Sydney-Informatics-Hub ONT-bacpac-nf issues

Sydney-Informatics-Hub / ONT-bacpac-nf

Bacterial profiling workflow for ONT data, written in Nextflow.

GNU General Public License v3.0

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issues

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Gadi project storage full

#63 fredjaya closed 20 hours ago
1
plassembler: insufficient read depth

#62 fredjaya opened 2 weeks ago
0
Revising trycycler and select assembly implementations

#61 fredjaya closed 3 days ago
2
Problem with trycyler

#60 fransamsing closed 5 hours ago
5
Implement solution for managing low-coverage samples

#59 georgiesamaha opened 1 month ago
0
Replace concat fq step with pigz

#58 georgiesamaha closed 1 month ago
0
Improve rendering of multiqc report

#57 georgiesamaha closed 1 month ago
1
Trycycler num contig check and improved flye assembly handling

#56 fredjaya closed 1 month ago
0
`create_phylogenytree_related_files.py` KeyError

#55 fredjaya closed 1 month ago
1
Explore reference-free assembly evaluation approach

#54 georgiesamaha closed 1 day ago
2
Clarify requirement to export singularity cache variables

#53 georgiesamaha opened 2 months ago
0
Fix broken tag for check_input

#52 georgiesamaha closed 2 months ago
0
Fix input directory typo

#51 georgiesamaha closed 2 months ago
0
Increasing assembly memory allocation for high accuracy basecalling samples

#50 georgiesamaha closed 2 months ago
0
Fix multiqc report

#49 georgiesamaha closed 1 month ago
1
Remove unused module

#48 georgiesamaha closed 3 months ago
0
Increase memory and threads for assemblies

#47 georgiesamaha closed 3 months ago
0
Fix docs typo

#46 georgiesamaha closed 3 months ago
0
Add samplesheet input

#45 georgiesamaha closed 3 months ago
0
Unicycler Error

#44 fransamsing closed 2 months ago
1
Revise trycycler method implementation

#43 georgiesamaha closed 1 day ago
2
Build custom trycycler container

#42 georgiesamaha closed 1 month ago
1
trycycler cluster issue workover, avoid building the tree; don't call the function

#41 nandan75 closed 2 months ago
0
Ingest a samplesheet, rather than a directory

#40 georgiesamaha closed 3 months ago
0
All non-zero exits to exit zero

#39 nandan75 closed 3 months ago
0
Updated gadi documentation for SINGULARITY_CACHEDIR

#38 nandan75 closed 3 months ago
0
Updated gadi documentation for SINGULARITY_CACHEDIR

#37 nandan75 closed 3 months ago
1
Change Python container

#36 nandan75 closed 3 months ago
0
Fixed nanoplot and pycoqc tags

#35 nandan75 closed 3 months ago
0
Testing with nf-test

#34 georgiesamaha opened 4 months ago
0
Add some test data

#33 georgiesamaha opened 4 months ago
0
Fix permissions and default assets preventing workflow execution

#32 georgiesamaha closed 4 months ago
0
Replaced wget with aria2 to parallelize and speed up the download

#31 gdmcdonald closed 2 months ago
1
Yesterday

#30 gdmcdonald closed 4 months ago
0
pull download edits to other branch

#29 gdmcdonald closed 4 months ago
0
Medaka output for consensus chromosomes is split into 2 subdirectories

#28 georgiesamaha closed 1 day ago
0
Update tags, results, docs for user testing

#27 georgiesamaha closed 4 months ago
0
Remove requirement to provide ONT summary sequencing file as file path

#26 georgiesamaha opened 4 months ago
0
Should we generate BUSCO plots?

#25 georgiesamaha opened 4 months ago
0
Should we add a process for visualising assembly graphs with Bandage?

#24 georgiesamaha opened 4 months ago
0
All consensus assemblies being polished by Medaka, even those that fail the check

#23 georgiesamaha closed 1 day ago
0
Porechop is abadonware

#22 georgiesamaha opened 4 months ago
1
Segmentation fault for 4 samples / 32 samples tested at run_trycycler_cluster.nf step

#21 nandan75 closed 1 month ago
3
create_phylogeny_And_heatmap.r - Image labels/size to be dynamically re-adjusted

#20 nandan75 closed 2 months ago
4
Workflow waits for all barcodes to complete before moving onto `select_assembly` step

#19 georgiesamaha closed 1 month ago
1
Speed up fastq concat

#18 georgiesamaha closed 1 month ago
1
Download reference databases and files

#17 georgiesamaha closed 1 month ago
1
Sequence QC: trimming with porechop

#16 georgiesamaha closed 5 months ago
0
Sequence QC: nanoplot

#15 georgiesamaha closed 5 months ago
0
Sequence QC: pycoqc

#14 georgiesamaha closed 5 months ago
0