diff --git a/modules/local/tools/star/starsolo_align/main.nf b/modules/local/tools/star/starsolo_align/main.nf index 6d71fcd..6ffd823 100644 --- a/modules/local/tools/star/starsolo_align/main.nf +++ b/modules/local/tools/star/starsolo_align/main.nf @@ -17,7 +17,7 @@ process STARSOLO_ALIGN { script: // Set default variables - def limitBAMsortRAM = (params.protocol == 'bd_rhapsody' || params.protocol == 'ultima_genomics') ? '--limitBAMsortRAM 50000000000' : '' + // def limitBAMsortRAM = (params.protocol == 'bd_rhapsody' || params.protocol == 'ultima_genomics') ? '--limitBAMsortRAM 50000000000' : '' // Retrieve settings from custom parameters if set, otherwise from conf/seqtech_parameters.config def star_soloTypestring = params.star_soloTypestring ?: params.seqtech_parameters[params.protocol].star_soloTypestring @@ -54,7 +54,7 @@ process STARSOLO_ALIGN { echo "Genome index directory: ${genome_index_files}" echo "Barcode whitelist: ${bc_whitelist}" echo "Expected cells: ${meta.expected_cells}" - echo "limitBAMsortRAM: ${limitBAMsortRAM}" + echo "star_limitBAMsortRAM: ${params.star_limitBAMsortRAM}" echo "star_solocellfilter: ${star_solocellfilter}" echo "star_soloTypestring: ${star_soloTypestring}" echo "star_generateBAM: ${params.star_generateBAM}" @@ -104,7 +104,7 @@ process STARSOLO_ALIGN { ${outSAMtype_option} \\ --outFileNamePrefix ${meta.id}_ \\ --genomeChrSetMitochondrial ${params.mt_contig} \\ - ${limitBAMsortRAM} \\ + --limitBAMsortRAM ${params.star_limitBAMsortRAM} \\ ${star_extraargs} """ } diff --git a/modules/local/tools/star/starsolo_genome_generate/main.nf b/modules/local/tools/star/starsolo_genome_generate/main.nf index 6116802..c8f5c8b 100644 --- a/modules/local/tools/star/starsolo_genome_generate/main.nf +++ b/modules/local/tools/star/starsolo_genome_generate/main.nf @@ -1,6 +1,6 @@ process STARSOLO_INDEX { publishDir "${params.outdir}/genome/star_index_${meta.id}", mode: 'copy' - label 'process_high' + label 'process_high_memory' input: tuple val(meta), path(fastq_cDNA), path(fastq_BC_UMI), path(fastq_indices), path(input_file) @@ -34,6 +34,7 @@ process STARSOLO_INDEX { --sjdbGTFfile ${ref_gtf} \\ --sjdbOverhang "\${sjdb_overhang}" \\ --genomeSAsparseD ${star_genomeSAsparseD} \\ - --genomeSAindexNbases ${star_genomeSAindexNbases} + --genomeSAindexNbases ${star_genomeSAindexNbases} \\ + --limitGenomeGenerateRAM ${params.star_limitGenomeGenerateRAM} """ } diff --git a/nextflow.config b/nextflow.config index 2725aca..1ec6ab1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -58,6 +58,8 @@ params { star_soloUMIdedup = null star_clipAdapterType = null star_generateBAM = true + star_limitBAMsortRAM = 0 + star_limitGenomeGenerateRAM = 31000000000 star_extraargs = null // Feature counting parameters