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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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|
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workflow { |
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read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) |
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|
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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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|
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process INDEX { |
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tag "$transcriptome.simpleName" |
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|
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input: |
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path transcriptome |
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|
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output: |
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path 'index' |
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|
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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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|
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process FASTQC { |
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tag "FASTQC on $sample_id" |
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publishDir params.outdir |
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|
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input: |
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tuple val(sample_id), path(reads) |
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|
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output: |
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path "fastqc_${sample_id}_logs" |
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|
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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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|
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process QUANT { |
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tag "$pair_id" |
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publishDir params.outdir |
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|
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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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|
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output: |
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path pair_id |
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|
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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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} |
