63 lines
1.2 KiB
Text
63 lines
1.2 KiB
Text
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/*
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* The following pipeline parameters specify the reference genomes
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* and read pairs and can be provided as command line options
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*/
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params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
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params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
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params.outdir = "results"
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workflow {
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read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
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INDEX(params.transcriptome)
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FASTQC(read_pairs_ch)
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QUANT(INDEX.out, read_pairs_ch)
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}
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process INDEX {
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tag "$transcriptome.simpleName"
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input:
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path transcriptome
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output:
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path 'index'
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script:
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"""
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salmon index --threads $task.cpus -t $transcriptome -i index
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"""
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}
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process FASTQC {
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tag "FASTQC on $sample_id"
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publishDir params.outdir
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input:
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tuple val(sample_id), path(reads)
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output:
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path "fastqc_${sample_id}_logs"
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script:
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"""
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fastqc.sh "$sample_id" "$reads"
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"""
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}
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process QUANT {
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tag "$pair_id"
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publishDir params.outdir
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input:
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path index
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tuple val(pair_id), path(reads)
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output:
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path pair_id
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script:
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"""
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salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
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"""
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}
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