Merge pull request #145 from TORCH-Consortium/abhinav/use-labels-with…

…-numbers Refactor labels to use the intuitive numbers
TORCH-Consortium · Mar 29, 2023 · 786d13d · 786d13d
2 parents 3ce641b + f5fa816
commit 786d13d
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Showing 18 changed files with 37 additions and 28 deletions.
diff --git a/conf/docker.config b/conf/docker.config
@@ -15,3 +15,8 @@ process {
     }
 
 }
+
+
+docker {
+    enabled = true
+}
diff --git a/modules/bgzip/bgzip.nf b/modules/bgzip/bgzip.nf
@@ -1,6 +1,6 @@
 process BGZIP {
     tag "${name}"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/bwa/mem.nf b/modules/bwa/mem.nf
@@ -1,6 +1,6 @@
 process BWA_MEM {
     tag "${sampleName}"
-    label 'cpu_high_memory_high'
+    label 'cpu_8_memory_8'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/fastqc/fastqc.nf b/modules/fastqc/fastqc.nf
@@ -1,6 +1,6 @@
 process FASTQC {
     tag "${sampleName}"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/gatk/apply_bqsr.nf b/modules/gatk/apply_bqsr.nf
@@ -1,6 +1,6 @@
 process GATK_APPLY_BQSR {
     tag "$sampleName"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/gatk/base_recalibrator.nf b/modules/gatk/base_recalibrator.nf
@@ -1,6 +1,6 @@
 process GATK_BASE_RECALIBRATOR {
     tag "$sampleName"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
 
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 

diff --git a/modules/gatk/collect_wgs_metrics.nf b/modules/gatk/collect_wgs_metrics.nf
@@ -1,6 +1,6 @@
 process GATK_COLLECT_WGS_METRICS {
     tag "${sampleName}"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/gatk/flag_stat.nf b/modules/gatk/flag_stat.nf
@@ -1,6 +1,6 @@
 process GATK_FLAG_STAT {
     tag "${sampleName}"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/gatk/haplotype_caller.nf b/modules/gatk/haplotype_caller.nf
@@ -1,6 +1,6 @@
 process GATK_HAPLOTYPE_CALLER {
     tag "$sampleName"
-    label 'cpu_medium_memory_medium'
+    label 'cpu_8_memory_8'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
 

diff --git a/modules/gatk/haplotype_caller__minor_variants.nf b/modules/gatk/haplotype_caller__minor_variants.nf
@@ -1,6 +1,6 @@
 process GATK_HAPLOTYPE_CALLER__MINOR_VARIANTS {
     tag "$sampleName"
-    label 'cpu_medium_memory_medium'
+    label 'cpu_4_memory_8'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
 

diff --git a/modules/gatk/mark_duplicates.nf b/modules/gatk/mark_duplicates.nf
@@ -1,6 +1,6 @@
 process GATK_MARK_DUPLICATES {
     tag "$sampleName"
-    label 'cpu_low_memory_high'
+    label 'cpu_4_memory_8'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/lofreq/call.nf b/modules/lofreq/call.nf
@@ -1,6 +1,6 @@
 process LOFREQ_CALL {
     tag "${sampleName}"
-    label 'cpu_high_memory_medium'
+    label 'cpu_8_memory_4'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/lofreq/indelqual.nf b/modules/lofreq/indelqual.nf
@@ -1,6 +1,6 @@
 process LOFREQ_INDELQUAL {
     tag "${sampleName}"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/multiqc/multiqc.nf b/modules/multiqc/multiqc.nf
@@ -1,6 +1,6 @@
 process MULTIQC {
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
-    label 'cpu_low_memory_high'
+    label 'cpu_4_memory_16'
 
     input:
         path("*")

diff --git a/modules/samtools/index.nf b/modules/samtools/index.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_INDEX {
     tag "${sampleName}"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/samtools/merge.nf b/modules/samtools/merge.nf
@@ -1,6 +1,5 @@
 process SAMTOOLS_MERGE {
     tag "${sampleName}"
-    label 'cpu_medium_memory_medium'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/modules/samtools/stats.nf b/modules/samtools/stats.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_STATS {
     tag "${sampleName}"
-    label 'cpu_low_memory_low'
+    label 'cpu_2_memory_2'
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     input:

diff --git a/nextflow.config b/nextflow.config
@@ -1,7 +1,7 @@
 manifest {
     name = 'MAGMA'
     description = 'MAGMA is a pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research.'
-    version = '1.0.0'
+    version = '1.0.1'
     author = 'TORCH-Consortium'
     defaultBranch = 'master'
     homePage = 'https://github.com/TORCH-Consortium/MAGMA'
@@ -11,34 +11,39 @@ params { includeConfig 'default_params.config' }
 
 process {
 
+    //Default values if a label hasn't been specified within a process
     cpus = 4
     memory = 4.GB
 
-    withLabel: 'cpu_low_memory_low' {
+    //Default action is to ignore the process if the second attempt fails
+    errorStrategy = { task.attempt < 3 ? 'retry' : 'ignore' }
+
+    //NOTE: These labels are ordered by number of cpus allocated and then the memory
+    withLabel: 'cpu_2_memory_2' {
         cpus = 2
         memory = 2.GB   
     }
 
-    withLabel: 'cpu_low_memory_high' {
-        cpus = 2
-        memory = 16.GB   
+    withLabel: 'cpu_4_memory_8' {
+        cpus = 4
+        memory = 8.GB   
     }
 
-    withLabel: 'cpu_medium_memory_medium' {
+    withLabel: 'cpu_4_memory_16' {
         cpus = 4
+        memory = 16.GB   
+    }
+
+    withLabel: 'cpu_8_memory_4' {
+        cpus = 8
         memory = 4.GB   
     }
 
-    withLabel: 'cpu_high_memory_high' {
+    withLabel: 'cpu_8_memory_8' {
         cpus = 8
         memory = 8.GB   
     }
 
-    withLabel: 'cpu_high_memory_medium' {
-        cpus = 8
-        memory = 4.GB   
-    }
-
     withName: 'SAMPLESHEET_VALIDATION' {
         //NOTE: If this process fails, terminate the pipeline execution
         errorStrategy = 'terminate'
-Original file line number
+Diff line change
@@ Expand Up / @@ -15,3 +15,8 @@ process { @@
         }
     }
+    docker {
+        enabled = true
+    }