My current run of the atacseq pipeline is failing at the step NFCORE_ATACSEQATACSEQMERGED_REPLICATE_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV with an out of memory error after retrying with up to 72G of RAM for one of the conditions. I modified the config file (passed on the command line with the -c option) to try to increase the memory allocation for bedtools genomecov, but this didn't work. I then read that for DSL2 pipelines the parameter block in a custom.config will not override the defaults, and that parameter override options must be provided with -params-file in yaml or json format. I've been searching for information about how to provide a process configuration for a specific tool in yaml or json format but have so far come up short. Could somebody provide some pointers for how to instruct the atacseq pipeline to require BEDTOOLS_GENOMECOV to execute with 96G of memory? This is the block I included in my .config file to try to achive the same result. withName : NFCORE_ATACSEQATACSEQMERGED_REPLICATE_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV { time = '8h' cpus = 6 memory = '96.G' }

Thank you for the explanation and the fix - my error was missing quotes around the process name. Appears to be working as expected now. Much appreciated!