diff --git a/CHANGELOG.md b/CHANGELOG.md index 9af07dcf..205f686d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#677](https://github.com/nf-core/ampliseq/pull/677) - Added cut_its information to SDBI export + ### `Fixed` - [#672](https://github.com/nf-core/ampliseq/pull/672) - Update output docs for collapsed abundance tables diff --git a/bin/sbdiexportreannotate.R b/bin/sbdiexportreannotate.R index 19d5e3ae..68a2b392 100755 --- a/bin/sbdiexportreannotate.R +++ b/bin/sbdiexportreannotate.R @@ -18,7 +18,10 @@ dbversion <- args[1] taxfile <- args[2] taxmethod <- args[3] wfversion <- args[4] -predfile <- args[5] +cut_its <- args[5] +predfile <- args[6] + +cut_its = ifelse(cut_its == 'none', '', paste(' cut_its:', cut_its, sep='')) # Read taxonomy table taxonomy <- read.delim(taxfile, sep = '\t', stringsAsFactors = FALSE) @@ -108,10 +111,10 @@ taxtable <- taxonomy %>% date_identified = as.character(lubridate::today()), reference_db = dbversion, annotation_algorithm = case_when( - (taxmethod == 'sintax') ~ paste('Ampliseq',wfversion,'(https://nf-co.re/ampliseq) VSEARCH:sintax', sep=' '), - (!(is.na(otu) | otu == '')) ~ paste('Ampliseq',wfversion,'(https://nf-co.re/ampliseq) addsh', sep=' '), - (!(is.na(species_exact) | species_exact == '')) ~ paste('Ampliseq',wfversion,'(https://nf-co.re/ampliseq) DADA2:assignTaxonomy:addSpecies', sep=' '), - TRUE ~ paste('Ampliseq',wfversion,'(https://nf-co.re/ampliseq) DADA2:assignTaxonomy', sep=' ') + (taxmethod == 'sintax') ~ paste('Ampliseq ',wfversion,' (https://nf-co.re/ampliseq) VSEARCH:sintax',cut_its, sep=' '), + (!(is.na(otu) | otu == '')) ~ paste('Ampliseq ',wfversion,' (https://nf-co.re/ampliseq) addsh',cut_its, sep=' '), + (!(is.na(species_exact) | species_exact == '')) ~ paste('Ampliseq ',wfversion,' (https://nf-co.re/ampliseq) DADA2:assignTaxonomy:addSpecies',cut_its, sep=' '), + TRUE ~ paste('Ampliseq ',wfversion,' (https://nf-co.re/ampliseq) DADA2:assignTaxonomy',cut_its, sep='') ), identification_references = 'https://docs.biodiversitydata.se/analyse-data/molecular-tools/#taxonomy-annotation', taxon_remarks = ifelse(!(is.na(domain) | domain == ''), paste('Domain = \'',domain,'\'',sep=''),''), diff --git a/modules/local/sbdiexportreannotate.nf b/modules/local/sbdiexportreannotate.nf index f06fae36..8ebe870c 100644 --- a/modules/local/sbdiexportreannotate.nf +++ b/modules/local/sbdiexportreannotate.nf @@ -11,6 +11,7 @@ process SBDIEXPORTREANNOTATE { path taxonomytable val taxonomymethod val dbversion + val cut_its path predictions output: @@ -28,7 +29,7 @@ process SBDIEXPORTREANNOTATE { ampliseq_version="v$workflow.manifest.version" fi - sbdiexportreannotate.R \"$dbversion\" $taxonomytable $taxonomymethod \"\$ampliseq_version\" $predictions + sbdiexportreannotate.R \"$dbversion\" $taxonomytable $taxonomymethod \"\$ampliseq_version\" $cut_its $predictions cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf index 05ddfee7..76a07726 100644 --- a/workflows/ampliseq.nf +++ b/workflows/ampliseq.nf @@ -722,11 +722,11 @@ workflow AMPLISEQ { if ( params.sintax_ref_taxonomy ) { SBDIEXPORT ( ch_dada2_asv, ch_sintax_tax, ch_metadata ) db_version = params.sintax_ref_databases[params.sintax_ref_taxonomy]["dbversion"] - SBDIEXPORTREANNOTATE ( ch_sintax_tax, "sintax", db_version, ch_barrnapsummary.ifEmpty([]) ) + SBDIEXPORTREANNOTATE ( ch_sintax_tax, "sintax", db_version, params.cut_its, ch_barrnapsummary.ifEmpty([]) ) } else { SBDIEXPORT ( ch_dada2_asv, ch_dada2_tax, ch_metadata ) db_version = params.dada_ref_databases[params.dada_ref_taxonomy]["dbversion"] - SBDIEXPORTREANNOTATE ( ch_dada2_tax, "dada2", db_version, ch_barrnapsummary.ifEmpty([]) ) + SBDIEXPORTREANNOTATE ( ch_dada2_tax, "dada2", db_version, params.cut_its, ch_barrnapsummary.ifEmpty([]) ) } ch_versions = ch_versions.mix(SBDIEXPORT.out.versions.first()) }