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last subworkflow for now; will likely move chimera removal into anoth…
…er one at a later point
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,36 +1,66 @@ | ||
| // TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :) | ||
| // https://github.com/nf-core/modules/tree/master/subworkflows | ||
| // You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace: | ||
| // https://nf-co.re/join | ||
| // TODO nf-core: A subworkflow SHOULD import at least two modules | ||
|
|
||
| include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' | ||
| include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' | ||
| include { BIOM } from '../../modules/local/biom' | ||
| 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' | ||
| include { SESSION_INFO } from '../../modules/local/rsessioninfo' | ||
|
|
||
| workflow GENERATE_OUTPUT { | ||
|
|
||
| // TODO: I'd like to have this simply be TSV files (no RDS) | ||
| // so we can generate from other subworkflows if needed | ||
| take: | ||
| // TODO nf-core: edit input (take) channels | ||
| ch_bam // channel: [ val(meta), [ bam ] ] | ||
| seq_table_rds | ||
| seq_table_qiime | ||
| tax_table_rds | ||
| tax_table_tsv | ||
| asvs | ||
| alignment | ||
| unrooted_tree | ||
| rooted_tree | ||
|
|
||
| main: | ||
|
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||
| ch_versions = Channel.empty() | ||
|
|
||
| // TODO nf-core: substitute modules here for the modules of your subworkflow | ||
| if (params.to_BIOM) { | ||
| BIOM( | ||
| seq_table_rds, | ||
| tax_table_rds | ||
| ) | ||
| } | ||
|
|
||
| SAMTOOLS_SORT ( ch_bam ) | ||
| ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) | ||
| if (params.to_QIIME2) { | ||
| QIIME2_FEATURETABLE( | ||
| seq_table_qiime | ||
| ) | ||
|
|
||
| SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) | ||
| ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) | ||
| QIIME2_TAXTABLE( | ||
| tax_table_tsv | ||
| ) | ||
|
|
||
| emit: | ||
| // TODO nf-core: edit emitted channels | ||
| bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] | ||
| bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] | ||
| csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] | ||
| QIIME2_SEQUENCE( | ||
| asvs | ||
| ) | ||
|
|
||
| if (!params.skip_alignment) { | ||
| QIIME2_ALIGNMENT( | ||
| alignment | ||
| ) | ||
| } | ||
|
|
||
| if (!params.skip_tree) { | ||
| QIIME2_TREE( | ||
| unrooted_tree, | ||
| rooted_tree | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| // TODO: May become redundant with versions | ||
| SESSION_INFO() | ||
|
|
||
| emit: | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,36 +1,49 @@ | ||
| // TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :) | ||
| // https://github.com/nf-core/modules/tree/master/subworkflows | ||
| // You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace: | ||
| // https://nf-co.re/join | ||
| // TODO nf-core: A subworkflow SHOULD import at least two modules | ||
|
|
||
| include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' | ||
| include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' | ||
| 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' | ||
|
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||
| workflow PHYLOGENY { | ||
|
|
||
| take: | ||
| // TODO nf-core: edit input (take) channels | ||
| ch_bam // channel: [ val(meta), [ bam ] ] | ||
| asvs | ||
|
|
||
| main: | ||
|
|
||
| ch_alignment = Channel.empty() | ||
| ch_unrooted_tree = Channel.empty() | ||
| ch_rooted_tree = Channel.empty() | ||
| ch_versions = Channel.empty() | ||
|
|
||
| // TODO nf-core: substitute modules here for the modules of your subworkflow | ||
|
|
||
| SAMTOOLS_SORT ( ch_bam ) | ||
| ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) | ||
|
|
||
| SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) | ||
| ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) | ||
| if (!params.skip_alignment) { | ||
| DECIPHER( | ||
| asvs | ||
| ) | ||
| ch_alignment = DECIPHER.out.alignment | ||
| if (!params.skip_tree) { | ||
| if (params.phylo_tool == 'phangorn') { | ||
| PHANGORN( | ||
| ch_alignment | ||
| ) | ||
| ch_unrooted_tree = PHANGORN.out.treeGTR | ||
| } else if (params.phylo_tool == 'fasttree') { | ||
| FASTTREE( | ||
| ch_alignment | ||
| ) | ||
| ch_unrooted_tree = FASTTREE.out.treeGTR | ||
| } | ||
|
|
||
| ROOT_TREE( | ||
| ch_unrooted_tree, | ||
| params.phylo_tool | ||
| ) | ||
| ch_rooted_tree = ROOT_TREE.out.rooted_tree | ||
| } | ||
| } | ||
|
|
||
| emit: | ||
| // TODO nf-core: edit emitted channels | ||
| bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] | ||
| bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] | ||
| csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] | ||
|
|
||
| versions = ch_versions // channel: [ versions.yml ] | ||
| ch_alignment | ||
| ch_unrooted_tree | ||
| ch_rooted_tree | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,36 +1,30 @@ | ||
| // TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :) | ||
| // https://github.com/nf-core/modules/tree/master/subworkflows | ||
| // You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace: | ||
| // https://nf-co.re/join | ||
| // TODO nf-core: A subworkflow SHOULD import at least two modules | ||
| include { READ_TRACKING } from '../../modules/local/readtracking' | ||
| include { PLOT_MERGED_HEATMAP } from '../../modules/local/plotmerged' | ||
| include { PLOT_ASV_DIST } from '../../modules/local/plotasvlen' | ||
|
|
||
| include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' | ||
| include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' | ||
|
|
||
| workflow QUALITYCONTROL { | ||
| workflow QUALITY_CONTROL { | ||
|
|
||
| take: | ||
| // TODO nf-core: edit input (take) channels | ||
| ch_bam // channel: [ val(meta), [ bam ] ] | ||
| ch_readtracking | ||
| merged_seqs | ||
| filtered_seqtable | ||
|
|
||
| main: | ||
|
|
||
| ch_versions = Channel.empty() | ||
|
|
||
| // TODO nf-core: substitute modules here for the modules of your subworkflow | ||
| READ_TRACKING( | ||
| ch_readtracking.collect() | ||
| ) | ||
|
|
||
| SAMTOOLS_SORT ( ch_bam ) | ||
| ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) | ||
| PLOT_MERGED_HEATMAP( | ||
| merged_seqs | ||
| ) | ||
|
|
||
| SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) | ||
| ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) | ||
| PLOT_ASV_DIST( | ||
| filtered_seqtable | ||
| ) | ||
|
|
||
| emit: | ||
| // TODO nf-core: edit emitted channels | ||
| bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] | ||
| bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] | ||
| csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] | ||
|
|
||
| versions = ch_versions // channel: [ versions.yml ] | ||
| } | ||
|
|
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