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#!/usr/bin/env nextflow
/*
========================================================================================
D A D A 2 P I P E L I N E
========================================================================================
DADA2 NEXTFLOW PIPELINE FOR UCT CBIO
----------------------------------------------------------------------------------------
*/
def helpMessage() {
log.info"""
===================================
${workflow.repository}/16S-rDNA-dada2-pipeline ~ version ${params.version}
===================================
Usage:
This pipeline can be run specifying parameters in a config file or with command line flags.
The typical example for running the pipeline with command line flags is as follows:
nextflow run uct-cbio/16S-rDNA-dada2-pipeline --reads '*_R{1,2}.fastq.gz' --trimFor 24 --trimRev 25 --reference 'gg_13_8_train_set_97.fa.gz' -profile uct_hex
The typical command for running the pipeline with your own config (instead of command line flags) is as follows:
nextflow run uct-cbio/16S-rDNA-dada2-pipeline -c dada2_user_input.config -profile uct_hex
where:
dada2_user_input.config is the configuration file (see example 'dada2_user_input.config')
NB: -profile uct_hex still needs to be specified from the command line
To override existing values from the command line, please type these parameters:
Mandatory arguments:
--reads Path to input data (must be surrounded with quotes)
-profile Hardware config to use. Currently profile available for UCT's HPC 'uct_hex' - create your own if necessary
NB -profile should always be specified on the command line, not in the config file
--trimFor integer. headcrop of read1 (set 0 if no trimming is needed)
--trimRev integer. headcrop of read2 (set 0 if no trimming is needed)
--reference Path to taxonomic database to be used for annotation (e.g. gg_13_8_train_set_97.fa.gz)
All available read preparation parameters:
--trimFor integer. headcrop of read1
--trimRev integer. headcrop of read2
--truncFor integer. truncate read1 here (i.e. if you want to trim 10bp off the end of a 250bp R1, truncFor should be set to 240). enforced before trimFor/trimRev
--truncRev integer. truncate read2 here ((i.e. if you want to trim 10bp off the end of a 250bp R2, truncRev should be set to 240). enforced before trimFor/trimRev
--maxEEFor integer. After truncation, R1 reads with higher than maxEE "expected errors" will be discarded. EE = sum(10^(-Q/10)), default=2
--maxEERev integer. After truncation, R1 reads with higher than maxEE "expected errors" will be discarded. EE = sum(10^(-Q/10)), default=2
--truncQ integer. Truncate reads at the first instance of a quality score less than or equal to truncQ; default=2
--maxN integer. Discard reads with more than maxN number of Ns in read; default=0
--maxLen integer. maximum length of sequence; maxLen is enforced before trimming and truncation; default=Inf (no maximum)
--minLen integer. minLen is enforced after trimming and truncation; default=50
--rmPhiX {"T","F"}. remove PhiX from read
--minOverlap integer. minimum length of the overlap required for merging R1 and R2; default=20 (dada2 package default=12)
--maxMismatch integer. The maximum mismatches allowed in the overlap region; default=0
--trimOverhang {"T","F"}. If "T" (true), "overhangs" in the alignment between R1 and R2 are trimmed off.
"Overhangs" are when R2 extends past the start of R1, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region. Default="F" (false)
Other arguments:
--pool Should sample pooling be used to aid identification of low-abundance ASVs? Options are
pseudo pooling: "pseudo", true: "T", false: "F"
--outdir The output directory where the results will be saved
--email Set this parameter to your e-mail address to get a summary e-mail with details of the run
sent to you when the workflow exits
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
Help:
--help Will print out summary above when executing nextflow run uct-cbio/16S-rDNA-dada2-pipeline
""".stripIndent()
}
/*
* SET UP CONFIGURATION VARIABLES
*/
// Configurable variables
params.name = false
params.project = false
params.email = false
params.plaintext_email = false
// Show help emssage
params.help = false
if (params.help){
helpMessage()
exit 0
}
//Validate inputs
if ( params.trimFor == false ) {
exit 1, "Must set length of R1 (--trimFor) that needs to be trimmed (set 0 if no trimming is needed)"
}
if ( params.trimRev == false ) {
exit 1, "Must set length of R2 (--trimRev) that needs to be trimmed (set 0 if no trimming is needed)"
}
if ( params.reference == false ) {
exit 1, "Must set reference database using --reference"
}
// Has the run name been specified by the user?
// this has the bonus effect of catching both -name and --name
custom_runName = params.name
if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
custom_runName = workflow.runName
}
Channel
.fromFilePairs( params.reads )
.ifEmpty { error "Cannot find any reads matching: ${params.reads}" }
.into { dada2ReadPairsToQual; dada2ReadPairs }
refFile = file(params.reference)
// Header log info
log.info "==================================="
log.info " uct-cbio/16S-rDNA-dada2-pipeline ~ version ${params.version}"
log.info "==================================="
def summary = [:]
summary['Run Name'] = custom_runName ?: workflow.runName
summary['Reads'] = params.reads
summary['trimFor'] = params.trimFor
summary['trimRev'] = params.trimRev
summary['truncFor'] = params.truncFor
summary['truncRev'] = params.truncRev
summary['truncQ'] = params.truncQ
summary['maxEEFor'] = params.maxEEFor
summary['maxEERev'] = params.maxEERev
summary['maxN'] = params.maxN
summary['maxLen'] = params.maxLen
summary['minLen'] = params.minLen
summary['rmPhiX'] = params.rmPhiX
summary['minOverlap'] = params.minOverlap
summary['maxMismatch'] = params.maxMismatch
summary['trimOverhang'] = params.trimOverhang
summary['species'] = params.species
summary['pool'] = params.pool
summary['Reference'] = params.reference
summary['Max Memory'] = params.max_memory
summary['Max CPUs'] = params.max_cpus
summary['Max Time'] = params.max_time
summary['Output dir'] = params.outdir
summary['Working dir'] = workflow.workDir
summary['Container'] = workflow.container
if(workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Current home'] = "$HOME"
summary['Current user'] = "$USER"
summary['Current path'] = "$PWD"
summary['Script dir'] = workflow.projectDir
summary['Config Profile'] = workflow.profile
if(params.email) {
summary['E-mail Address'] = params.email
}
log.info summary.collect { k,v -> "${k.padRight(15)}: $v" }.join("\n")
log.info "========================================="
/*
*
* Step 1: Filter and trim (run per sample?)
*
*/
process runFastQC {
tag { "rFQC.${pairId}" }
publishDir "${params.outdir}/dada2-FilterAndTrim", mode: "copy", overwrite: false
input:
set pairId, file(in_fastq) from dada2ReadPairsToQual
output:
file("${pairId}_fastqc/*.zip") into fastqc_files
"""
mkdir ${pairId}_fastqc
fastqc --outdir ${pairId}_fastqc \
${in_fastq.get(0)} \
${in_fastq.get(1)}
"""
}
process runMultiQC{
tag { "rMQC" }
publishDir "${params.outdir}/dada2-FilterAndTrim", mode: 'copy', overwrite: false
input:
file('*') from fastqc_files.collect()
output:
file('multiqc_report.html')
"""
multiqc .
"""
}
process filterAndTrim {
tag { "filterAndTrim" }
publishDir "${params.outdir}/dada2-FilterAndTrim", mode: "copy", overwrite: false
input:
set pairId, file(reads) from dada2ReadPairs
output:
set val(pairId), "*.R1.filtered.fastq.gz", "*.R2.filtered.fastq.gz" into filteredReadsforQC, filteredReads
file "*.R1.filtered.fastq.gz" into forReads
file "*.R2.filtered.fastq.gz" into revReads
file "*.trimmed.txt" into trimTracking
script:
"""
#!/usr/bin/env Rscript
library(dada2); packageVersion("dada2")
#Variable selection from CLI input flag --rmPhix
if("${params.rmPhiX}"=="F"){
rm.phix <- FALSE
} else if("${params.rmPhiX}"=="T"){
rm.phix <- TRUE
}
print(rm.phix)
out <- filterAndTrim(fwd = "${reads[0]}",
filt = paste0("${pairId}", ".R1.filtered.fastq.gz"),
rev = "${reads[1]}",
filt.rev = paste0("${pairId}", ".R2.filtered.fastq.gz"),
trimLeft = c(${params.trimFor},${params.trimRev}),
truncLen = c(${params.truncFor},${params.truncRev}),
maxEE = c(${params.maxEEFor},${params.maxEERev}),
truncQ = ${params.truncQ},
maxN = ${params.maxN},
rm.phix = rm.phix,
maxLen = ${params.maxLen},
minLen = ${params.minLen},
compress = TRUE,
verbose = TRUE,
multithread = ${task.cpus})
write.csv(out, paste0("${pairId}", ".trimmed.txt"))
"""
}
process runFastQC_postfilterandtrim {
tag { "rFQC_post_FT.${pairId}" }
publishDir "${params.outdir}/FastQC_post_filter_trim", mode: "copy", overwrite: false
input:
set val(pairId), file(filtFor), file(filtRev) from filteredReadsforQC
output:
file("${pairId}_fastqc_postfiltertrim/*.zip") into fastqc_files_2
"""
mkdir ${pairId}_fastqc_postfiltertrim
fastqc --outdir ${pairId}_fastqc_postfiltertrim \
${filtFor} \
${filtRev}
"""
}
process runMultiQC_postfilterandtrim {
tag { "rMQC_post_FT" }
publishDir "${params.outdir}/FastQC_post_filter_trim", mode: 'copy', overwrite: false
input:
file('*') from fastqc_files_2.collect()
output:
file('multiqc_report.html')
"""
multiqc .
"""
}
process mergeTrimmedTable {
tag { "mergTrimmedTable" }
publishDir "${params.outdir}/dada2-FilterAndTrim", mode: "copy", overwrite: false
input:
file trimData from trimTracking.collect()
output:
file "all.trimmed.csv" into trimmedReadTracking
script:
"""
#!/usr/bin/env Rscript
trimmedFiles <- list.files(path = '.', pattern = '*.trimmed.txt')
sample.names <- sub('.trimmed.txt', '', trimmedFiles)
trimmed <- do.call("rbind", lapply(trimmedFiles, function (x) as.data.frame(read.csv(x))))
colnames(trimmed)[1] <- "Sequence"
trimmed\$SampleID <- sample.names
write.csv(trimmed, "all.trimmed.csv", row.names = FALSE)
"""
}
/*
*
* Step 2: Learn error rates (run on all samples)
*
*/
// TODO: combine For and Rev process to reduce code duplication?
process LearnErrorsFor {
tag { "LearnErrorsFor" }
publishDir "${params.outdir}/dada2-LearnErrors", mode: "copy", overwrite: false
input:
file fReads from forReads.collect()
output:
file "errorsF.RDS" into errorsFor
script:
"""
#!/usr/bin/env Rscript
library(dada2);
packageVersion("dada2")
# File parsing
filtFs <- list.files('.', pattern="R1.filtered.fastq.gz", full.names = TRUE)
sample.namesF <- sapply(strsplit(basename(filtFs), "_"), `[`, 1) # Assumes filename = samplename_XXX.fastq.gz
set.seed(100)
# Learn forward error rates
errF <- learnErrors(filtFs, multithread=${task.cpus})
pdf("R1.err.pdf")
plotErrors(errF, nominalQ=TRUE)
dev.off()
saveRDS(errF, "errorsF.RDS")
"""
}
process LearnErrorsRev {
tag { "LearnErrorsRev" }
publishDir "${params.outdir}/dada2-LearnErrors", mode: "copy", overwrite: false
input:
file rReads from revReads.collect()
output:
file "errorsR.RDS" into errorsRev
script:
"""
#!/usr/bin/env Rscript
library(dada2);
packageVersion("dada2")
# load error profiles
# File parsing
filtRs <- list.files('.', pattern="R2.filtered.fastq.gz", full.names = TRUE)
sample.namesR <- sapply(strsplit(basename(filtRs), "_"), `[`, 1) # Assumes filename = samplename_XXX.fastq.gz
set.seed(100)
# Learn forward error rates
errR <- learnErrors(filtRs, multithread=${task.cpus})
pdf("R2.err.pdf")
plotErrors(errR, nominalQ=TRUE)
dev.off()
saveRDS(errR, "errorsR.RDS")
"""
}
/*
*
* Step 3: Dereplication, Sample Inference, Merge Pairs
*
*/
// TODO: allow serial processing of this step?
process SampleInferDerepAndMerge {
tag { "SampleInferDerepAndMerge" }
publishDir "${params.outdir}/dada2-Derep", mode: "copy", overwrite: false
input:
set val(pairId), file(filtFor), file(filtRev) from filteredReads
file errFor from errorsFor
file errRev from errorsRev
output:
file "*.merged.RDS" into mergedReads
file "*.ddF.RDS" into dadaFor
file "*.ddR.RDS" into dadaRev
script:
"""
#!/usr/bin/env Rscript
library(dada2)
packageVersion("dada2")
errF <- readRDS("${errFor}")
errR <- readRDS("${errRev}")
cat("Processing:", "${pairId}", "\\n")
#Variable selection from CLI input flag --pool
if("${params.pool}"=="pseudo"){
pool <- "pseudo"
} else if("${params.pool}"=="F"){
pool <- FALSE
} else if("${params.pool}"=="T"){
pool <- TRUE
}
print(pool)
derepF <- derepFastq("${filtFor}")
ddF <- dada(derepF, err=errF, multithread=${task.cpus}, pool=pool)
derepR <- derepFastq("${filtRev}")
ddR <- dada(derepR, err=errR, multithread=${task.cpus},pool=pool)
#Variable selection from CLI input flag --trimOverhang
if("${params.trimOverhang}"=="F"){
trimOverhang <- FALSE
} else if("${params.trimOverhang}"=="T"){
trimOverhang <- TRUE
}
print(trimOverhang)
merger <- mergePairs(ddF, derepF, ddR, derepR,
minOverlap = ${params.minOverlap},
maxMismatch = ${params.maxMismatch},
trimOverhang = trimOverhang
)
# TODO: make this a single item list with ID as the name, this is lost
# further on
saveRDS(merger, paste("${pairId}", "merged", "RDS", sep="."))
saveRDS(ddF, paste("${pairId}", "ddF", "RDS", sep="."))
saveRDS(ddR, paste("${pairId}", "ddR", "RDS", sep="."))
"""
}
// TODO: step may be obsolete if we run the above serially
process mergeDadaRDS {
tag { "mergeDadaRDS" }
publishDir "${params.outdir}/dada2-Inference", mode: "copy", overwrite: false
input:
file ddFs from dadaFor.collect()
file ddRs from dadaRev.collect()
output:
file "all.ddF.RDS" into dadaForReadTracking
file "all.ddR.RDS" into dadaRevReadTracking
script:
'''
#!/usr/bin/env Rscript
library(dada2)
packageVersion("dada2")
dadaFs <- lapply(list.files(path = '.', pattern = '.ddF.RDS$'), function (x) readRDS(x))
names(dadaFs) <- sub('.ddF.RDS', '', list.files('.', pattern = '.ddF.RDS'))
dadaRs <- lapply(list.files(path = '.', pattern = '.ddR.RDS$'), function (x) readRDS(x))
names(dadaRs) <- sub('.ddR.RDS', '', list.files('.', pattern = '.ddR.RDS'))
saveRDS(dadaFs, "all.ddF.RDS")
saveRDS(dadaRs, "all.ddR.RDS")
'''
}
/*
*
* Step 4: Construct sequence table
*
*/
process SequenceTable {
tag { "SequenceTable" }
publishDir "${params.outdir}/dada2-SeqTable", mode: "copy", overwrite: false
input:
file mr from mergedReads.collect()
output:
file "seqtab.RDS" into seqTable
file "mergers.RDS" into mergerTracking
script:
'''
#!/usr/bin/env Rscript
library(dada2)
packageVersion("dada2")
mergerFiles <- list.files(path = '.', pattern = '.*.RDS$')
pairIds <- sub('.merged.RDS', '', mergerFiles)
mergers <- lapply(mergerFiles, function (x) readRDS(x))
names(mergers) <- pairIds
seqtab <- makeSequenceTable(mergers)
saveRDS(seqtab, "seqtab.RDS")
saveRDS(mergers, "mergers.RDS")
'''
}
/*
*
* Step 8: Remove chimeras
*
*/
if (params.species) {
speciesFile = file(params.species)
process ChimeraTaxonomySpecies {
tag { "ChimeraTaxonomySpecies" }
publishDir "${params.outdir}/dada2-Chimera-Taxonomy", mode: "copy", overwrite: false
input:
file st from seqTable
file ref from refFile
file sp from speciesFile
output:
file "seqtab_final.RDS" into seqTableFinal,seqTableFinalTree,seqTableFinalTracking
file "tax_final.RDS" into taxFinal
script:
"""
#!/usr/bin/env Rscript
library(dada2)
packageVersion("dada2")
st.all <- readRDS("${st}")
# Remove chimeras
seqtab <- removeBimeraDenovo(st.all, method="consensus", multithread=${task.cpus})
# Assign taxonomy
tax <- assignTaxonomy(seqtab, "${ref}", multithread=${task.cpus})
tax <- addSpecies(tax, "${sp}")
# Write to disk
saveRDS(seqtab, "seqtab_final.RDS")
saveRDS(tax, "tax_final.RDS")
"""
}
} else {
process ChimeraTaxonomy {
tag { "ChimeraTaxonomy" }
publishDir "${params.outdir}/dada2-Chimera-Taxonomy", mode: "copy", overwrite: false
input:
file st from seqTable
file ref from refFile
output:
file "seqtab_final.RDS" into seqTableFinal,seqTableFinalTree,seqTableFinalTracking
file "tax_final.RDS" into taxFinal
script:
"""
#!/usr/bin/env Rscript
library(dada2)
packageVersion("dada2")
st.all <- readRDS("${st}")
# Remove chimeras
seqtab <- removeBimeraDenovo(st.all, method="consensus", multithread=${task.cpus})
# Assign taxonomy
tax <- assignTaxonomy(seqtab, "${ref}", multithread=${task.cpus})
# Write to disk
saveRDS(seqtab, "seqtab_final.RDS")
saveRDS(tax, "tax_final.RDS")
"""
}
}
/*
*
* Step 9: Construct phylogenetic tree
*
*/
// TODO: break into more steps? phangorn takes a long time...
process AlignAndGenerateTree {
tag { "AlignAndGenerateTree" }
publishDir "${params.outdir}/dada2-Alignment", mode: "copy", overwrite: false
input:
file sTable from seqTableFinalTree
output:
file "aligned_seqs.fasta" into alnFile
file "phangorn.tree.RDS" into treeRDS
file "tree.newick" into treeFile
file "tree.GTR.newick" into treeGTRFile
script:
"""
#!/usr/bin/env Rscript
library(dada2)
library(DECIPHER)
library(phangorn)
seqs <- getSequences(readRDS("${sTable}"))
names(seqs) <- seqs # This propagates to the tip labels of the tree
alignment <- AlignSeqs(DNAStringSet(seqs),
anchor=NA,
processors = ${task.cpus})
writeXStringSet(alignment, "aligned_seqs.fasta")
# TODO: optimize this, or maybe split into a second step?
phang.align <- phyDat(as(alignment, "matrix"), type="DNA")
dm <- dist.ml(phang.align)
treeNJ <- NJ(dm) # Note, tip order != sequence order
fit = pml(treeNJ, data=phang.align)
write.tree(fit\$tree, file = "tree.newick")
## negative edges length changed to 0!
fitGTR <- update(fit, k=4, inv=0.2)
fitGTR <- optim.pml(fitGTR, model="GTR", optInv=TRUE, optGamma=TRUE,
rearrangement = "stochastic", control = pml.control(trace = 0))
saveRDS(fitGTR, "phangorn.tree.RDS")
write.tree(fitGTR\$tree, file = "tree.GTR.newick")
"""
}
process BiomFile {
tag { "BiomFile" }
publishDir "${params.outdir}/dada2-BIOM", mode: "copy", overwrite: false
input:
file sTable from seqTableFinal
file tTable from taxFinal
output:
file "dada2.biom" into biomFile
script:
"""
#!/usr/bin/env Rscript
library(biomformat)
packageVersion("biomformat")
seqtab <- readRDS("${sTable}")
taxtab <- readRDS("${tTable}")
st.biom <- make_biom(t(seqtab), observation_metadata = taxtab)
write_biom(st.biom, "dada2.biom")
"""
}
/*
*
* Step 10: Track reads
*
*/
// Broken: needs a left-join on the initial table
process ReadTracking {
tag { "ReadTracking" }
publishDir "${params.outdir}/dada2-ReadTracking", mode: "copy", overwrite: false
input:
file trimmedTable from trimmedReadTracking
file sTable from seqTableFinalTracking
file mergers from mergerTracking
file ddFs from dadaForReadTracking
file ddRs from dadaRevReadTracking
output:
file "all.readtracking.txt"
script:
"""
#!/usr/bin/env Rscript
library(dada2)
packageVersion("dada2")
library(dplyr)
getN <- function(x) sum(getUniques(x))
dadaFs <- as.data.frame(sapply(readRDS("${ddFs}"), getN))
dadaFs\$SampleID <- rownames(dadaFs)
dadaRs <- as.data.frame(sapply(readRDS("${ddRs}"), getN))
dadaRs\$SampleID <- rownames(dadaRs)
mergers <- as.data.frame(sapply(readRDS("${mergers}"), getN))
mergers\$SampleID <- rownames(mergers)
seqtab.nochim <- as.data.frame(rowSums(readRDS("${sTable}")))
seqtab.nochim\$SampleID <- rownames(seqtab.nochim)
trimmed <- read.csv("${trimmedTable}")
track <- Reduce(function(...) merge(..., by = "SampleID"), list(trimmed, dadaFs, dadaRs, mergers, seqtab.nochim))
colnames(track) <- c("SampleID", "SequenceR1", "input", "filtered", "denoisedF", "denoisedR", "merged", "nonchim")
write.table(track, "all.readtracking.txt", sep = "\t", row.names = FALSE)
"""
}
/*
* Completion e-mail notification
*/
workflow.onComplete {
def subject = "[uct-cbio/16S-rDNA-dada2-pipeline] Successful: $workflow.runName"
if(!workflow.success){
subject = "[uct-cbio/16S-rDNA-dada2-pipeline] FAILED: $workflow.runName"
}
def email_fields = [:]
email_fields['version'] = params.version
email_fields['runName'] = custom_runName ?: workflow.runName
email_fields['success'] = workflow.success
email_fields['dateComplete'] = workflow.complete
email_fields['duration'] = workflow.duration
email_fields['exitStatus'] = workflow.exitStatus
email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
email_fields['errorReport'] = (workflow.errorReport ?: 'None')
email_fields['commandLine'] = workflow.commandLine
email_fields['projectDir'] = workflow.projectDir
email_fields['summary'] = summary
email_fields['summary']['Date Started'] = workflow.start
email_fields['summary']['Date Completed'] = workflow.complete
email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
if(workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
if(workflow.container) email_fields['summary']['Docker image'] = workflow.container
// Render the TXT template
def engine = new groovy.text.GStringTemplateEngine()
def tf = new File("$baseDir/assets/email_template.txt")
def txt_template = engine.createTemplate(tf).make(email_fields)
def email_txt = txt_template.toString()
// Render the HTML template
def hf = new File("$baseDir/assets/email_template.html")
def html_template = engine.createTemplate(hf).make(email_fields)
def email_html = html_template.toString()
// Render the sendmail template
def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir" ]
def sf = new File("$baseDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString()
// Send the HTML e-mail
if (params.email) {
try {
if( params.plaintext_email ){ throw GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
[ 'sendmail', '-t' ].execute() << sendmail_html
log.info "[uct-cbio/16S-rDNA-dada2-pipeline] Sent summary e-mail to $params.email (sendmail)"
} catch (all) {
// Catch failures and try with plaintext
[ 'mail', '-s', subject, params.email ].execute() << email_txt
log.info "[uct-cbio/16S-rDNA-dada2-pipeline] Sent summary e-mail to $params.email (mail)"
}
}
}