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georgiesamaha
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configBuilder-nf
Nextflow config builder scripts for supported HPC infrastructures.
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Ask user if they want to set NXF_TEMP
#48
georgiesamaha
opened
5 months ago
2
Autodetect which queues are available for detected scheduler
#47
georgiesamaha
closed
5 months ago
4
Add question and selection of optional container/conda cache dirs
#46
jfy133
opened
5 months ago
2
Fix broken autodetection of PBSpro schedulder
#45
georgiesamaha
closed
5 months ago
0
Sort detected container options for consistency
#44
jfy133
closed
5 months ago
0
Add final nf-core specific questions for infrastructure questions
#43
jfy133
closed
5 months ago
3
Add nf-core specific parameters questions (name, url etc)
#42
jfy133
closed
6 months ago
1
Add cleanup y/N question for infra config
#41
jfy133
closed
6 months ago
0
Add cleanup option (untested: requires previous PRs merged)
#40
jfy133
closed
6 months ago
2
Add basic container detection for local installations
#39
jfy133
closed
6 months ago
4
Fix writing of config to ensure no 'nonsense' output
#38
jfy133
closed
6 months ago
0
Restructures pipeline config initialisation
#37
jfy133
closed
6 months ago
0
Remove cloud option from infrastructure options
#36
jfy133
closed
7 months ago
0
Feature: `--fast` mode
#35
jfy133
opened
8 months ago
1
Infrastructure config - autodetect: which schedulers are available
#34
jfy133
closed
5 months ago
1
Pipeline config - new question: would you like to update another module?
#33
jfy133
opened
8 months ago
0
Pipeline config - new question: what walltime would you like to set for the process
#32
jfy133
opened
8 months ago
0
Pipeline config - new question: how many CPUs would you like to set for the process
#31
jfy133
opened
8 months ago
0
Pipeline config - new question: what memory would you like to set for the process
#30
jfy133
opened
8 months ago
0
Pipeline config - new question: what process would you like to configure?
#29
jfy133
opened
8 months ago
0
Pipeline config - autodetect: possible modules/processes
#28
jfy133
opened
8 months ago
0
Pipeline config - new question: what is the path to a pipeline you wish to make config for (if not nf-core)
#27
jfy133
opened
8 months ago
0
Pipeline config - new question: is this for a nf-core pipeline?
#26
jfy133
opened
8 months ago
0
Infrastructure config - new question: do you want to specify a certain number of retries
#25
jfy133
opened
8 months ago
0
Infrastructure config - new question: do you want autocleanup of work?
#24
jfy133
closed
6 months ago
0
Infrastructure config - new question: do you want to specify a specific scratch/TMPDIR space
#23
jfy133
opened
8 months ago
2
Infrastructure config - new question: do you want to define a global cache directory
#22
jfy133
opened
8 months ago
0
Infrastructure config - new question: do you have/want a iGenomes cache
#21
jfy133
opened
8 months ago
0
Infrastructure config - autodetect: is a cachedir variable already set, for resuse
#20
jfy133
opened
8 months ago
1
Infrastructure config - autodetect: [nf-core only] try to autoscale default process labels depending on max resources
#19
jfy133
opened
8 months ago
0
Infrastructure config - autodetect: [nf-core only?] find maximum resources across all nodes/machine
#18
jfy133
opened
8 months ago
0
Infrastructure config - autodetect step: detect options for container/software systems
#17
jfy133
opened
8 months ago
2
Infrastructure config - new question: is this config for a HPC?
#16
jfy133
opened
8 months ago
0
Infrastructure config - new question: is this for an nf-core config?
#15
jfy133
closed
6 months ago
0
Fix AttributeError in create_custom.py
#14
georgiesamaha
closed
8 months ago
5
Rename infrastructure questions and functions, add improved question flow and user response feedback
#13
jfy133
closed
8 months ago
1
Add Developer notes
#12
georgiesamaha
closed
8 months ago
0
Modularise the code base and add HPC automated checks
#11
georgiesamaha
closed
8 months ago
1
Reformat codebase for improved modularity
#10
georgiesamaha
closed
8 months ago
0
Saying 'yes' for unique resource for a specific processes asks again what executor to use?
#9
jfy133
opened
9 months ago
1
Not clear what 'Specify cluster options that should be applied to each process:' means
#8
jfy133
opened
9 months ago
2
Infrastructure config - autodetect: possible queues
#7
jfy133
closed
5 months ago
1
Auto-detect if `modules` is used on the system
#6
jfy133
closed
8 months ago
0
Consider autodetection of job scheduler
#5
jfy133
closed
8 months ago
0
Improve documentation on what is a 'custom' vs 'nf-core' configuration...
#4
jfy133
closed
5 months ago
2
Create conda environment.yml
#3
jfy133
closed
8 months ago
1
Possible issues with requirements
#2
jfy133
closed
8 months ago
0
Add documentation and instructions
#1
georgiesamaha
closed
9 months ago
0