fix: add more mem to junction_filter

mskilab-org · Jul 5, 2024 · 7347141 · 7347141
1 parent 386ded5
commit 7347141
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Showing 4 changed files with 30 additions and 26 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -162,36 +162,35 @@
                 "format": "file-path",
                 "exists": true
             },
-            "ploidy": {
-                "errorMessage": "purityploidy file must have extension '.rds' or be a number",
+            "cov": {
+                "errorMessage": "COV file cannot contain spaces and must have extension '.rds' or '.txt'",
                 "anyOf": [
                     {
                         "type": "string",
-                        "pattern": "^\\S+\\.rds$"
+                        "pattern": "^\\S+\\.(rds|txt)$"
                     },
                     {
                         "type": "string",
-                        "pattern": "^NA$"
-                    },
+                        "maxLength": 0
+                    }
+                ],
+                "format": "file-path",
+                "exists": true
+            },
+            "hets": {
+                "errorMessage": "Pileups file and must have extension '.txt'",
+                "anyOf": [
                     {
                         "type": "string",
-                        "pattern": "^/dev/null$"
+                        "pattern": "^\\S+\\.txt$"
                     },
                     {
                         "type": "string",
-                        "maxLength": 0
+                        "pattern": "^NA$"
                     },
-                    {
-                        "type": "number"
-                    }
-                ],
-            },
-            "cov": {
-                "errorMessage": "COV file cannot contain spaces and must have extension '.rds' or '.txt'",
-                "anyOf": [
                     {
                         "type": "string",
-                        "pattern": "^\\S+\\.(rds|txt)$"
+                        "pattern": "^/dev/null$"
                     },
                     {
                         "type": "string",
@@ -201,12 +200,12 @@
                 "format": "file-path",
                 "exists": true
             },
-            "hets": {
-                "errorMessage": "Pileups file and must have extension '.txt'",
+            "ploidy": {
+                "errorMessage": "purityploidy file must have extension '.rds' or be a number",
                 "anyOf": [
                     {
                         "type": "string",
-                        "pattern": "^\\S+\\.txt$"
+                        "pattern": "^\\S+\\.rds$"
                     },
                     {
                         "type": "string",
@@ -219,10 +218,11 @@
                     {
                         "type": "string",
                         "maxLength": 0
+                    },
+                    {
+                        "type": "number"
                     }
                 ],
-                "format": "file-path",
-                "exists": true
             },
             "vcf": {
                 "errorMessage": "VCF file for reads 1 cannot contain spaces and must have extension '.vcf' or '.vcf.gz'",

diff --git a/conf/base.config b/conf/base.config
@@ -116,6 +116,11 @@ process {
         memory          = { check_max( 48.GB * task.attempt, 'memory' ) }
         time            = { check_max( 8.h  * task.attempt, 'time'    ) }
     }
+    withName: 'JUNCTION_FILTER' {
+        cpus            = { check_max( 2 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 128.GB * task.attempt, 'memory' ) }
+        time            = { check_max( 16.h  * task.attempt, 'time'    ) }
+    }
     withName: 'HETPILEUPS' {
         cpus            = { check_max( 4 * task.attempt, 'cpus' ) }
         memory          = { check_max( 8.GB * task.attempt, 'memory' ) }

diff --git a/conf/modules/snv_calling.config b/conf/modules/snv_calling.config
@@ -32,7 +32,7 @@ process {
                 pattern: "*{vcf.gz,txt.gz,vcf*,.command.*}"
             ]
     }
-    withName: '.*SAGE_SOMATIC' {
+    withName: '.*SAGE_SOMATIC|SAGE_PASS_FILTER' {
         ext.when         = { params.tools && params.tools.split(',').contains('sage') }
         publishDir       = [
                 mode: params.publish_dir_mode,

diff --git a/workflows/nfjabba.nf b/workflows/nfjabba.nf
@@ -130,9 +130,9 @@ def handleError(step, dataType) {
 }
 
 input_sample = ch_from_samplesheet
-        .map{ meta, fastq_1, fastq_2, table, cram, crai, bam, bai, ploidy, cov, hets, vcf, vcf2, snv_vcf_somatic, snv_tbi_somatic, snv_vcf_germline, snv_tbi_germline, seg, nseg, ggraph, variantcaller ->
+        .map{ meta, fastq_1, fastq_2, table, cram, crai, bam, bai, cov, hets, ploidy, vcf, vcf2, snv_vcf_somatic, snv_tbi_somatic, snv_vcf_germline, snv_tbi_germline, seg, nseg, ggraph, variantcaller ->
             // generate patient_sample key to group lanes together
-            [ meta.patient + meta.sample, [meta, fastq_1, fastq_2, table, cram, crai, bam, bai, ploidy, cov, hets, vcf, vcf2, snv_vcf_somatic, snv_tbi_somatic, snv_vcf_germline, snv_tbi_germline, seg, nseg, ggraph, variantcaller] ]
+            [ meta.patient + meta.sample, [meta, fastq_1, fastq_2, table, cram, crai, bam, bai, cov, hets, ploidy, vcf, vcf2, snv_vcf_somatic, snv_tbi_somatic, snv_vcf_germline, snv_tbi_germline, seg, nseg, ggraph, variantcaller] ]
         }
         .tap{ ch_with_patient_sample } // save the channel
         .groupTuple() //group by patient_sample to get all lanes
@@ -143,7 +143,7 @@ input_sample = ch_from_samplesheet
         .combine(ch_with_patient_sample, by: 0) // for each entry add numLanes
         .map { patient_sample, num_lanes, ch_items ->
 
-            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, ploidy, cov, hets, vcf, vcf2, snv_vcf_somatic, snv_tbi_somatic, snv_vcf_germline, snv_tbi_germline, seg, nseg, ggraph, variantcaller) = ch_items
+            (meta, fastq_1, fastq_2, table, cram, crai, bam, bai, cov, hets, ploidy, vcf, vcf2, snv_vcf_somatic, snv_tbi_somatic, snv_vcf_germline, snv_tbi_germline, seg, nseg, ggraph, variantcaller) = ch_items
             if (meta.lane && fastq_2) {
                 meta           = meta + [id: "${meta.sample}-${meta.lane}".toString()]
                 def CN         = params.seq_center ? "CN:${params.seq_center}\\t" : ''
@@ -1835,7 +1835,6 @@ workflow NFJABBA {
                                 []
                             ]
                         }
-                    jabba_inputs.dump(tag: 'trace2')
                 } else {
                     // join all previous outputs to be used as input for jabba
                     // excluding svs since they can come from either svaba or gridss