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/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Andromeda
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Ayu Dark
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Ayu Mirage
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Ayu Light
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Cobalt2
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Night Owl
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Night Owl Light
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Azureus
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Bordo
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Hibernus
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Lilac
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Lux
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Minimus
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Obscuro
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Sereno
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Uva
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Noctis Viola
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Palenight
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Pico 8
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Shades of Purple
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Shades of Purple SD
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Synthwave '84
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Tokyo Night
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Tokyo Night Storm
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Tokyo Night Light
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Winter is Coming
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Winter is Coming Light
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
Winter is Coming Dark
/*
* The following pipeline parameters specify the reference genomes
* and read pairs and can be provided as command line options
*/
params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
INDEX(params.transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
}
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process FASTQC {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple val(sample_id), path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
fastqc.sh "$sample_id" "$reads"
"""
}
process QUANT {
tag "$pair_id"
publishDir params.outdir
input:
path index
tuple val(pair_id), path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}