diff --git a/workflows/tada.nf b/workflows/tada.nf index f6893b6..a345ad7 100644 --- a/workflows/tada.nf +++ b/workflows/tada.nf @@ -12,36 +12,34 @@ include { VSEARCH_EESTATS } from '../modules/local/vsearch_eestats' include { FILTER_AND_TRIM } from '../subworkflows/local/filter_and_trim' include { DADA2_DENOISE } from '../subworkflows/local/dada2_denoise' -// TODO: may want to move into a subworkflow since we will likely implement a -// few additional methods (q2-feature-classifier, IDTAXA, etc) +// include { TAXONOMIC_ASSIGNMENT } from '../subworkflows/local/taxonomic_assignment' include { ASSIGN_TAXA_SPECIES } from '../modules/local/assigntaxaspecies' // TODO: Move into phylogenetic subworkflow +// include { PHYLOGENETICS } from '../subworkflows/local/taxonomic_assignment' include { DECIPHER } from '../modules/local/decipher' include { PHANGORN } from '../modules/local/phangorn' include { FASTTREE } from '../modules/local/fasttree' include { ROOT_TREE } from '../modules/local/roottree' // TODO: Move into subworkflow(s) +// include { QUALITY_CONTROL } from '../subworkflows/local/taxonomic_assignment' include { READ_TRACKING } from '../modules/local/readtracking' include { PLOT_MERGED_HEATMAP } from '../modules/local/plotmerged' include { PLOT_ASV_DIST } from '../modules/local/plotasvlen' +include { SESSION_INFO } from '../modules/local/rsessioninfo' // TODO: Move into subworkflow(s) +// include { OUTPUT } from '../subworkflows/local/taxonomic_assignment' include { BIOM } from '../modules/local/biom' include { SEQTABLE2TEXT } from '../modules/local/seqtable2txt' include { TAXTABLE2TEXT } from '../modules/local/taxtable2txt' - -// TODO: Move into subworkflow(s) include { QIIME2_FEATURETABLE } from '../modules/local/qiime2featuretable' include { QIIME2_TAXTABLE } from '../modules/local/qiime2taxtable' include { QIIME2_SEQUENCE } from '../modules/local/qiime2seqs' include { QIIME2_ALIGNMENT } from '../modules/local/qiime2aln' include { QIIME2_TREE } from '../modules/local/qiime2tree' -// TODO: this can be captured in scripts and used in the versions.yml -include { SESSION_INFO } from '../modules/local/rsessioninfo' - include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'