fix: memory blowup

mskilab-org · Jan 7, 2025 · a778eff · a778eff
1 parent 51c4e9f
commit a778eff
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Showing 7 changed files with 27 additions and 9 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -65,9 +65,9 @@ process {
         cpus            = { check_max( 12 * task.attempt, 'cpus' ) }
         memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
     }
-    withName: 'BWAMEM1_MEM|BWAMEM2_MEM' {
+    withName: 'BWAMEM2_MEM|BWAMEM2_MEM' {
         cpus            = { check_max( 24 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 30.GB * task.attempt, 'memory' ) }
+        memory          = { check_max( 72.GB * task.attempt, 'memory' ) }
     }
     withName: 'PARABRICKS_FQ2BAM' {
         cpus            = { check_max( 24 * task.attempt, 'cpus' ) }

diff --git a/conf/modules/aligner.config b/conf/modules/aligner.config
@@ -84,4 +84,14 @@ process {
     withName: 'MERGE_BAM' {
         ext.prefix = { "${meta.id}.sorted" }
     }
+
+
+    withName: 'CRAM_TO_BAM_FINAL' {
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/alignment/final/${meta.id}/" },
+            pattern: "*{bam,bai}",
+        ]
+    }
 }
+
diff --git a/conf/modules/recalibrate.config b/conf/modules/recalibrate.config
@@ -18,7 +18,7 @@ process {
     withName: 'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK' {
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
         publishDir       = [
-            enabled: !params.save_output_as_bam,
+            enabled: params.save_mapped,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/alignment/" },
             pattern: "*cram",
@@ -30,7 +30,7 @@ process {
             ext.prefix       = { "${meta.id}.recal" }
 
             publishDir       = [
-                enabled: !params.save_output_as_bam,
+                enabled: params.save_mapped,
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/alignment/recalibrated/${meta.id}/" },
                 pattern: "*cram"
@@ -39,7 +39,7 @@ process {
 
         withName: 'MSKILABORG_NFJABBA:NFJABBA:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM' {
             publishDir       = [
-                enabled: !params.save_output_as_bam,
+                enabled: params.save_mapped,
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/alignment/recalibrated/${meta.id}/" },
                 pattern: "*{recal.cram,recal.cram.crai}"
@@ -50,7 +50,7 @@ process {
         ext.prefix       = { "${meta.id}.recal" }
 
         publishDir       = [
-            enabled: params.save_output_as_bam,
+            enabled: params.save_mapped,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/alignment/recalibrated/${meta.id}/" },
             pattern: "*{recal.bam,recal.bam.bai}"

diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -48,7 +48,7 @@ params {
     fq2bam_mark_duplicates     = true                            // Whether fq2bam should mark duplicates, set false if not using fq2bam
     fq2bam_low_memory          = false                           // Set to true if using fq2bam with gpus that have <24GB memory
     optical_duplicate_pixel_distance = 2500                      // For computing optical duplicates, 2500 for NovaSeqX+
-	save_mapped                = true                            // Mapped BAMs are saved
+	save_mapped                = false                            // Mapped BAMs are saved
 	save_output_as_bam         = true                            // Output files from alignment are saved as bam by default and not as cram files
 	seq_center                 = null                            // No sequencing center to be written in read group CN field by aligner
 	seq_platform               = null                            // Default platform written in read group PL field by aligner, null by default.

diff --git a/tests/test_runs/full_test/params.json b/tests/test_runs/full_test/params.json
@@ -6,7 +6,7 @@
     "bwa": "/gpfs/commons/home/sdider/DB/GATK/bwa/",
     "outdir": "./results",
     "pon_dryclean": "/gpfs/commons/home/tdey/data/dryclean/MONSTER_PON_RAW/MONSTER_PON_RAW_SORTED/fixed.detergent.rds",
-    "tools": "fusions",
+    "tools": "bamqc",
     "field_dryclean": "reads",
     "genome": "GATK.GRCh37",
     "email": "[email protected]"

diff --git a/workflows/nfcasereports.nf b/workflows/nfcasereports.nf
@@ -368,6 +368,14 @@ inputs = inputs
 
             ch_items.meta           = ch_items.meta - ch_items.meta.subMap('lane') + [num_lanes: num_lanes.toInteger(), read_group: read_group.toString(), size: 1]
 
+        } else if (ch_items.fastq_2) {
+            ch_items.meta   = ch_items.meta + [id: ch_items.meta.sample.toString()]
+            def CN         = params.seq_center ? "CN:${params.seq_center}\\t" : ''
+
+            def flowcell   = flowcellLaneFromFastq(ch_items.fastq_1)
+            def read_group = "\"@RG\\tID:${flowcell}.${ch_items.meta.sample}\\t${CN}PU:${ch_items.meta.sample}\\tSM:${ch_items.meta.patient}_${ch_items.meta.sample}\\tLB:${ch_items.meta.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\""
+
+            ch_items.meta = ch_items.meta + [num_lanes: num_lanes.toInteger(), read_group: read_group.toString(), size: 1]
         } else if (ch_items.meta.lane && ch_items.bam) {
             ch_items.meta   = ch_items.meta + [id: "${ch_items.meta.sample}-${ch_items.meta.lane}".toString()]
             def CN          = params.seq_center ? "CN:${params.seq_center}\\t" : ''