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set limitGenomeGenerateRAM and limitBAMsortRAM as custom config variables #42

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Merged
bonitavw merged 1 commit into from
Jan 26, 2026
Merged

set limitGenomeGenerateRAM and limitBAMsortRAM as custom config variables #42

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6 changes: 3 additions & 3 deletions modules/local/tools/star/starsolo_align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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}"
Expand Down Expand Up @@ -104,7 +104,7 @@ process STARSOLO_ALIGN {
${outSAMtype_option} \\
--outFileNamePrefix ${meta.id}_ \\
--genomeChrSetMitochondrial ${params.mt_contig} \\
${limitBAMsortRAM} \\
--limitBAMsortRAM ${params.star_limitBAMsortRAM} \\
${star_extraargs}
"""
}
5 changes: 3 additions & 2 deletions modules/local/tools/star/starsolo_genome_generate/main.nf
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@@ -1,6 +1,6 @@
process STARSOLO_INDEX {
publishDir "${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)
Expand Down Expand Up @@ -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}
"""
}
2 changes: 2 additions & 0 deletions nextflow.config
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Expand Up @@ -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
Expand Down
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