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placeholders for subworkflows
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cjfields committed Jan 8, 2025
1 parent 7464ec0 commit 607c862
Showing 1 changed file with 5 additions and 7 deletions.
12 changes: 5 additions & 7 deletions workflows/tada.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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'
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