Table Of Conents¶
- Front Page
- Installing and Updating YMP
- Configuration
- Command Line
- ymp
- env
- init
- make
- show
- stage
- submit
-P--pdb-q--quiet-v--verbose--log-file-n--dryrun-p--printshellcmds-k--keepgoing--lock--no-lock--rerun-incomplete--ri-F--forceall-f--force--notemp-t--touch--shadow-prefix-r--reason-N--nohup-P--profile-c--snake-config-d--drmaa-s--sync-i--immediate--command--wrapper--max-jobs-per-second-l--latency-wait-J--cluster-cores-j--cores--args--scriptnameTARGET_FILES
-P--pdb-q--quiet-v--verbose--log-file--version--install-completion--profile
- ymp
- Stages
annotate_blastannotate_diamondannotate_prodigalannotate_tblastnassemble_megahitassemble_metaspadesassemble_trinitybin_metabat2checkcluster_cdhitcorrect_bbmapcount_diamondcount_stringtiecoverage_samtoolsdedup_bbmapdust_bbmapextract_readsextract_seqsfilter_bmtaggerformat_bbmaphumann2index_bbmapindex_blastindex_bmtaggerindex_bowtie2index_diamondmap_bbmapmap_bowtie2map_diamondmap_hisat2map_starmetaphlan2primermatch_bbmapprofile_centrifugeqc_fastqcqc_multiqcqc_quastquant_rsemreferencesremove_bbmapsort_bamsplit_librarytrim_bbmaptrim_sickletrim_trimmomaticdownload_file_ftpdownload_file_httpprefetchfastq_dumpcombine_with_refalign_mafftblast7_mergeblast7_extractblast7_extract_mergeblast7_allblast7_reportsblast7_eval_histblast7_eval_plotcdhit_fna_single878889909192faa_fastpfasta_to_fastp_gzgunzipmkdirfq2famake_otu_tableotu_to_qiime_txtotu_to_biomblast7_coverage_per_otupick_open_otuspick_closed_otusrarefy_tableconvert_to_closed_refenv_waitticktocknoopnormalize_16Spredict_metagenomecategorize_by_functionraxml_treersem_indexscnic_within_minsampscnic_within_sparcc_filterstar_index
- API
- ymp package
- Subpackages
- ymp.cli package
- ymp.stage package
- Submodules
- ymp.stage.base module
- ymp.stage.expander module
- ymp.stage.groupby module
- ymp.stage.pipeline module
- ymp.stage.project module
PandasProjectDataPandasTableBuilderProjectKEY_BCCOLKEY_DATAKEY_IDCOLKEY_READCOLSRE_FILERE_REMOTERE_SRRchoose_fq_columnschoose_id_columndataencode_barcode_pathfq_namesfwd_fq_namesfwd_pe_fq_namesget_fq_namesget_idsidcoliter_samplesminimize_variablesoutputspe_fq_namesproject_nameraw_reads_source_pathrev_pe_fq_namesrunsse_fq_namessource_cfgsource_pathunsplit_pathvariables
SQLiteProjectData
- ymp.stage.reference module
- ymp.stage.stack module
- ymp.stage.stage module
- Submodules
- ymp.blast module
- ymp.blast2gff module
- ymp.cluster module
- ymp.common module
- ymp.config module
- ymp.dna module
- ymp.download module
- ymp.env module
- ymp.exceptions module
- ymp.gff module
- ymp.helpers module
- ymp.map2otu module
- ymp.nuc2aa module
- ymp.snakemake module
BaseExpanderCircularReferenceExceptionColonExpanderDefaultExpanderExpandLateExceptionExpandableWorkflowFormatExpanderInheritanceExceptionInheritanceExpanderNamedListRecursiveExpanderSnakemakeExpanderWorkflowObjectcheck_snakemakeget_workflowload_workflowmake_rulenetworkxprint_ruleinforuleinfo_fields
- ymp.snakemakelexer module
- ymp.sphinxext module
- ymp.string module
- ymp.util module
- ymp.yaml module
get_configprint_rulesnakemake_versions
- Subpackages
- ymp package