diff --git a/conf/base.conf b/conf/base.conf index cf23bd4c..dca769de 100755 --- a/conf/base.conf +++ b/conf/base.conf @@ -362,5 +362,4 @@ process { singularity { enabled = true - runOptions = '--bind /lustre --bind /software --bind /nfs --no-home' } diff --git a/conf/extra_confs/leicester/alice_new_setup.conf b/conf/extra_confs/leicester/alice_new_setup.conf new file mode 100644 index 00000000..e73be459 --- /dev/null +++ b/conf/extra_confs/leicester/alice_new_setup.conf @@ -0,0 +1,33 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'ALICE and SPECTRE cluster profile provided by nf-core/configs.' + config_profile_contact = 'Matiss Ozols - mo246@leichester.ac.uk | mo11@sanger.ac.uk | matiss.ozols@manchester.ac.uk | mo513@cam.ac.uk' + + max_cpus = 24 + max_memory = 240.GB + max_time = 168.h + +} + +singularity { + enabled = true + envWhitelist = 'TZ' +} + +process { + + executor = 'slurm' + cpus = 1 + pollInterval = '1 min' + queueStatInterval = '2 min' + memory = 24.GB + time = 12.h + + + //queue = { task.time <= 24.h ? 'short' : task.time > 672.h ? 'long' : 'medium'} + withLabel: gpu { + beforeScript = 'module load cuda11.4/toolkit/11.4.1' + clusterOptions = '-l nodes=1:ppn=4:gpus=1 -l vmem=24g' + queue = 'gpu' + } +} \ No newline at end of file diff --git a/modules/nf-core/modules/umap/main.nf b/modules/nf-core/modules/umap/main.nf index 4e20317d..ac55b871 100755 --- a/modules/nf-core/modules/umap/main.nf +++ b/modules/nf-core/modules/umap/main.nf @@ -55,9 +55,6 @@ workflow UMAP { // the 'flatMap' emits each of these // aggregation list as a single item - Channel.of('key',outdir,anndata,metadata,pcs,reduced_dims,all_umaps).set{all_umaps2} - umap_gather_input.view() - all_umaps2.view() // Gather step. // Gather by tuple ... if we just to a collect, then will get all // umap_calculate calls, not split by reduced_dims. See link below: