Update resource allocation for ADD_GENE_ANNOTATION processes (#155)

Moved ADD_GENE_ANNOTATIONS and ADD_GENE_ANNOTATIONS_RRNA_RM from 1CPU/2GB RAM section to 4CPU/16GB RAM section in local.config and slurm.config

Author: bnovak32

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/local.config

@@ -17,7 +17,7 @@ process {
     maxErrors     = '-1'
 
     // https://www.nextflow.io/docs/latest/config.html#config-process-selectors
-    withName:'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|PARSE_ANNOTATIONS_TABLE|COPY_READS|DOWNLOAD_REFERENCES|DOWNLOAD_ERCC|CONCAT_ERCC|GTF_TO_PRED|PRED_TO_BED|GET_MAX_READ_LENGTH|INFER_EXPERIMENT|ASSESS_STRANDEDNESS|QUANTIFY_STAR_GENES|EXTRACT_RRNA|REMOVE_RRNA|QUANTIFY_RSEM_GENES|ADD_GENE_ANNOTATIONS|ADD_GENE_ANNOTATIONS_RRNA_RM|RAW_READS_MULTIQC|TRIMMED_READS_MULTIQC|ALIGN_MULTIQC|INFER_EXPERIMENT_MULTIQC|GENEBODY_COVERAGE_MULTIQC|INNER_DISTANCE_MULTIQC|READ_DISTRIBUTION_MULTIQC|COUNT_MULTIQC|ALL_MULTIQC|PARSE_QC_METRICS|VV_RAW_READS|VV_TRIMMED_READS|VV_STAR_ALIGNMENT|VV_RSEQC|VV_RSEM_COUNTS|VV_DGE_DESEQ2|VV_CONCAT_FILTER|SOFTWARE_VERSIONS|GENERATE_PROTOCOL' {
+    withName:'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|PARSE_ANNOTATIONS_TABLE|COPY_READS|DOWNLOAD_REFERENCES|DOWNLOAD_ERCC|CONCAT_ERCC|GTF_TO_PRED|PRED_TO_BED|GET_MAX_READ_LENGTH|INFER_EXPERIMENT|ASSESS_STRANDEDNESS|QUANTIFY_STAR_GENES|EXTRACT_RRNA|REMOVE_RRNA|QUANTIFY_RSEM_GENES|RAW_READS_MULTIQC|TRIMMED_READS_MULTIQC|ALIGN_MULTIQC|INFER_EXPERIMENT_MULTIQC|GENEBODY_COVERAGE_MULTIQC|INNER_DISTANCE_MULTIQC|READ_DISTRIBUTION_MULTIQC|COUNT_MULTIQC|ALL_MULTIQC|PARSE_QC_METRICS|VV_RAW_READS|VV_TRIMMED_READS|VV_STAR_ALIGNMENT|VV_RSEQC|VV_RSEM_COUNTS|VV_DGE_DESEQ2|VV_CONCAT_FILTER|SOFTWARE_VERSIONS|GENERATE_PROTOCOL' {
         cpus   = { 1    * task.attempt }
         memory = { 2.GB * task.attempt }
     }
@@ -41,7 +41,7 @@ process {
         cpus   = { 2    * task.attempt  }
         memory = { 8.GB * task.attempt  }
     }
-    withName:'SORT_AND_INDEX_BAM|DGE_DESEQ2|DGE_DESEQ2_RRNA_RM' {
+    withName:'SORT_AND_INDEX_BAM|DGE_DESEQ2|DGE_DESEQ2_RRNA_RM|ADD_GENE_ANNOTATIONS|ADD_GENE_ANNOTATIONS_RRNA_RM' {
         // DGE To do: Test resource usage w/ Wald parallelization enabled
         cpus   = { 4     * task.attempt }
         memory = { 16.GB * task.attempt }
@@ -104,4 +104,4 @@ executor { // entire executor scope parameters. I.E. parameters that define how
     $local {
         queueSize = 12
     }
-}
+}

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/slurm.config

@@ -18,7 +18,7 @@ process {
     cache = 'lenient'
 
     // https://www.nextflow.io/docs/latest/config.html#config-process-selectors
-    withName:'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|PARSE_ANNOTATIONS_TABLE|COPY_READS|DOWNLOAD_REFERENCES|DOWNLOAD_ERCC|CONCAT_ERCC|GTF_TO_PRED|PRED_TO_BED|GET_MAX_READ_LENGTH|INFER_EXPERIMENT|ASSESS_STRANDEDNESS|QUANTIFY_STAR_GENES|EXTRACT_RRNA|REMOVE_RRNA|QUANTIFY_RSEM_GENES|ADD_GENE_ANNOTATIONS|ADD_GENE_ANNOTATIONS_RRNA_RM|RAW_READS_MULTIQC|TRIMMED_READS_MULTIQC|ALIGN_MULTIQC|INFER_EXPERIMENT_MULTIQC|GENEBODY_COVERAGE_MULTIQC|INNER_DISTANCE_MULTIQC|READ_DISTRIBUTION_MULTIQC|COUNT_MULTIQC|ALL_MULTIQC|PARSE_QC_METRICS|VV_RAW_READS|VV_TRIMMED_READS|VV_STAR_ALIGNMENT|VV_RSEQC|VV_RSEM_COUNTS|VV_DGE_DESEQ2|VV_CONCAT_FILTER|SOFTWARE_VERSIONS|GENERATE_PROTOCOL' {
+    withName:'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|PARSE_ANNOTATIONS_TABLE|COPY_READS|DOWNLOAD_REFERENCES|DOWNLOAD_ERCC|CONCAT_ERCC|GTF_TO_PRED|PRED_TO_BED|GET_MAX_READ_LENGTH|INFER_EXPERIMENT|ASSESS_STRANDEDNESS|QUANTIFY_STAR_GENES|EXTRACT_RRNA|REMOVE_RRNA|QUANTIFY_RSEM_GENES|RAW_READS_MULTIQC|TRIMMED_READS_MULTIQC|ALIGN_MULTIQC|INFER_EXPERIMENT_MULTIQC|GENEBODY_COVERAGE_MULTIQC|INNER_DISTANCE_MULTIQC|READ_DISTRIBUTION_MULTIQC|COUNT_MULTIQC|ALL_MULTIQC|PARSE_QC_METRICS|VV_RAW_READS|VV_TRIMMED_READS|VV_STAR_ALIGNMENT|VV_RSEQC|VV_RSEM_COUNTS|VV_DGE_DESEQ2|VV_CONCAT_FILTER|SOFTWARE_VERSIONS|GENERATE_PROTOCOL' {
         cpus   = { 1    * task.attempt }
         memory = { 2.GB * task.attempt }
     }
@@ -42,7 +42,7 @@ process {
         cpus   = { 2    * task.attempt  }
         memory = { 8.GB * task.attempt  }
     }
-    withName:'SORT_AND_INDEX_BAM|DGE_DESEQ2|DGE_DESEQ2_RRNA_RM' {
+    withName:'SORT_AND_INDEX_BAM|DGE_DESEQ2|DGE_DESEQ2_RRNA_RM|ADD_GENE_ANNOTATIONS|ADD_GENE_ANNOTATIONS_RRNA_RM' {
         // DGE To do: Test resource usage w/ Wald parallelization enabled
         cpus   = { 4     * task.attempt }
         memory = { 16.GB * task.attempt }
@@ -117,4 +117,4 @@ executor {
         queueStatInterval = '2 min'  // Set the time interval between queue status checks; default 1 min
         submitRateLimit = '1 sec'  // Set the job submission rate limit (1 per second); default unlimited
     }
-}
+}