diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 2b7753fd8..3332d000e 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -7,6 +7,8 @@ process SAMTOOLS_SORT { 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" + errorStrategy { task.exitStatus == 140 && task.dumpStderr().matches("\\[bam_sort_core\\] merging from \\d+\\ files and \\d+\\ in-memory blocks...") ? 'ignore' : 'terminate' } + input: tuple val(meta), path(bam) @@ -28,7 +30,7 @@ process SAMTOOLS_SORT { -@ $task.cpus \\ -o ${prefix}.bam \\ -T $prefix \\ - $bam + $bam cat <<-END_VERSIONS > versions.yml "${task.process}":