Fixes minor bugs related to JaBbA

mskilab-org · Nov 7, 2023 · 3bdb964 · 3bdb964
1 parent c9fe005
commit 3bdb964
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Showing 5 changed files with 30 additions and 75 deletions.
diff --git a/main.nf b/main.nf
@@ -60,6 +60,7 @@ params.build_dryclean        = WorkflowMain.getGenomeAttribute(params, 'build_dr
 params.hapmap_sites          = WorkflowMain.getGenomeAttribute(params, 'hapmap_sites')
 params.pon_dryclean          = WorkflowMain.getGenomeAttribute(params, 'pon_dryclean')
 params.blacklist_coverage_jabba     = WorkflowMain.getGenomeAttribute(params, 'blacklist_coverage_jabba')
+//params.blacklist_junctions_jabba     = WorkflowMain.getGenomeAttribute(params, 'blacklist_junctions_jabba')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/modules/local/jabba/main.nf b/modules/local/jabba/main.nf
@@ -14,7 +14,7 @@ process JABBA {
     tuple val(meta), path(cbs_seg_rds, stageAs: "cbs_seg.rds")
     tuple val(meta), path(cbs_nseg_rds, stageAs: "cbs_nseg.rds")
     tuple val(meta), path(j_supp)
-    path(blacklist_junctions)
+    val(blacklist_junctions)
     val(geno)
     val(indel)
     val(tfield)
@@ -68,29 +68,7 @@ process JABBA {
 
     set -o allexport
 
-    # Check if the environment has the module program installed
-    if command -v module &> /dev/null
-    then
-        # Check if the required modules are available
-        if module avail R/4.0.2 &> /dev/null && module avail gcc/9.2.0 &> /dev/null
-        then
-            ## load correct R and gcc versions
-            module unload R
-            module load R/4.0.2
-            module unload gcc
-            module load gcc/9.2.0
-        fi
-    fi
-
-    set -x
-    R_LIB_PATH="/gpfs/commons/groups/imielinski_lab/lib/R-4.0.2"
-    if [ -d "\$R_LIB_PATH" ]; then
-        export R_LIBS=\$R_LIB_PATH
-    fi
 
-    export R_DATATABLE_NUM_THREADS=1
-    #unset R_HOME
-    #R_PROFILE_USER="/dev/null"
 
     ## find R installation
     echo "USING LIBRARIES: \$(Rscript -e 'print(.libPaths())')"
@@ -100,46 +78,26 @@ process JABBA {
     echo \$jba
     set +x
 
-    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 \\
-    --name                  $name \\
-    --cores                 $task.cpus \\
-    --mem                   $task.memory \\
-    --fix.thres				$fix_thres \\
-    --lp					$lp \\
-    --ism					$ism \\
-    --filter_loose			$filter_loose \\
-    --gurobi				$gurobi \\
-    --nonintegral			$nonintegral \\
-    --verbose				$verbose \\
-    --help					$help \\
+    export cmd="Rscript \$jba ${junction} ${cov_rds} \\
+    --j.supp                ${j_supp} \\
+    --indel					${indel} \\
+    --tfield				${tfield} \\
+    --field					${field} \\
+    --seg			        ${cbs_seg_rds} \\
+    --blacklist.coverage	${blacklist_coverage} \\
+    --nseg			        ${cbs_nseg_rds} \\
+    --hets		            ${het_pileups_wgs} \\
+    --ploidy				${ploidy} \\
+    --purity				${purity} \\
+    --ppmethod				${pp_method} \\
+    --cores                 ${task.cpus} \\
     "
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        JaBbA: ${VERSION}
+    END_VERSIONS
+
     { echo "Running:" && echo "\$(echo \$cmd)" && echo && eval \$cmd; }
     cmdsig=\$?
     if [ "\$cmdsig" = 0 ]; then
@@ -148,13 +106,7 @@ process JABBA {
         echo "Broke!"
         exit \$cmdsig
     fi
-
-    exit 0
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        JaBbA: ${VERSION}
-    END_VERSIONS
+    
     """
 
     stub:

diff --git a/nextflow.config b/nextflow.config
@@ -60,7 +60,7 @@ params {
 
 	// fragCounter options
 	midpoint_frag              = "TRUE"                           // If TRUE only count midpoint if FALSE then count bin footprint of every fragment interval: Default=TRUE
-	windowsize_frag            = 1000                            // Window / bin size : Default=200 (but dryclean uses 1000 binsize)
+	windowsize_frag            = 200                            // Window / bin size : Default=200 (but dryclean uses 1000 binsize)
 	minmapq_frag               = 1                              // Minimal map quality : Default = 1
 	paired_frag                = "TRUE"                           // Is the dataset paired : Default = TRUE
 	exome_frag                 = "FALSE"	                        // Use exons as bins instead of fixed window : Default = FALSE
@@ -92,7 +92,7 @@ params {
     name_cbs                            = "tumor"
 
 	// JaBbA options
-    blacklist_junctions_jabba = "/dev/null"
+    blacklist_junctions_jabba = "NULL"
     geno_jabba = "FALSE"
     indel_jabba = "exclude"
     tfield_jabba = "tier"
@@ -112,7 +112,7 @@ params {
     slack_jabba = 100
     linear_jabba = "TRUE"
     tilim_jabba = 7200
-    epgap_jabba = 1e-8
+    epgap_jabba = 0.00000001
     fix_thres_jabba = -1
     lp_jabba = "TRUE"
     ism_jabba = "TRUE"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -535,7 +535,6 @@
             "properties": {
                 "blacklist_junctions_jabba": {
                     "type": "string",
-                    "default": "/dev/null",
                     "description": "rearrangement junctions to be excluded from consideration",
                     "fa_icon": "fas fa-file"
                 },
@@ -661,7 +660,6 @@
                 },
                 "epgap_jabba": {
                     "type": "number",
-                    "default": 1e-8,
                     "description": "threshold for calling convergence",
                     "fa_icon": "fas fa-wrench"
                 },

diff --git a/workflows/heisenbio.nf b/workflows/heisenbio.nf
@@ -264,7 +264,7 @@ blacklist_path_dryclean      = params.blacklist_path_dryclean      ? Channel.fro
 germline_file_dryclean      = params.germline_file_dryclean      ? Channel.fromPath(params.germline_file_dryclean).collect()     : Channel.empty()   // This is the path to the germline mask for dryclean (optional).
 
 // JaBbA
-blacklist_junctions_jabba		= params.blacklist_junctions_jabba        ? Channel.fromPath(params.blacklist_junctions_jabba).collect() : Channel.empty()
+//blacklist_junctions_jabba		= params.blacklist_junctions_jabba        ? Channel.fromPath(params.blacklist_junctions_jabba).collect() : Channel.empty()
 blacklist_coverage_jabba		= params.blacklist_coverage_jabba		  ? Channel.fromPath(params.blacklist_coverage_jabba).collect() : Channel.empty()
 
 // Initialize value channels based on params, defined in the params.genomes[params.genome] scope
@@ -314,6 +314,7 @@ field_cbs                       = params.field_cbs                  ?: Channel.e
 name_cbs                        = params.name_cbs                   ?: Channel.empty()
 
 // JaBbA
+blacklist_junctions_jabba       = params.blacklist_junctions_jabba      ?: Channel.empty()
 geno_jabba					    = params.geno_jabba			            ?: Channel.empty()
 indel_jabba					    = params.indel_jabba			        ?: Channel.empty()
 tfield_jabba					= params.tfield_jabba			        ?: Channel.empty()
@@ -327,6 +328,7 @@ allin_jabba					    = params.allin_jabba			        ?: Channel.empty()
 field_jabba					    = params.field_jabba			        ?: Channel.empty()
 maxna_jabba					    = params.maxna_jabba			        ?: Channel.empty()
 purity_jabba					= params.purity_jabba                   ?: Channel.empty()
+//ploidy_jabba					= params.ploidy_jabba                   ?: Channel.empty()
 pp_method_jabba					= params.pp_method_jabba                ?: Channel.empty()
 cnsignif_jabba					= params.cnsignif_jabba                 ?: Channel.empty()
 slack_jabba					    = params.slack_jabba                    ?: Channel.empty()
@@ -965,7 +967,9 @@ workflow HEISENBIO {
 
             all_sv_vcfs = Channel.empty()
             all_sv_vcfs = all_sv_vcfs.mix(BAM_SVCALLING_SVABA.out.all_output)                                                      //This one contains multiple files of vcf, to get individual files, call individual output
+
             vcf_from_sv_calling = Channel.empty().mix(BAM_SVCALLING_SVABA.out.som_sv)
+
             unfiltered_som_sv = Channel.empty()
             unfiltered_som_sv = unfiltered_som_sv.mix(BAM_SVCALLING_SVABA.out.unfiltered_som_sv)
         }
@@ -984,7 +988,7 @@ workflow HEISENBIO {
             versions = versions.mix(BAM_SVCALLING_GRIDSS_SOMATIC.out.versions)
 
             vcf_from_sv_calling = Channel.empty().mix(BAM_SVCALLING_GRIDSS_SOMATIC.out.all_vcf)
-            vcf_from_sv_calling.view()
+            //vcf_from_sv_calling.view()
         }
 
         // TODO: CHANNEL_SVCALLING_CREATE_CSV(vcf_from_sv_calling, params.tools, params.outdir) // Need to fix this!!!!!