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initialize channels for pangenome tool outputs and confindr outputs t… #105

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initialize channels for pangenome tool outputs and confindr outputs t… #105

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8 changes: 8 additions & 0 deletions subworkflows/local/pangenome_analysis.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,14 @@ workflow PANGENOME_ANALYSIS {
main:

ch_versions = Channel.empty()
roary_results = Channel.empty()
roary_alignment = Channel.empty()
pirate_results = Channel.empty()
pirate_alignment = Channel.empty()
panaroo_results = Channel.empty()
panaroo_alignment = Channel.empty()
peppan_gff = Channel.empty()
peppan_fna = Channel.empty()

if (params.reference_gff) {
ch_reference_gff = params.reference_gff
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5 changes: 5 additions & 0 deletions subworkflows/local/raw_reads_qc.nf
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Expand Up @@ -34,6 +34,11 @@ workflow RAW_READS_QC {
raw_fastqc = Channel.empty()
trim_fastqc = Channel.empty()

confindr_csv = Channel.empty()
confindr_log = Channel.empty()
confindr_report = Channel.empty()
confindr_rmlst = Channel.empty()
aggregate_confidr = Channel.empty()

//
// Validate database paths
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