47 lines
1.3 KiB
Plaintext
47 lines
1.3 KiB
Plaintext
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process jaffal{
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label "isoforms"
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input:
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tuple val(sample_id), path(fastq)
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path refBase
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val genome
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val annotation
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output:
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tuple val(sample_id), path("jaffal_output_$sample_id"), emit: results
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tuple val(sample_id), path("jaffal_output_$sample_id/*jaffa_results.csv"), emit: results_csv
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script:
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"""
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JAFFAOUT=jaffal_output_$sample_id
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$params.jaffal_dir/tools/bin/bpipe run \
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-n $params.threads \
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-p jaffa_output="\$JAFFAOUT/" \
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-p refBase=$refBase \
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-p genome=$genome \
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-p annotation=$annotation \
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-p fastqInputFormat="*.fastq" \
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$params.jaffal_dir/JAFFAL.groovy \
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$fastq
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mv "\$JAFFAOUT/jaffa_results.csv" "\$JAFFAOUT/${sample_id}_jaffa_results.csv"
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# Add sample id column
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sed "s/\$/,${sample_id}/" \$JAFFAOUT/${sample_id}_jaffa_results.csv > tmp1
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# Add header
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sed "1 s/${sample_id}/sample_id/" tmp1 > tmp2
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mv tmp2 \$JAFFAOUT/${sample_id}_jaffa_results.csv
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"""
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}
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// workflow module
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workflow gene_fusions {
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take:
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fastq
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refBase
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genome
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annotation
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main:
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jaffal(fastq, refBase, genome, annotation)
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emit:
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results_csv = jaffal.out.results_csv
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results = jaffal.out.results
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}
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