From bbe6583f0d3a2b1c42b2c5f31ba3af916331cc81 Mon Sep 17 00:00:00 2001 From: liuyangzzu Date: Sat, 16 Mar 2024 18:20:34 -0400 Subject: [PATCH] add support pod5 add sumner2 node support --- modules/UNTAR.nf | 4 ++-- nextflow.config | 49 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+), 2 deletions(-) diff --git a/modules/UNTAR.nf b/modules/UNTAR.nf index fb26cdfb..46410a84 100644 --- a/modules/UNTAR.nf +++ b/modules/UNTAR.nf @@ -39,8 +39,8 @@ process UNTAR { ### deal with tar.gz tar -xzf !{fast5Input} -C untarTempDir elif [[ -d !{fast5Input} ]]; then - ## Copy files, do not change original files such as old analyses data - find !{fast5Input}/ -name '*.fast5' | \ + ## For dir, should copy files, we do not want to change original files such as old analyses data in fast5 + find !{fast5Input}/ \\( -name "*.fast5" -o -name "*.pod5" \\) | \ parallel -j!{cores} cp -L -f {} untarTempDir/ else echo "### Untar error for input=!{fast5Input}" diff --git a/nextflow.config b/nextflow.config index f5d8e226..154d32a8 100755 --- a/nextflow.config +++ b/nextflow.config @@ -441,6 +441,55 @@ profiles { } } + sumner2 { + params{ + max_cpus = 72 + max_memory = 768.GB + + gpu_queue = 'gpus' // winter only have one partition + gpu_qos = 'gpu_training' // or use training, time can be 14 days + gpu_processors = 8 + gpu_memory = '128GB' + gpu_time = '14.d' + gpu_gresOptions = 'gpu:1' // null/false if no gpu needed + + cpu_queue = 'compute' // winter only have one partition + cpu_qos = 'long' // or use training, time can be 14 days + cpu_processors = 8 + cpu_memory = '128GB' + cpu_time = '14.d' + + queueSize = 24 + } + + process{ + executor = "slurm" + module = "slurm:singularity" + + withName: 'UNTAR|ALIGNMENT|QCEXPORT|RESQUIGGLE|NANOPOLISH|Tombo|Guppy6Comb|METEORE|CLAIR3|PHASING|CONSENSUS|EVAL|REPORT|NPLSHCOMB|MGLDNCOMB|DPSIGCOMB|DEEPSIGNAL2COMB|GuppyComb|TomboComb|DpmodComb|Guppy6Comb' { + queue = params.cpu_queue + cpus = params.cpu_processors + memory = params.cpu_memory + time = params.cpu_time + clusterOptions = "-q ${params.cpu_qos}" + } + + withName: 'ENVCHECK|BASECALL|MEGALODON|Guppy6|Guppy|DEEPSIGNAL|DEEPSIGNAL2|DeepMod|METEORE' { + queue = params.gpu_queue + cpus = params.gpu_processors + memory = params.gpu_memory + time = params.gpu_time + clusterOptions = "-q ${params.gpu_qos} ${params.gpu_gresOptions ? '--gres=' + params.gpu_gresOptions : ' '}" + } + + + } + + executor { + queueSize = params.queueSize + } + } + // Google cloud computing platform // ref doc: https://www.nextflow.io/docs/latest/google.html // ref doc: https://www.nextflow.io/docs/latest/google.html#configuration