Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)
GNU General Public License v3.0
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Remove Nextflow workaround for Docker CPU Limit #26
Currently when using Docker as the container engine, if --cpus is not specify in the runOptions and there is no cpus directive in the process, the underlying docker run launched by Nextflow uses --cpus=1 by default.
Currently when using Docker as the container engine, if
--cpusis not specify in the runOptions and there is nocpusdirective in the process, the underlyingdocker runlaunched by Nextflow uses--cpus=1by default.Queried at https://github.com/nextflow-io/nextflow/issues/3808, fix available at https://github.com/nextflow-io/nextflow/commit/b38c38806e11dfdbf32f3fa41287a05f9eb3d430 and will be released as part of 23.04.0 (ETA 2023 April)
Remove workarounds from the beneath sections when the included Nextflow is updated to 23.04.0 https://github.com/HarryHung/gps-unified-pipeline/blob/121cb37f68040381f6e67bef491999f0c6e8d63f/nextflow.config#L110-L112