Skip to content
Snippets Groups Projects
Commit 292c183a authored by elabaron's avatar elabaron
Browse files

add src/nf_modules/stringtie/transcriptome_{sohrt,long}Reads.nf

parent 34661ee9
No related branches found
No related tags found
No related merge requests found
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
withName: stringtie {
cpus = 1
container = "informationsea/stringtie:2.1.1"
}
}
}
}
params.bam = "$baseDir/data/bam/*.bam"
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { bam_files }
///////////////////////////////////////////////////////////////////////////////
// TRANSCRIPTOME BUILDING
process stringtie {
tag "$file_id"
publishDir "results/stringtie/${file_id}", mode: 'copy'
input:
set file_id, file(bam) from bam_files
output:
file "*.gtf" into gtf_transcriptome
script:
"""
stringtie -L \
-o ${file_id}.gtf \
-f 0.001 \
-j 0.5 ${bam}
"""
}
// END STRNGTIE
params.bam = "$baseDir/data/bam/*.bam"
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { bam_files }
///////////////////////////////////////////////////////////////////////////////
// TRANSCRIPTOME BUILDING
process stringtie {
tag "$file_id"
publishDir "results/stringtie/${file_id}", mode: 'copy'
input:
set file_id, file(bam) from bam_files
output:
file "*.gtf" into gtf_files
script:
"""
stringtie -o ${file_id}.gtf \
-f 0.01 \
-j 0.5 ${bam}
"""
}
// END STRNGTIE
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment