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fixing translation to dsl2, pending to update to last arriba version #1

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fixing translation to dsl2, pending to update to last arriba version #1

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23 changes: 12 additions & 11 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -52,11 +52,11 @@ process build_star_index {
publishDir params.outdir, mode: 'copy'

input:
file(fasta)
file(gtf)
path(fasta)
path(gtf)

output:
file("star-index")
path("star-index"), emit: index

when: !(params.star_index)

Expand Down Expand Up @@ -95,7 +95,7 @@ process star_mapping{
file(star_index)
output:
//star bam files
tuple val(sample), file("${sample}_STAR.bam")
tuple val(sample), file("${sample}_STAR.bam"), emit: bams
//star mapping stats and gene counts *.{tsv,txt}
tuple val(sample), file("${sample}.{Log.final.out,ReadsPerGene.out.tab,fastq.log}") optional true

Expand Down Expand Up @@ -352,13 +352,14 @@ if(params.reads_csv) {
read_files_star = Channel.fromPath(file(params.reads_csv)).splitCsv(header: true, sep: '\t', strip: true)
.map{row -> [ row.sampleID, [file(row.fwd), file(row.rev)]]}
.ifEmpty{exit 1, "params.reads_csv was empty - no input files supplied" }
//read_files_star.view()

}else if(params.bams){
//we process the bam files
if (file(params.bams).listFiles().findAll { it.name ==~ /.*bam/ }.size() > 0){
if (file(params.bams).listFiles().findAll { it.name ==~ /.*cram/ }.size() > 0){
println "BAM files found, proceed with arriba";
read_files_star=Channel.fromPath( params.bams+'/*.bam' )
.map { path -> [ path.name.replace(".bam",""), path] }//.view()
read_files_star=Channel.fromPath( params.bams+'/*.cram' )
.map { path -> [ path.name.replace(".cram",""), path] }//.view()
mode="BAM"
}else{
println "ERROR: input folder contains no fastq nor BAM files"; System.exit(0)
Expand All @@ -384,13 +385,12 @@ if (params.svs){
// Build STAR index
if(mode!="BAM"){
build_star_index(ch_fasta,ch_gtf)
ch_star_index = params.star_index ? Channel.value(file(params.star_index)).ifEmpty{exit 1, "STAR index not found: ${params.star_index}" } : build_star_index.out
ch_star_index = ch_star_index.dump(tag:'ch_star_index')
ch_star_index = params.star_index ? Channel.value(file(params.star_index)).ifEmpty{exit 1, "STAR index not found: ${params.star_index}" } : build_star_index.out.index
//ch_star_index = ch_star_index
//map the rna-seq reads to the genome
star_mapping(read_files_star,ch_star_index)
read_files_star = star_mapping.out
read_files_star = star_mapping.out.bams
}

//run arriba
if(params.svs){
println "Run arriba in SV mode";
Expand All @@ -400,6 +400,7 @@ if(params.svs){
println "Run arriba";
arriba(read_files_star,ch_fasta,ch_gtf)
}

//we merge into a single channel the arriba result + the star mapping
plot_arriba = params.svs ? read_files_star.join(arriba_sv.out[0]):read_files_star.join(arriba.out[0])

Expand Down
10 changes: 6 additions & 4 deletions nextflow.config
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Expand Up @@ -68,26 +68,28 @@ debug = false

}

// Define timestamp, to avoid overwriting existing trace
def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')

// nextflow run information
timeline {
enabled = true
file = "${params.tracedir}/${manifest.name}_timeline.html"
file = "${params.tracedir}/${manifest.name}_${timestamp}_timeline.html"
}

report {
enabled = true
file = "${params.tracedir}/${manifest.name}_report.html"
file = "${params.tracedir}/${manifest.name}_${timestamp}_report.html"
}

trace {
enabled = true
file = "${params.tracedir}/${manifest.name}_trace.txt"
file = "${params.tracedir}/${manifest.name}_${timestamp}_trace.txt"
}

dag {
enabled = true
file = "${params.tracedir}/${manifest.name}_dag.html"
file = "${params.tracedir}/${manifest.name}_${timestamp}_dag.html"
}

//Mesage regarding errors or complete
Expand Down