diff --git a/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/local.config b/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/local.config index cb970bf6..2b3c0aa1 100644 --- a/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/local.config +++ b/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 } -} \ No newline at end of file +} diff --git a/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/slurm.config b/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/slurm.config index caf7ca0f..f6483c6f 100644 --- a/RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/slurm.config +++ b/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 } -} \ No newline at end of file +}