arg_skip_deeparg: true
+run_bgc_screening: true
+bgc_skip_hmmsearch: true
+outdir: 'results_sampleARC'
\ No newline at end of file
diff --git a/runs/samplesheet_yam.csv b/runs/samplesheet_yam.csv
new file mode 100644
index 0000000..8eeb5de
--- /dev/null
+++ b/runs/samplesheet_yam.csv
@@ -0,0 +1,6 @@
+sample,fasta
+BRI,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/706/625/GCA_900706625.1_ORDI_BRI6/GCA_900706625.1_ORDI_BRI6_genomic.fna.gz
+IVO,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/706/695/GCA_900706695.1_ORDI_IVO3/GCA_900706695.1_ORDI_IVO3_genomic.fna.gz
+AMP,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/706/525/GCA_900706525.1_ORDI_AMP9/GCA_900706525.1_ORDI_AMP9_genomic.fna.gz
+AMB,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/883/635/GCA_900883635.1_ORDI_AMB_3/GCA_900883635.1_ORDI_AMB_3_genomic.fna.gz
+RAN,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/706/685/GCA_900706685.1_ORDI_RAN3/GCA_900706685.1_ORDI_RAN3_genomic.fna.gz
\ No newline at end of file
diff --git a/studies/YamDataset/isa.study.xlsx b/studies/YamDataset/isa.study.xlsx
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diff --git a/workflows/nfcore_funcscan.cwl b/workflows/nfcore_funcscan.cwl
new file mode 100644
index 0000000..9678de2
--- /dev/null
+++ b/workflows/nfcore_funcscan.cwl
@@ -0,0 +1,712 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements: []
+
+inputs:
+- id: input
+ type: string?
+ inputBinding:
+ prefix: --input
+- id: outdir
+ type: string?
+ inputBinding:
+ prefix: --outdir
+- id: email
+ type: string?
+ inputBinding:
+ prefix: --email
+- id: multiqc_title
+ type: string?
+ inputBinding:
+ prefix: --multiqc_title
+- id: run_amp_screening
+ type: boolean?
+ inputBinding:
+ prefix: --run_amp_screening
+- id: run_arg_screening
+ type: boolean?
+ inputBinding:
+ prefix: --run_arg_screening
+- id: run_bgc_screening
+ type: boolean?
+ inputBinding:
+ prefix: --run_bgc_screening
+- id: annotation_tool
+ type: string?
+ default: prodigal
+ inputBinding:
+ prefix: --annotation_tool
+- id: save_annotations
+ type: boolean?
+ inputBinding:
+ prefix: --save_annotations
+- id: annotation_bakta_db
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --annotation_bakta_db
+- id: annotation_bakta_mincontiglen
+ type: int?
+ default: 1
+ inputBinding:
+ prefix: --annotation_bakta_mincontiglen
+- id: annotation_bakta_translationtable
+ type: int?
+ default: 11
+ inputBinding:
+ prefix: --annotation_bakta_translationtable
+- id: annotation_bakta_gram
+ type: string?
+ default: '?'
+ inputBinding:
+ prefix: --annotation_bakta_gram
+- id: annotation_bakta_complete
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_complete
+- id: annotation_bakta_renamecontigheaders
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_renamecontigheaders
+- id: annotation_bakta_compliant
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_compliant
+- id: annotation_bakta_skiptrna
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skiptrna
+- id: annotation_bakta_skiptmrna
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skiptmrna
+- id: annotation_bakta_skiprrna
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skiprrna
+- id: annotation_bakta_skipncrna
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skipncrna
+- id: annotation_bakta_skipncrnaregion
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skipncrnaregion
+- id: annotation_bakta_skipcrispr
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skipcrispr
+- id: annotation_bakta_skipcds
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skipcds
+- id: annotation_bakta_skippseudo
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skippseudo
+- id: annotation_bakta_skipsorf
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skipsorf
+- id: annotation_bakta_skipgap
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skipgap
+- id: annotation_bakta_skipori
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_bakta_skipori
+- id: annotation_prokka_singlemode
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prokka_singlemode
+- id: annotation_prokka_rawproduct
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prokka_rawproduct
+- id: annotation_prokka_kingdom
+ type: string?
+ default: Bacteria
+ inputBinding:
+ prefix: --annotation_prokka_kingdom
+- id: annotation_prokka_gcode
+ type: int?
+ default: 11
+ inputBinding:
+ prefix: --annotation_prokka_gcode
+- id: annotation_prokka_mincontiglen
+ type: int?
+ default: 1
+ inputBinding:
+ prefix: --annotation_prokka_mincontiglen
+- id: annotation_prokka_evalue
+ type: float?
+ default: 0.000001
+ inputBinding:
+ prefix: --annotation_prokka_evalue
+- id: annotation_prokka_coverage
+ type: int?
+ default: 80
+ inputBinding:
+ prefix: --annotation_prokka_coverage
+- id: annotation_prokka_cdsrnaolap
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prokka_cdsrnaolap
+- id: annotation_prokka_rnammer
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prokka_rnammer
+- id: annotation_prokka_centre
+ type: string?
+ inputBinding:
+ prefix: --annotation_prokka_centre
+- id: annotation_prokka_compliant
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prokka_compliant
+- id: annotation_prokka_locustag
+ type: string?
+ default: Prokka
+ inputBinding:
+ prefix: --annotation_prokka_locustag
+- id: annotation_prokka_addgenes
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prokka_addgenes
+- id: annotation_prodigal_singlemode
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prodigal_singlemode
+- id: annotation_prodigal_closed
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prodigal_closed
+- id: annotation_prodigal_transtable
+ type: int?
+ default: 11
+ inputBinding:
+ prefix: --annotation_prodigal_transtable
+- id: annotation_prodigal_forcenonsd
+ type: boolean?
+ inputBinding:
+ prefix: --annotation_prodigal_forcenonsd
+- id: save_databases
+ type: boolean?
+ inputBinding:
+ prefix: --save_databases
+- id: amp_skip_amplify
+ type: boolean?
+ inputBinding:
+ prefix: --amp_skip_amplify
+- id: amp_skip_ampir
+ type: boolean?
+ inputBinding:
+ prefix: --amp_skip_ampir
+- id: amp_ampir_model
+ type: string?
+ default: precursor
+ inputBinding:
+ prefix: --amp_ampir_model
+- id: amp_ampir_minlength
+ type: int?
+ default: 10
+ inputBinding:
+ prefix: --amp_ampir_minlength
+- id: amp_skip_hmmsearch
+ type: boolean?
+ inputBinding:
+ prefix: --amp_skip_hmmsearch
+- id: amp_hmmsearch_models
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --amp_hmmsearch_models
+- id: amp_hmmsearch_savealignments
+ type: boolean?
+ inputBinding:
+ prefix: --amp_hmmsearch_savealignments
+- id: amp_hmmsearch_savetargets
+ type: boolean?
+ inputBinding:
+ prefix: --amp_hmmsearch_savetargets
+- id: amp_hmmsearch_savedomains
+ type: boolean?
+ inputBinding:
+ prefix: --amp_hmmsearch_savedomains
+- id: amp_skip_macrel
+ type: boolean?
+ inputBinding:
+ prefix: --amp_skip_macrel
+- id: amp_ampcombi_db
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --amp_ampcombi_db
+- id: amp_ampcombi_cutoff
+ type: float?
+ default: 0.4
+ inputBinding:
+ prefix: --amp_ampcombi_cutoff
+- id: arg_skip_amrfinderplus
+ type: boolean?
+ inputBinding:
+ prefix: --arg_skip_amrfinderplus
+- id: arg_amrfinderplus_db
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --arg_amrfinderplus_db
+- id: arg_amrfinderplus_identmin
+ type: float?
+ default: -1
+ inputBinding:
+ prefix: --arg_amrfinderplus_identmin
+- id: arg_amrfinderplus_coveragemin
+ type: float?
+ default: 0.5
+ inputBinding:
+ prefix: --arg_amrfinderplus_coveragemin
+- id: arg_amrfinderplus_translationtable
+ type: int?
+ default: 11
+ inputBinding:
+ prefix: --arg_amrfinderplus_translationtable
+- id: arg_amrfinderplus_plus
+ type: boolean?
+ inputBinding:
+ prefix: --arg_amrfinderplus_plus
+- id: arg_amrfinderplus_name
+ type: boolean?
+ inputBinding:
+ prefix: --arg_amrfinderplus_name
+- id: arg_skip_deeparg
+ type: boolean?
+ inputBinding:
+ prefix: --arg_skip_deeparg
+- id: arg_deeparg_data
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --arg_deeparg_data
+- id: arg_deeparg_data_version
+ type: int?
+ default: 2
+ inputBinding:
+ prefix: --arg_deeparg_data_version
+- id: arg_deeparg_model
+ type: string?
+ default: LS
+ inputBinding:
+ prefix: --arg_deeparg_model
+- id: arg_deeparg_minprob
+ type: float?
+ default: 0.8
+ inputBinding:
+ prefix: --arg_deeparg_minprob
+- id: arg_deeparg_alignmentevalue
+ type: float?
+ default: 1e-10
+ inputBinding:
+ prefix: --arg_deeparg_alignmentevalue
+- id: arg_deeparg_alignmentidentity
+ type: int?
+ default: 50
+ inputBinding:
+ prefix: --arg_deeparg_alignmentidentity
+- id: arg_deeparg_alignmentoverlap
+ type: float?
+ default: 0.8
+ inputBinding:
+ prefix: --arg_deeparg_alignmentoverlap
+- id: arg_deeparg_numalignmentsperentry
+ type: int?
+ default: 1000
+ inputBinding:
+ prefix: --arg_deeparg_numalignmentsperentry
+- id: arg_skip_fargene
+ type: boolean?
+ inputBinding:
+ prefix: --arg_skip_fargene
+- id: arg_fargene_hmmmodel
+ type: string?
+ default: |-
+ class_a,class_b_1_2,class_b_3,class_c,class_d_1,class_d_2,qnr,tet_efflux,tet_rpg,tet_enzyme
+ inputBinding:
+ prefix: --arg_fargene_hmmmodel
+- id: arg_fargene_savetmpfiles
+ type: boolean?
+ inputBinding:
+ prefix: --arg_fargene_savetmpfiles
+- id: arg_fargene_score
+ type: float?
+ inputBinding:
+ prefix: --arg_fargene_score
+- id: arg_fargene_minorflength
+ type: int?
+ default: 90
+ inputBinding:
+ prefix: --arg_fargene_minorflength
+- id: arg_fargene_orffinder
+ type: boolean?
+ inputBinding:
+ prefix: --arg_fargene_orffinder
+- id: arg_fargene_translationformat
+ type: string?
+ default: pearson
+ inputBinding:
+ prefix: --arg_fargene_translationformat
+- id: arg_skip_rgi
+ type: boolean?
+ inputBinding:
+ prefix: --arg_skip_rgi
+- id: arg_rgi_savetmpfiles
+ type: boolean?
+ inputBinding:
+ prefix: --arg_rgi_savetmpfiles
+- id: arg_rgi_alignmenttool
+ type: string?
+ default: BLAST
+ inputBinding:
+ prefix: --arg_rgi_alignmenttool
+- id: arg_rgi_includeloose
+ type: boolean?
+ default: true
+ inputBinding:
+ prefix: --arg_rgi_includeloose
+- id: arg_rgi_excludenudge
+ type: boolean?
+ default: true
+ inputBinding:
+ prefix: --arg_rgi_excludenudge
+- id: arg_rgi_lowquality
+ type: boolean?
+ inputBinding:
+ prefix: --arg_rgi_lowquality
+- id: arg_rgi_data
+ type: string?
+ default: NA
+ inputBinding:
+ prefix: --arg_rgi_data
+- id: arg_skip_abricate
+ type: boolean?
+ inputBinding:
+ prefix: --arg_skip_abricate
+- id: arg_abricate_db
+ type: string?
+ default: ncbi
+ inputBinding:
+ prefix: --arg_abricate_db
+- id: arg_abricate_minid
+ type: int?
+ default: 80
+ inputBinding:
+ prefix: --arg_abricate_minid
+- id: arg_abricate_mincov
+ type: int?
+ default: 80
+ inputBinding:
+ prefix: --arg_abricate_mincov
+- id: bgc_skip_antismash
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_skip_antismash
+- id: bgc_antismash_databases
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --bgc_antismash_databases
+- id: bgc_antismash_installationdirectory
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --bgc_antismash_installationdirectory
+- id: bgc_antismash_sampleminlength
+ type: int?
+ default: 1000
+ inputBinding:
+ prefix: --bgc_antismash_sampleminlength
+- id: bgc_antismash_contigminlength
+ type: int?
+ default: 1000
+ inputBinding:
+ prefix: --bgc_antismash_contigminlength
+- id: bgc_antismash_cbgeneral
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_antismash_cbgeneral
+- id: bgc_antismash_cbknownclusters
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_antismash_cbknownclusters
+- id: bgc_antismash_cbsubclusters
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_antismash_cbsubclusters
+- id: bgc_antismash_ccmibig
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_antismash_ccmibig
+- id: bgc_antismash_smcogtrees
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_antismash_smcogtrees
+- id: bgc_antismash_hmmdetectionstrictness
+ type: string?
+ default: relaxed
+ inputBinding:
+ prefix: --bgc_antismash_hmmdetectionstrictness
+- id: bgc_antismash_taxon
+ type: string?
+ default: bacteria
+ inputBinding:
+ prefix: --bgc_antismash_taxon
+- id: bgc_skip_deepbgc
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_skip_deepbgc
+- id: bgc_deepbgc_database
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --bgc_deepbgc_database
+- id: bgc_deepbgc_score
+ type: float?
+ default: 0.5
+ inputBinding:
+ prefix: --bgc_deepbgc_score
+- id: bgc_deepbgc_prodigalsinglemode
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_deepbgc_prodigalsinglemode
+- id: bgc_deepbgc_mergemaxproteingap
+ type: int?
+ inputBinding:
+ prefix: --bgc_deepbgc_mergemaxproteingap
+- id: bgc_deepbgc_mergemaxnuclgap
+ type: int?
+ inputBinding:
+ prefix: --bgc_deepbgc_mergemaxnuclgap
+- id: bgc_deepbgc_minnucl
+ type: int?
+ default: 1
+ inputBinding:
+ prefix: --bgc_deepbgc_minnucl
+- id: bgc_deepbgc_minproteins
+ type: int?
+ default: 1
+ inputBinding:
+ prefix: --bgc_deepbgc_minproteins
+- id: bgc_deepbgc_mindomains
+ type: int?
+ default: 1
+ inputBinding:
+ prefix: --bgc_deepbgc_mindomains
+- id: bgc_deepbgc_minbiodomains
+ type: int?
+ inputBinding:
+ prefix: --bgc_deepbgc_minbiodomains
+- id: bgc_deepbgc_classifierscore
+ type: float?
+ default: 0.5
+ inputBinding:
+ prefix: --bgc_deepbgc_classifierscore
+- id: bgc_skip_gecco
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_skip_gecco
+- id: bgc_gecco_mask
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_gecco_mask
+- id: bgc_gecco_cds
+ type: int?
+ default: 3
+ inputBinding:
+ prefix: --bgc_gecco_cds
+- id: bgc_gecco_pfilter
+ type: float?
+ default: 1e-9
+ inputBinding:
+ prefix: --bgc_gecco_pfilter
+- id: bgc_gecco_threshold
+ type: float?
+ default: 0.8
+ inputBinding:
+ prefix: --bgc_gecco_threshold
+- id: bgc_gecco_edgedistance
+ type: int?
+ inputBinding:
+ prefix: --bgc_gecco_edgedistance
+- id: bgc_skip_hmmsearch
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_skip_hmmsearch
+- id: bgc_hmmsearch_models
+ type: string?
+ default: None
+ inputBinding:
+ prefix: --bgc_hmmsearch_models
+- id: bgc_hmmsearch_savealignments
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_hmmsearch_savealignments
+- id: bgc_hmmsearch_savetargets
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_hmmsearch_savetargets
+- id: bgc_hmmsearch_savedomains
+ type: boolean?
+ inputBinding:
+ prefix: --bgc_hmmsearch_savedomains
+- id: arg_hamronization_summarizeformat
+ type: string?
+ default: tsv
+ inputBinding:
+ prefix: --arg_hamronization_summarizeformat
+- id: genome
+ type: string?
+ inputBinding:
+ prefix: --genome
+- id: fasta
+ type: string?
+ inputBinding:
+ prefix: --fasta
+- id: igenomes_base
+ type: string?
+ default: s3://ngi-igenomes/igenomes
+ inputBinding:
+ prefix: --igenomes_base
+- id: igenomes_ignore
+ type: boolean?
+ inputBinding:
+ prefix: --igenomes_ignore
+- id: custom_config_version
+ type: string?
+ default: master
+ inputBinding:
+ prefix: --custom_config_version
+- id: custom_config_base
+ type: string?
+ default: https://raw.githubusercontent.com/nf-core/configs/master
+ inputBinding:
+ prefix: --custom_config_base
+- id: config_profile_name
+ type: string?
+ inputBinding:
+ prefix: --config_profile_name
+- id: config_profile_description
+ type: string?
+ inputBinding:
+ prefix: --config_profile_description
+- id: config_profile_contact
+ type: string?
+ inputBinding:
+ prefix: --config_profile_contact
+- id: config_profile_url
+ type: string?
+ inputBinding:
+ prefix: --config_profile_url
+- id: max_cpus
+ type: int?
+ default: 16
+ inputBinding:
+ prefix: --max_cpus
+- id: max_memory
+ type: string?
+ default: 128.GB
+ inputBinding:
+ prefix: --max_memory
+- id: max_time
+ type: string?
+ default: 240.h
+ inputBinding:
+ prefix: --max_time
+- id: help
+ type: boolean?
+ inputBinding:
+ prefix: --help
+- id: version
+ type: boolean?
+ inputBinding:
+ prefix: --version
+- id: publish_dir_mode
+ type: string?
+ default: copy
+ inputBinding:
+ prefix: --publish_dir_mode
+- id: email_on_fail
+ type: string?
+ inputBinding:
+ prefix: --email_on_fail
+- id: plaintext_email
+ type: boolean?
+ inputBinding:
+ prefix: --plaintext_email
+- id: max_multiqc_email_size
+ type: string?
+ default: 25.MB
+ inputBinding:
+ prefix: --max_multiqc_email_size
+- id: monochrome_logs
+ type: boolean?
+ inputBinding:
+ prefix: --monochrome_logs
+- id: hook_url
+ type: string?
+ inputBinding:
+ prefix: --hook_url
+- id: multiqc_config
+ type: string?
+ inputBinding:
+ prefix: --multiqc_config
+- id: multiqc_logo
+ type: string?
+ inputBinding:
+ prefix: --multiqc_logo
+- id: multiqc_methods_description
+ type: string?
+ inputBinding:
+ prefix: --multiqc_methods_description
+- id: tracedir
+ type: string?
+ default: ${params.outdir}/pipeline_info
+ inputBinding:
+ prefix: --tracedir
+- id: validate_params
+ type: boolean?
+ default: true
+ inputBinding:
+ prefix: --validate_params
+- id: show_hidden_params
+ type: boolean?
+ inputBinding:
+ prefix: --show_hidden_params
+- id: release
+ type: string?
+ default: 1.0.1
+ inputBinding:
+ prefix: -r
+- id: profile
+ type: string?
+ default: singularity
+ inputBinding:
+ prefix: -profile
+
+outputs:
+- id: out_folder
+ type:
+ type: array
+ items: Directory
+ outputBinding:
+ glob: $(inputs.outdir)
+
+baseCommand:
+- nextflow
+- run
+- nf-core/funcscan
+
+hints: []
--
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