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default_workflowconfig.settings
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default_workflowconfig.settings
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from snakemake.utils import update_config
config_default = {
"workflows" : {
"seqscreen_workflow" :{
"method":['fast'],
"qual" : ["2","30"],
"db" : "data/SeqScreenDB_21.4/"
},
"samples_input_workflow" : {
# Global parameter for the sample input to run on.
# This replaces having samnples in every workflow
"samples" : ["SRR606249_subset10"]
},
"read_filtering_pretrim_workflow" : {
},
"read_filtering_posttrim_workflow" : {
"qual" : ["2","30"]
},
"read_filtering_multiqc_workflow" : {
},
"read_filtering_khmer_interleave_reads_workflow" : {
"qual" : ["2","30"]
},
"read_filtering_khmer_subsample_interleaved_reads_workflow" : {
"qual" : ["2","30"]
},
"read_filtering_khmer_split_interleaved_reads_workflow" : {
"qual" : ["2","30"]
},
"read_filtering_khmer_count_unique_kmers_workflow" : {
"qual" : ["2","30"],
"kmers" : [21,31,51]
},
"read_filtering_convert_PE_to_SE_workflow":{
"qual" : ["2","30"]
},
"assembly_metaspades_workflow" : {
# the assembly workflow will be run on.
# (metaspades assembler only).
"qual" : ["2","30"],
},
"assembly_spades_workflow" : {
# the assembly workflow will be run on.
# (spades assembler only).
"qual" : ["2","30"],
},
"assembly_plasmidspades_workflow" : {
# the assembly workflow will be run on.
# (plasmidspades assembler only).
"qual" : ["2","30"],
},
"assembly_rnaspades_workflow" : {
# the assembly workflow will be run on.
# (rnaspades assembler only).
"qual" : ["2","30"],
},
"assembly_megahit_workflow" : {
# the assembly workflow will be run on
# (megahit assembler only).
"qual" : ["2","30"],
},
"assembly_all_workflow" : {
# the assembly workflow will be run on
# (all assemblers).
"qual" : ["2","30"],
},
"assembly_quast_workflow" : {
"assembler" : ["megahit","metaspades"],
"qual" : ["2","30"],
},
"assembly_metaquast_workflow" : {
"assembler" : ["megahit","metaspades"],
"qual" : ["2","30"],
},
"assembly_quast_spades_workflow" : {
"qual" : ["2","30"],
},
"assembly_quast_plasmidspades_workflow" : {
"qual" : ["2","30"],
},
"assembly_multiqc_workflow" : {
# #which assembler to get input from
"multiqc_assembler" : ["megahit","metaspades"],
},
"assembly_metaquast_rnaspades_workflow" : {
"qual" : ["2","30"],
},
"assembly_multiqc_rnaspades_workflow" : {
"qual" : ["2","30"],
},
"comparison_reads_workflow": {
# these parameters determine which reads
# the comparison workflow will be run on
"kvalue" : ["21","31","51"],
},
"comparison_assembly_workflow" : {
# these parameters determine which assembled reads
# the comparison workflow will be run on
"kvalue" : ["21","31","51"],
},
"comparison_reads_assembly_workflow" : {
# these parameters determine which reads and assembled
# reads the comparison workflow will be run on
"kvalue" : ["21","31","51"],
},
"tax_class_signatures_workflow" : {
"qual" : ["2","30"],
},
"tax_class_gather_workflow" : {
"qual" : ["2","30"],
"kvalues" : ["21","31","51"]
},
"tax_class_kaijureport_workflow" : {
"qual" : ["2","30"],
},
"tax_class_kaijureport_contigs_workflow" : {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_kaijureport_filtered_workflow" : {
"qual" : ["2","30"],
},
"tax_class_kaijureport_filteredclass_workflow" : {
"qual" : ["2","30"],
},
"tax_class_kaijureport_filteredclass_contigs_workflow" : {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_kaijureport_filtered_contigs_workflow": {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_add_taxonnames_workflow" : {
"qual" : ["2","30"],
},
"tax_class_add_taxonnames_contigs_workflow" : {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_convert_kaiju_to_krona_workflow" : {
"qual" : ["2","30"],
},
"tax_class_kaiju_species_summary_workflow" : {
"qual" : ["2","30"],
},
"tax_class_kaiju_species_summary_contigs_workflow" : {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_visualize_krona_kaijureport_workflow" : {
"qual" : ["2","30"],
},
"tax_class_visualize_krona_kaijureport_contigs_workflow" : {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_visualize_krona_kaijureport_filtered_workflow" : {
"qual" : ["2","30"],
},
"tax_class_visualize_krona_kaijureport_filtered_contigs_workflow" : {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_visualize_krona_kaijureport_filteredclass_workflow" : {
"qual" : ["2","30"],
},
"tax_class_visualize_krona_kaijureport_filteredclass_contigs_workflow": {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_visualize_krona_species_summary_workflow" : {
"qual" : ["2","30"],
},
"tax_class_visualize_krona_species_summary_contigs_workflow" : {
"qual" : ["2","30"],
"assembler" : ["megahit","metaspades"]
},
"tax_class_kraken2_workflow" : {
"qual" : ["2","30"],
# db to run against, this is the default DB downloaded from download python script.
"db" : "minikraken_8GB_20200312",
# confidence score between 0 and 1
"confidence" : 0,
},
"tax_class_krakenuniq_workflow" : {
"qual" : ["2","30"],
# db to run against, this is the default DB downloaded from download python script.
"db" : "minikraken_20171019_8GB",
# hll-precision score between 10 and 18
"hll_precision" : 12
},
"tax_class_bracken_workflow" : {
"read_length" : 100,
"level" : "S",
"threshold" : 0,
#directory that has DB dir. defaults to default dir
"bdb" : "minikraken_8GB_20200312"
},
"tax_class_mash_dist_workflow" : {
"qual" : ["2","30"],
#mash db
"mash_db" : "RefSeq_10K_Sketches.msh",
},
"tax_class_mash_screen_workflow" : {
"qual" : ["2","30"],
#mash db
"mash_db" : "RefSeq_10K_Sketches.msh",
},
"tax_class_mtsv_workflow" : {
"qual" : ["2","30"],
},
"functional_humann2_workflow" : {
"qual" : ["2","30"],
},
"functional_humann3_workflow" : {
"qual" : ["2","30"],
},
"functional_prokka_with_megahit_workflow" : {
# these parameters determine which contig params
# from megahit to run prokka on
"qual" : ["2","30"],
},
"functional_prokka_metatrans_with_rnaspades_workflow" : {
"qual" : ["2","30"],
},
"functional_prokka_trans_with_rnaspades_workflow" : {
"qual" : ["2","30"],
},
"functional_prokka_with_metaspades_workflow" : {
# these parameters determine which contig params
# from metaspades to run prokka on
"qual" : ["2","30"],
},
"functional_prokka_with_spades_workflow" : {
# these parameters determine which contig params
# from spades to run prokka on
"qual" : ["2","30"],
},
"functional_abricate_with_megahit_workflow" : {
# these parameters determine which contig params
# from megahit to run abricate on
"qual" : ["2","30"],
# abricate db's - card, vfdb, argannot, resfinder, ncbibetalactamase, plasmidfinder
#to use custom/external DB file "customDBabricate"
"db" : ["card", "vfdb"],
#"db" : ["customDBabricate"],
},
"functional_abricate_with_metaspades_workflow" : {
# these parameters determine which contig params
# from metaspades to run abricate on
"qual" : ["2","30"],
# abricate internal db's - card, vfdb, argannot, resfinder, ncbibetalactamase, plasmidfinder
#to use custom/external DB file "customDBabricate"
"db" : ["card", "vfdb"],
#"db" : ["customDBabricate"],
},
"functional_abricate_with_spades_workflow" : {
# these parameters determine which contig params
# from spades to run abricate on
"qual" : ["2","30"],
# abricate internal db's - card, vfdb, argannot, resfinder, ncbibetalactamase, plasmidfinder
#to use custom/external DB file "customDBabricate"
"db" : ["card", "vfdb"],
#"db" : ["customDBabricate"],
},
"functional_with_srst2_workflow" : {
# these paramters determine srst2 input
"qual" : ["2","30"],
#srst2 db's - {ARGannot.r3.fasta, ResFinder.fasta, PlasmidFinder.fasta, EcOH.fasta} or external DBs
"db" : ["ARGannot.r3.fasta", "ResFinder.fasta"]
},
"read_filtering_low_complexity_workflow":{
"qual" : ["2", "30"]
}
},
}
update_config(config_default, config)
config = config_default