f5ceventalign.nf

/*
 * Eventalign using f5c / nanopolish
 */

process f5ceventalign {

    publishDir "$params.outdir/eventalign_native_16s", pattern: "native*16s*", mode:'copy'
    publishDir "$params.outdir/eventalign_native_23s", pattern: "native*23s*", mode:'copy'
    publishDir "$params.outdir/eventalign_ivt_16s", pattern: "ivt*16s*", mode:'copy'
    publishDir "$params.outdir/eventalign_ivt_23s", pattern: "ivt*23s*", mode:'copy'

    input:
    tuple path(fastq), path(index), path(fai), path(gzi), path(readdb)
    tuple path(bam), path(bai)
    path referencefasta
    val flag

    output:
    path "*_summary.txt", emit: f5csummary_ch
    path "*_eventalign.txt", emit: f5ceventalign_ch
    val true, emit: f5ceventaligndone_ch

    script:
    """
    /home/bhargavam/f5c-v0.7/f5c eventalign --scale-events --signal-index --print-read-names --rna -r $fastq -b $bam -g $referencefasta --summary ${fastq.simpleName}_summary.txt --threads 40 > ${fastq.simpleName}_eventalign.txt
    """
}