UPDATE: pipeline path variables and config options

bbglab · Nov 10, 2023 · 7d001df · 7d001df
1 parent 844ea1a
commit 7d001df
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Showing 4 changed files with 7 additions and 63 deletions.
diff --git a/01_training.nf b/01_training.nf
@@ -200,10 +200,6 @@ process SplitCV {
     label "boostdm"
     publishDir "${OUTPUT}/splitcv", mode: 'copy'
 
-    memory { task.memory * task.attempt }
-    errorStrategy { task.attempt > 3 ? 'ignore': 'retry' }
-
-
     input:
         tuple val(cohort), path(input) from IN_CV
 
@@ -231,10 +227,6 @@ process SplitCVMetacohort {
     label "boostdm"
     publishDir "${OUTPUT}", mode: 'copy'
 
-    memory { task.memory * task.attempt }
-    errorStrategy { task.attempt > 3 ? 'ignore': 'retry' }
-
-
     input:
         path(input) from OUT_CV_COHORTS.collect()
 

diff --git a/config/bbglab.conf b/config/bbglab.conf
@@ -11,23 +11,17 @@ process {
 
     withName: TrainingMeta {
         cpus = 4
-    }
-
-    withName: AutoEvaluationMeta {
         memory = 20.GB
     }
 
-    withName: AnnotateSaturation {
-        memory = 8.GB
+    withName: CrossValidation {
+        memory = 20.GB
     }
 
-    withLabel: prediction {
-        memory = 8.GB
-    }
 }
 
 
 executor {
     name = 'slurm'
-    queueSize = 100
+    queueSize = 150
 }
diff --git a/model-selection.nf b/model-selection.nf
diff --git a/nextflow.config b/nextflow.config
@@ -8,23 +8,9 @@ env {
     GENOME_BUILD = "hg38"
     INTOGEN_DATASETS = "/workspace/projects/intogen_plus/fixdatasets-20230223/intogen-plus/run_20230224_ALL/intogen_analysis/"
     BOOSTDM_DATASETS = "/workspace/projects/intogen_plus/fixdatasets-20230223/intogen-plus/datasets/boostdm/"
-    VEP_SATURATION = env.INTOGEN_DATASETS + "/steps/boostDM/saturation_clean/"
-    PIPELINE = "/workspace/datasets/boostdm_runs/boostdm-pipeline-20230307"
-    OUTPUT = env.PIPELINE + "/output"
-
-    /* old stuff */
-
-    // CANONICAL_REGIONS = "/workspace/datasets/boostdm_runs/boostdm-pipeline-20230307/canonical.regions.gz"
-    // VEP_VERSION = "92"
-    // INTOGEN_DATASETS = "/workspace/projects/intogen_2017/pipeline/datasets/hg38_vep92_v20191009"
-    // DRIVERS_PATH = env.INTOGEN_DATASETS + "/drivers.tsv"
-    // COHORTS_PATH = env.INTOGEN_DATASETS + "/cohorts.tsv"
-    // VEP_SATURATION = env.INTOGEN_DATASETS + "/steps/boostDM/saturation/"
-    // BGDATA_LOCAL = env.INTOGEN_DATASETS + "/bgdata"
-    // INTOGEN_FOLDER = "/workspace/projects/intogen_2017/runs/20200102"
-    // HARTWIG_FOLDER = "/workspace/projects/hartwig/intogen/runs/20200117_20200121"
-    // STJUDE_FOLDER = "/workspace/projects/stjude/intogen/runs/20191022"
-
+    VEP_SATURATION = env.INTOGEN_DATASETS + "/steps/boostDM/saturationHotFIX/"
+    PIPELINE = "/workspace/datasets/boostdm_runs/boostdm-pipeline-20230307/"
+    OUTPUT = env.PIPELINE + "/output_20230710/"
 }
 
 singularity {
@@ -37,7 +23,7 @@ process {
     cpus = 1
     errorStrategy = 'ignore'
     withLabel: boostdm {
-    	container = "file:///${singularity.cacheDir}/boostdm.simg"
+	container = "file:///${singularity.cacheDir}/boostdm.simg"
     }
 }