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Merge pull request #43 from hoelzer/analysis
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add analysis only workflow for ideel
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@hoelzer
hoelzer committed Jul 7, 2020
2 parents 1f5ba63 + 814db48 commit 67c2918
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Showing 2 changed files with 97 additions and 75 deletions.
171 changes: 96 additions & 75 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -33,9 +33,11 @@ if( !nextflow.version.matches('20.01+') ) {
}

if (params.profile) { exit 1, "--profile is WRONG use -profile" }
if (params.nano == '' || (params.nano == '' && params.illumina == '')) {
if (params.sra == '') {
exit 1, "input missing, use [--nano] or [--sra] or [--nano] and [--illumina]"
if (params.fasta == '') {
if (params.nano == '' || (params.nano == '' && params.illumina == '')) {
if (params.sra == '') {
exit 1, "input missing, use [--nano] or [--sra] or [--nano] and [--illumina] or [--fasta]"
}
}
}

Expand Down Expand Up @@ -64,6 +66,18 @@ else if (params.illumina) { illumina_input_ch = Channel
.fromFilePairs( params.illumina , checkIfExists: true )
.view() }

// fasta assembly input & --list support
if (params.fasta && params.list) { fasta_input_ch = Channel
.fromPath( params.fasta, checkIfExists: true )
.splitCsv()
.map { row -> ["${row[0]}", file("${row[1]}", checkIfExists: true)] }
.view() }
else if (params.fasta) { fasta_input_ch = Channel
.fromPath( params.fasta, checkIfExists: true)
.map { file -> tuple(file.simpleName, file) }
.view() }


// SRA reads input
if (params.sra) {
nano_input_ch = Channel
Expand Down Expand Up @@ -320,90 +334,96 @@ workflow index_wf {

workflow {

clean_ont_ch = false
clean_ill_ch = false // uses bbduk per default
clean_assembly_ch = false
if (params.illumina && params.nano) {
clean_assembly_ch = file("${baseDir}/clean/assembly/NC_001422_DCS.mmi", checkIfExists: true)
} else {
if (params.illumina) {
clean_assembly_ch = file("${baseDir}/clean/assembly/NC_001422_FNA.mmi", checkIfExists: true)
}
if (params.nano) {
clean_assembly_ch = file("${baseDir}/clean/assembly/DCS_FNA.mmi", checkIfExists: true)
}
if (params.fasta) {
assemblies = fasta_input_ch
}
else {
clean_ont_ch = false
clean_ill_ch = false // uses bbduk per default
clean_assembly_ch = false
if (params.illumina && params.nano) {
clean_assembly_ch = file("${baseDir}/clean/assembly/NC_001422_DCS.mmi", checkIfExists: true)
} else {
if (params.illumina) {
clean_assembly_ch = file("${baseDir}/clean/assembly/NC_001422_FNA.mmi", checkIfExists: true)
}
if (params.nano) {
clean_assembly_ch = file("${baseDir}/clean/assembly/DCS_FNA.mmi", checkIfExists: true)
}
}

// 1) check for user defined minimap2 indices
if (params.clean_ont) { clean_ont_ch = file(params.clean_ont, checkIfExists: true) }
if (params.clean_ill) { clean_ill_ch = file(params.clean_ill, checkIfExists: true) }
if (params.clean_assembly) {
// 1) check for user defined minimap2 indices
if (params.clean_ont) { clean_ont_ch = file(params.clean_ont, checkIfExists: true) }
if (params.clean_ill) { clean_ill_ch = file(params.clean_ill, checkIfExists: true) }
if (params.clean_assembly) {

clean_assembly_ch = file(params.clean_assembly, checkIfExists: true)
}
clean_assembly_ch = file(params.clean_assembly, checkIfExists: true)
}

// 2) build indices if just a fasta is provided
// WIP
if (params.host) {
index_wf(host_input_ch)
clean_ont_ch = index_wf.out[0]
clean_assembly_ch = index_wf.out[1]
}

// 2) build indices if just a fasta is provided
// WIP
if (params.host) {
index_wf(host_input_ch)
clean_ont_ch = index_wf.out[0]
clean_assembly_ch = index_wf.out[1]
}

// 3) download genome and build indices
// WIP
if (params.species) {
download_host_genome()
genome = download_host_genome.out
host_input_ch = Channel.of( [params.species, genome] )
index_wf(host_input_ch)
clean_ont_ch = index_wf.out[0]
clean_assembly_ch = index_wf.out[1]
}
// 3) download genome and build indices
// WIP
if (params.species) {
download_host_genome()
genome = download_host_genome.out
host_input_ch = Channel.of( [params.species, genome] )
index_wf(host_input_ch)
clean_ont_ch = index_wf.out[0]
clean_assembly_ch = index_wf.out[1]
}

// ONT preprocess
nanopore_preprocess_wf(nano_input_ch, clean_ont_ch)
// ONT preprocess
if (params.nano) {
nanopore_preprocess_wf(nano_input_ch, clean_ont_ch)
}

// ILL preprocess
if (params.illumina ) {
illumina_preprocess_wf(illumina_input_ch, clean_ill_ch)
}
// ILL preprocess
if (params.illumina ) {
illumina_preprocess_wf(illumina_input_ch, clean_ill_ch)
}

// Flye-based assembly followed by optional short-read polishing
if (!params.illumina || params.assemblerHybrid != 'spades') {
// assembly w/ flye
nanopore_assembly_wf(nanopore_preprocess_wf.out)
assemblyRaw = nanopore_assembly_wf.out[0]
assemblyRacon = nanopore_assembly_wf.out[1]
assemblyReady = nanopore_assembly_wf.out[2]

// combine for analysis step
assemblies = assemblyRaw.concat(assemblyRacon).concat(assemblyReady)

// polish with short reads
if (params.illumina) {
illumina_polishing_wf(assemblyReady, illumina_preprocess_wf.out)
assemblyReady = illumina_polishing_wf.out
assemblies = assemblies.concat(assemblyReady)
// Flye-based assembly followed by optional short-read polishing
if (!params.illumina || params.assemblerHybrid != 'spades') {
// assembly w/ flye
nanopore_assembly_wf(nanopore_preprocess_wf.out)
assemblyRaw = nanopore_assembly_wf.out[0]
assemblyRacon = nanopore_assembly_wf.out[1]
assemblyReady = nanopore_assembly_wf.out[2]

// combine for analysis step
assemblies = assemblyRaw.concat(assemblyRacon).concat(assemblyReady)

// polish with short reads
if (params.illumina) {
illumina_polishing_wf(assemblyReady, illumina_preprocess_wf.out)
assemblyReady = illumina_polishing_wf.out
assemblies = assemblies.concat(assemblyReady)
}
}
}

// Hybrid SPAdes
if (params.nano && params.illumina && params.assemblerHybrid == 'spades') {
// assembly w/ spades
hybrid_assembly_wf(nanopore_preprocess_wf.out, illumina_preprocess_wf.out)
assemblyReady = hybrid_assembly_wf.out
// Hybrid SPAdes
if (params.nano && params.illumina && params.assemblerHybrid == 'spades') {
// assembly w/ spades
hybrid_assembly_wf(nanopore_preprocess_wf.out, illumina_preprocess_wf.out)
assemblyReady = hybrid_assembly_wf.out

// collect for analysis step
assemblies = assemblyReady
}
// collect for analysis step
assemblies = assemblyReady
}

// clean assembly
if (clean_assembly_ch) {
clean_assembly_wf(assemblyReady, clean_assembly_ch)
assemblyReady = clean_assembly_wf.out
assemblies = assemblies.concat(assemblyReady)
// clean assembly
if (clean_assembly_ch) {
clean_assembly_wf(assemblyReady, clean_assembly_ch)
assemblyReady = clean_assembly_wf.out
assemblies = assemblies.concat(assemblyReady)
}
}

// analysis workflow
Expand Down Expand Up @@ -448,6 +468,7 @@ def helpMSG() {
${c_yellow}Input:${c_reset}
${c_green} --nano ${c_reset} '*.fasta' or '*.fastq.gz' -> one sample per file
${c_green} --illumina ${c_reset} '*.R{1,2}.fastq.gz' -> file pairs
${c_green} --fasta ${c_reset} '*.fasta' or '*.fasta.gz' -> one sample per file
${c_green} --sra ${c_reset} ERR3407986 -> Run acc, currently only for ONT data supported
${c_dim} ..change above input to csv:${c_reset} ${c_green}--list ${c_reset}
Expand Down
1 change: 1 addition & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ params {
// input
nano = ''
illumina = ''
fasta = ''
sra = ''
list = false

Expand Down

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