SamStudio8 reticulatus issues

SamStudio8 / reticulatus

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads

MIT License

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issues

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Test sample

#56 GiangLeN opened 2 years ago
1
Update and pin dependencies

#55 SamStudio8 opened 2 years ago
2
Kraken rule throws InputFunctionException when provided with Ilm reads

#54 tanaes opened 3 years ago
5
Incorrect config gives unhelpful error

#53 Mulecc opened 3 years ago
1
k2kc (ktkit count) file should be bonded with reads.cfg

#52 SamStudio8 closed 3 years ago
0
Create LICENSE

#51 SamStudio8 closed 3 years ago
0
Provide overview figure

#50 Kirk3gaard opened 3 years ago
3
Recent changes to pre-medaka rules have forced the simg container to be required even for CPU

#49 SamStudio8 closed 4 years ago
8
Override of medaka calls_to_draft is not working

#48 jagos01 closed 4 years ago
20
Conda installation issue

#47 emmadoughty closed 4 years ago
8
Snakemake enhancement tracking issue

#46 SamStudio8 opened 4 years ago
0
assembly stats script is well slow

#45 SamStudio8 opened 4 years ago
0
Allow enforcing of a maximum number of attempts

#44 SamStudio8 opened 4 years ago
0
Globally define wildcard_constraints

#43 SamStudio8 closed 4 years ago
0
[pomoxis] Reticulatus-pomoxis tracking issue

#42 SamStudio8 opened 4 years ago
0
Rebaled assemblies fail jts_fastmer rule

#41 SamStudio8 closed 4 years ago
5
Expected assembly size is hardcoded in the default spellbook, which isn't a very good idea

#40 SamStudio8 opened 4 years ago
1
Error when running the pipeline

#39 nbargues closed 4 years ago
14
Ensure GPU devices are provisioned

#38 SamStudio8 closed 4 years ago
0
Add a method to mock entries in the manifest (eg. for comparison of known refs etc)

#37 SamStudio8 opened 4 years ago
0
Permit use of multiple ref.cfg, bound together by a config

#36 SamStudio8 closed 4 years ago
0
Read length statistics by reference

#35 SamStudio8 closed 4 years ago
0
Use ktkit for `extract_kraken_contigs` rule

#34 SamStudio8 opened 4 years ago
1
ktkit, download taxonomy database to config.yaml location

#33 SamStudio8 closed 4 years ago
1
Add links to ref.cfg.example to online Zymo refs

#32 SamStudio8 closed 4 years ago
0
Use of flye --meta should be configurable

#31 SamStudio8 closed 4 years ago
0
Is this for isolates or metagenomes?

#30 tseemann closed 4 years ago
2
Assembly battery graph

#29 SamStudio8 opened 4 years ago
0
Per taxon final assembly coverage based on kraken / ktkit

#28 SamStudio8 closed 4 years ago
1
Read taxon summaries with kraken / ktkit

#27 SamStudio8 closed 4 years ago
2
Add option to manifest to trash contigs with low support (low depth)

#26 SamStudio8 opened 4 years ago
0
Add medaka `consensus_probs.hdf` to rule output and set it as temp to destroy it afterwards

#25 SamStudio8 closed 4 years ago
1
Update to new SlackLogger (when it becomes available)

#24 SamStudio8 closed 4 years ago
2
Hook subsample_bam to be usable from manifest

#23 SamStudio8 closed 4 years ago
6
Benchmark summariser can't get time spent by medaka_consensus on samtools operations

#22 SamStudio8 closed 4 years ago
2
Override ${SORT} in pomoxis mini_align to reduce medaka sort overhead

#21 SamStudio8 closed 4 years ago
5
Validate manifest

#20 SamStudio8 opened 4 years ago
1
Make use of the {attempt} key to reduce GPU requirements

#19 SamStudio8 opened 4 years ago
2
General workspace/ tidying

#18 SamStudio8 opened 4 years ago
0
General tidying

#17 SamStudio8 closed 4 years ago
1
Automatically assign log and rtbenchmark with callable

#16 SamStudio8 opened 4 years ago
1
Rename `Snakefile-full` to `Snakefile-zymo` and decouple the rules

#15 SamStudio8 closed 4 years ago
5
Using pigz to speed up gzip steps causes flye to fail

#14 SamStudio8 opened 4 years ago
3
Full benchmark mode

#13 SamStudio8 closed 4 years ago
10
Generate citations for rules

#12 SamStudio8 opened 4 years ago
1
Consider process specific reporting of GPU information

#11 SamStudio8 opened 4 years ago
1
Override snakemake benchmark timer for GPU information

#10 SamStudio8 closed 4 years ago
6
Helper commands to initialise a pipeline

#9 SamStudio8 opened 4 years ago
2
Add option to flye spell to turn off built-in polishing

#8 SamStudio8 closed 4 years ago
0
Juggle GPU medaka automatically with CUDA_VISIBLE_DEVICES

#7 SamStudio8 closed 4 years ago
1