feat: Add JaBbA workflow wiring

Some parameters were removed since they are no longer present in the
current jba executable. Others were modified. Did not add ASCAT since
the default purity/ploidy caller is actually sequenza which is imported
by default (the JaBbA docker container also has it installed).

modules/local/jabba/main.nf

@@ -8,33 +8,43 @@ process JABBA {
 
     input:
     tuple val(meta), path(cov_rds)
-    tuple val(meta), path(junctionFilePath)
-    val(field)
-    path(junctionUnfiltered)
+    tuple val(meta), path(junction)
+    path(j_supp)
+    path(blacklist_junctions)
+    val(geno)
+    val(indel)
     val(tfield)
-    path(cbs_nseg_rds)
+    val(iter)
+    val(rescue_window)
+    val(rescue_all)
+    val(nudgebalanced)
+    val(edgenudge)
+    val(strict)
+    val(allin)
+    val(field)
     path(cbs_seg_rds)
-    val(slack)
+    val(maxna)
+    path(blacklist_coverage)
+    path(cbs_nseg_rds)
     path(het_pileups_wgs)
-    val(purity)
     val(ploidy)
-    val(tilim)
-    val(epgap)
+    val(purity)
     val(pp_method)
-    val(maxna)
-    val(flags)
-    path(blacklist_coverage)
-    path(blacklist_junctions)
-    val(iter)
-    val(pair)
-    val(indel)
     val(cnsignif)
+    val(slack)
+    val(linear)
+    val(tilim)
+    val(epgap)
+    val(outdir)
+    val(name)
+    val(fix_thres)
     val(lp)
     val(ism)
-    val(treemem)
-    val(fix_thres)
+    val(filter_loose)
     val(gurobi)
     val(nonintegral)
+    val(verbose)
+    val(help)
 
     output:
     tuple val(meta), path("*.jabba.simple.rds")      , emit: jabba_rds, optional: true
@@ -53,12 +63,7 @@ process JABBA {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def VERSION    = '1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    def VERSION    = '1.1'
     """
     #!/bin/bash
 
@@ -95,7 +100,46 @@ process JABBA {
     echo $jba
     set +x
 
-    export cmd="Rscript $jba \$@"
+    export cmd="Rscript $jba $cov_rds $junction \\
+    --j.supp                $j_supp \\
+    --blacklist.junctions	$blacklist_junctions \\
+    --geno					$geno \\
+    --indel					$indel \\
+    --tfield				$tfield \\
+    --iterate				$iter \\
+    --rescue.window			$rescue_window \\
+    --rescue.all			$rescue_all \\
+    --nudgebalanced			$nudgebalanced \\
+    --edgenudge				$edgenudge \\
+    --strict				$strict \\
+    --allin					$allin \\
+    --field					$field \\
+    --seg			        $cbs_seg_rds \\
+    --maxna					$maxna \\
+    --blacklist.coverage	$blacklist_coverage \\
+    --nseg			        $cbs_nseg_rds \\
+    --hets		            $het_pileups_wgs \\
+    --ploidy				$ploidy \\
+    --purity				$purity \\
+    --ppmethod				$pp_method \\
+    --cnsignif				$cnsignif \\
+    --slack					$slack \\
+    --linear				$linear \\
+    --tilim					$tilim \\
+    --epgap					$epgap \\
+    --outdir                $outdir \\
+    --name                  $name \\
+    --cores                 $task.cpus \\
+    --mem                   $task.mem \\
+    --fix.thres				$fix_thres \\
+    --lp					$lp \\
+    --ism					$ism \\
+    --filter_loose			$filter_loose \\
+    --gurobi				$gurobi \\
+    --nonintegral			$nonintegral \\
+    --verbose				$verbose \\
+    --help					$help \\
+    "
 
     { echo "Running:" && echo "\$(echo $cmd)" && echo && eval $cmd; }
     cmdsig=\$?
@@ -107,6 +151,11 @@ process JABBA {
     fi
 
     exit 0
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        JaBbA: ${VERSION}
+    END_VERSIONS
     """
 
     stub:

nextflow.config

@@ -75,32 +75,38 @@ params {
     build_dryclean                       = "hg19"
 
 	// JaBbA options
-    field = "ratio"
-    junctionUnfiltered = file("/dev/null")
+    blacklist_junctions = "/dev/null"
+    geno = "FALSE"
+    indel = "exclude"
     tfield = "tier"
-    cbs_nseg_rds = file("/dev/null")
-    cbs_seg_rds = file("/dev/null")
-    slack = 100
-    het_pileups_wgs = file("/dev/null")
-    purity = "NA"
+    iter = 2
+    rescue_window = 10000
+    rescue_all = "TRUE"
+    nudgebalanced = "TRUE"
+    edgenudge = 0.1
+    strict = "FALSE"
+    allin = "FALSE"
+    field = "foreground"
+    cbs_seg_rds = "/dev/null"
+    maxna = 0.9
+    cbs_nseg_rds = "/dev/null"
+    het_pileups_wgs = "/dev/null"
     ploidy = "NA"
-    tilim = 6000
-    epgap = 1e-8
+    purity = "NA"
     pp_method = "ppgrid"
-    maxna = 0.8
-    flags = ""
-    blacklist_coverage = file("/dev/null")
-    blacklist_junctions = file("/dev/null")
-    iter = 0
-    pair = "tumor"
-    indel = "exclude"
     cnsignif = 0.00001
+    slack = 100
+    linear = "TRUE"
+    tilim = 7200
+    epgap = 1e-8
+    fix_thres = -1
     lp = "TRUE"
     ism = "TRUE"
-    treemem = 16
-    fix_thres = -1
+    filter_loose = "FALSE"
     gurobi = "FALSE"
     nonintegral = "FALSE"
+    verbose = "TRUE"
+    help = "FALSE"
 
     // Variant Calling
     only_paired_variant_calling   = false // if true, skips germline variant calling for normal-paired samples

subworkflows/local/jabba/main.nf

@@ -0,0 +1,91 @@
+//
+// JaBbA
+//
+
+include { JABBA } from '../../../modules/local/jabba/main.nf'
+
+workflow COV_JUNC_JABBA {
+
+    take:
+    cov_rds_jabba
+    junction_jabba
+    j_supp_jabba
+    blacklist_junctions_jabba
+    geno_jabba
+    indel_jabba
+    tfield_jabba
+    iter_jabba
+    rescue_window_jabba
+    rescue_all_jabba
+    nudgebalanced_jabba
+    edgenudge_jabba
+    strict_jabba
+    allin_jabba
+    field_jabba
+    cbs_seg_rds_jabba
+    maxna_jabba
+    blacklist_coverage_jabba
+    cbs_nseg_rds_jabba
+    het_pileups_wgs_jabba
+    ploidy_jabba
+    purity_jabba
+    pp_method_jabba
+    cnsignif_jabba
+    slack_jabba
+    linear_jabba
+    tilim_jabba
+    epgap_jabba
+    outdir_jabba
+    name_jabba
+    fix_thres_jabba
+    lp_jabba
+    ism_jabba
+    filter_loose_jabba
+    gurobi_jabba
+    nonintegral_jabba
+    verbose_jabba
+    help_jabba
+
+    main:
+    versions            = Channel.empty()
+    jabba_rds           = Channel.empty()
+    jabba_gg            = Channel.empty()
+    jabba_vcf           = Channel.empty()
+    jabba_raw_rds       = Channel.empty()
+    opti                = Channel.empty()
+    jabba_seg           = Channel.empty()
+    karyograph          = Channel.empty()
+
+    JABBA(cov_rds_jabba, junction_jabba, j_supp_jabba,
+    blacklist_junctions_jabba, geno_jabba, indel_jabba, tfield_jabba,
+    iter_jabba, rescue_window_jabba, rescue_all_jabba, nudgebalanced_jabba,
+    edgenudge_jabba, strict_jabba, allin_jabba, field_jabba, cbs_seg_rds_jabba,
+    maxna_jabba, blacklist_coverage_jabba, cbs_nseg_rds_jabba,
+    het_pileups_wgs_jabba, ploidy_jabba, purity_jabba, pp_method_jabba,
+    cnsignif_jabba, slack_jabba, linear_jabba, tilim_jabba, epgap_jabba,
+    outdir_jabba, name_jabba, fix_thres_jabba, lp_jabba, ism_jabba,
+    filter_loose_jabba, gurobi_jabba, nonintegral_jabba, verbose_jabba,
+    help_jabba)
+
+    jabba_rds           = JABBA.out.jabba_rds
+    jabba_gg            = JABBA.out.jabba_gg
+    jabba_vcf           = JABBA.out.jabba_vcf
+    jabba_raw_rds       = JABBA.out.jabba_raw_rds
+    opti                = JABBA.out.opti
+    jabba_seg           = JABBA.out.jabba_seg
+    karyograph          = JABBA.out.karyograph
+
+    versions          = JABBA.out.versions
+
+    emit:
+    jabba_rds
+    jabba_gg
+    jabba_vcf
+    jabba_raw_rds
+    opti
+    jabba_seg
+    karyograph
+
+    versions
+}
+