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mycobactopia-org
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MTBseq-nf
MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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Modifications after extensively iterations on Virtual Machine
#86
Mxrcon
closed
2 months ago
1
[PATCH] Using biocontainers and removing custom container version
#85
Mxrcon
closed
2 months ago
0
Use nf-core template for the pipeline to facilitate standardisation
#84
abhi18av
closed
4 months ago
4
update nf-core tool and run `nf-core create` again [hotfix]
#82
Mxrcon
closed
1 year ago
0
Single-end reads
#81
AroobAlhumaidy
closed
1 year ago
1
Update the resistance database
#80
abhi18av
opened
1 year ago
0
Using `nf-core` :green_apple: template on MTBseq-nf step :two: :
#79
Mxrcon
closed
8 months ago
2
Using `nf-core` :green_apple: template on MTBseq-nf step :one:
#78
Mxrcon
closed
1 year ago
0
Refactor the pipeline to rely upon the nf-core template
#77
abhi18av
opened
1 year ago
0
Error related to log4j2 (with gatk `v3.8.0`)
#76
Mxrcon
closed
1 year ago
6
Bundle the gatk jar in the container
#75
abhi18av
closed
1 year ago
0
Improvements to the design and defaults
#74
abhi18av
closed
1 year ago
3
Updating the documentation for `MEDTROP` presentation
#73
Mxrcon
closed
1 year ago
1
GATK/Nextflow Java environment differences
#70
jloubser
closed
1 year ago
4
[FIX] Found errors in qc after debbuging
#69
Mxrcon
closed
2 years ago
3
Consider creating a custom container with all the necessary deps.
#67
abhi18av
closed
1 year ago
1
[Fix] Preventing workflows from caching the `samples.tsv` for cohort steps
#66
Mxrcon
closed
2 years ago
3
[DEV] Creating a Bash script to check logs
#65
Mxrcon
opened
2 years ago
1
[FIX] Adding specific tag to conda recipe
#64
Mxrcon
closed
2 years ago
0
Evaluate the use of hard-coded exit status as a fallback for mtbseq statuses
#63
abhi18av
opened
2 years ago
5
[MAINTENANCE] Adding a test workflow and updating the `Makefile`
#61
Mxrcon
closed
2 years ago
4
Submit a multi-container image to biocontainers
#60
abhi18av
closed
1 year ago
2
Evaluate upgrading the project to use mtbseq-1.0.4
#59
abhi18av
closed
2 years ago
10
[DEV] Adding a gatk_jar downloader
#58
Mxrcon
closed
1 year ago
15
Automatically download and extract the GATK jar
#57
abhi18av
opened
2 years ago
0
[DEV ] Adding a qc report report workflow
#56
Mxrcon
closed
2 years ago
2
Add QC_REPORTS workflow
#55
abhi18av
closed
2 years ago
4
[BUG] cannot create regular file ‘GenomeAnalysisTK.jar’ File exists - conda executor
#54
Mxrcon
opened
2 years ago
6
Allow the users to specify their own MTB references
#53
abhi18av
opened
2 years ago
1
Publish Logs
#52
abhi18av
opened
2 years ago
2
[BUG] conda package name
#51
Mxrcon
closed
2 years ago
2
Release 0.9.3
#50
emilyncosta
closed
2 years ago
0
Add reference files for MTB
#49
emilyncosta
closed
2 years ago
0
[DEV] Adding a channel for references
#48
Mxrcon
closed
2 years ago
6
[BONUS-BRANCH] Adding trimmomatic as optional tool
#47
Mxrcon
closed
2 years ago
11
Add optional trimmomatic module
#46
emilyncosta
closed
2 years ago
0
Generate nextflow schema
#45
emilyncosta
opened
2 years ago
0
[DEV] Adding notes about the native commands
#44
Mxrcon
closed
2 years ago
2
Release 0.9.2
#43
abhi18av
closed
2 years ago
2
Update error strategy
#42
abhi18av
closed
2 years ago
0
[DEV] adding dag resources
#41
Mxrcon
closed
2 years ago
2
Add github issue/contribution templates
#40
abhi18av
opened
2 years ago
0
Stubs and DAG file
#39
abhi18av
closed
2 years ago
0
[FIX] Syncing stubs and scripts
#38
Mxrcon
closed
2 years ago
0
Add a basic nextflow_schema file
#37
abhi18av
closed
2 years ago
0
Add nextflow_schema file
#36
abhi18av
closed
2 years ago
0
Create a documentation website
#35
abhi18av
opened
2 years ago
3
First public release
#34
abhi18av
closed
2 years ago
0
Allow users to input a CSV/TSV file
#33
abhi18av
closed
2 years ago
1
Create a DAG file for the batch/parallel workflows
#32
abhi18av
closed
2 years ago
3
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