64 lines
1.9 KiB
Plaintext
64 lines
1.9 KiB
Plaintext
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process jaffal{
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label "isoforms"
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cpus params.threads
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memory "31 GB"
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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_$sample_id
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# JAFFAL exists with status code 1 when there's 0 fusion hits. Prevent this with '||:'
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$params.jaffal_dir/tools/bin/bpipe run \
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-n "${task.cpus}" \
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-p jaffa_output="\$JAFFAOUT/" \
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-p refBase=$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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summary="\$JAFFAOUT/all/all.summary"
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if [ -f \$summary ]; then
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# The summary is writtten so assume JAFFAL completed.
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if [ ! -s \$summary ]; then
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echo "JAFFAL failed to find any fusion transcripts for ${sample_id}"
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touch "\$JAFFAOUT/${sample_id}_jaffa_results.csv"
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else
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echo JAFFAL found fusion transcripts for ${sample_id}
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mv "\$JAFFAOUT/jaffa_results.csv" "\$JAFFAOUT/${sample_id}_jaffa_results.csv"
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# Add sample id column and header
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sed "s/\$/,${sample_id}/" \$JAFFAOUT/${sample_id}_jaffa_results.csv \
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| sed "1 s/${sample_id}/sample_id/" > tmp
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mv tmp \$JAFFAOUT/${sample_id}_jaffa_results.csv
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fi
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else
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echo JAFFAL encountered an error while prosessing ${sample_id}
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fi
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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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