Merge branch 'jabba_workflow' into dev

modules/local/ascat/main.nf

@@ -10,7 +10,7 @@ process ASCAT_SEG {
     input:
     tuple val(meta), path(hets)                                      // channel: [mandatory] [ meta, hets ]
     tuple val(meta), path(cbs_cov)                                   // channel: [mandatory] [ meta, cbs_cov ]
-    val(field)                                                       // channel: [mandatory] "foreground" for dryclean/ "ratio" 
+    val(field)                                                       // channel: [mandatory] "foreground" for dryclean/ "ratio"
     val(hets_thresh)                                                 // channel: cutoff for hetpileups; default=0.2
     val(penalty)                                                     // channel: penalty for ASCAT; default=70
     val(gc)                                                          // channel: perform GC correction? Default=TRUE
@@ -60,9 +60,9 @@ process ASCAT_SEG {
 
     ## find R installation and dryclean exec
     echo "USING LIBRARIES: \$(Rscript -e 'print(.libPaths())')"
-    
+
     RSCRIPT_PATH=\$(if [[ ${workflow.containerEngine} == "singularity" && !task.ext.singularity_pull_docker_container ]]; then echo "./ascat_seg.R"; else echo "\${baseDir}/bin/ascat_seg.R"; fi)
-    
+
     Rscript \$RSCRIPT_PATH       \\
     --id          ${meta.id}     \\
     --variants    ${hets}        \\
@@ -102,4 +102,4 @@ process ASCAT_SEG {
 
     """
 
-}
+}

modules/local/cbs/main.nf

@@ -15,9 +15,9 @@ process CBS {
     val name
 
     output:
-    path "*.cov.rds", emit: cbs_cov_rds
-    path "*seg.rds", emit: cbs_seg_rds
-    path "*nseg.rds", emit: cbs_nseg_rds
+    tuple val(meta), path "*.cov.rds", emit: cbs_cov_rds
+    tuple val(meta), path "*seg.rds", emit: cbs_seg_rds
+    tuple val(meta), path "*nseg.rds", emit: cbs_nseg_rds
 
     when:
     task.ext.when == null || task.ext.when

modules/local/hetpileups/main.nf

@@ -15,7 +15,7 @@ process HETPILEUPS {
 
     output:
     path "versions.yml"                                     , emit: versions
-    path "sites.txt"                                        , emit: het_pileups_wgs
+    tuple val(meta), path("*sites.txt")                     , emit: het_pileups_wgs
 
     when:
     task.ext.when == null || task.ext.when

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)
+    tuple val(meta), val(ploidy)
+    tuple val(meta), path(het_pileups_wgs)
+    tuple val(meta), 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)
-    path(het_pileups_wgs)
-    val(purity)
-    val(ploidy)
-    val(tilim)
-    val(epgap)
-    val(pp_method)
     val(maxna)
-    val(flags)
     path(blacklist_coverage)
-    path(blacklist_junctions)
-    val(iter)
-    val(pair)
-    val(indel)
+    path(cbs_nseg_rds)
+    val(purity)
+    val(pp_method)
     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

@@ -92,32 +92,38 @@ params {
     name                                = "tumor"
 
 	// JaBbA options
-    //field = "ratio"
-    //junctionUnfiltered = file("/dev/null")
-    //tfield = "tier"
-    //cbs_nseg_rds = file("/dev/null")
-    //cbs_seg_rds = file("/dev/null")
-    //slack = 100
-    //het_pileups_wgs = file("/dev/null")
-    //purity = "NA"
-    //ploidy = "NA"
-    //tilim = 6000
-    //epgap = 1e-8
-    //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
-    //lp = "TRUE"
-    //ism = "TRUE"
-    //treemem = 16
-    //fix_thres = -1
-    //gurobi = "FALSE"
-    //nonintegral = "FALSE"
+    blacklist_junctions = "/dev/null"
+    geno = "FALSE"
+    indel = "exclude"
+    tfield = "tier"
+    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"
+    purity = "NA"
+    pp_method = "ppgrid"
+    cnsignif = 0.00001
+    slack = 100
+    linear = "TRUE"
+    tilim = 7200
+    epgap = 1e-8
+    fix_thres = -1
+    lp = "TRUE"
+    ism = "TRUE"
+    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/cov_ascat/main.nf

@@ -10,7 +10,7 @@ workflow COV_ASCAT {
     take:
     hetpileups                                        // channel: [mandatory] [ meta, hets ]
     cbs_cov                                           // channel: [mandatory] [ meta, cbs_cov ]
-    field                                             // channel: [mandatory] "foreground" for dryclean/ "ratio" 
+    field                                             // channel: [mandatory] "foreground" for dryclean/ "ratio"
     hets_threshold                                    // channel: cutoff for hetpileups; default=0.2
     penalty                                           // channel: penalty for ASCAT; default=70
     gc_correct                                        // channel: perform GC correction? Default=TRUE
@@ -40,4 +40,4 @@ workflow COV_ASCAT {
     ploidy
 
     versions
-}
+}

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           // [ meta, cov]
+    junction_jabba          // [ meta, junction]
+    ploidy_jabba            // [ meta, ploidy ]
+    het_pileups_wgs_jabba   // [ meta, hets ]
+    cbs_seg_rds_jabba       // [ meta, seg_cbs ]
+    cbs_nseg_rds_jabba      // [ meta, nseg_cbs ]
+    j_supp_jabba            // [ meta, unfiltered_som_sv ]
+    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
+    maxna_jabba
+    blacklist_coverage_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
+}
+