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KwanLab
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Autometa
Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
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"No markers for contigs in table. Unable to assess binning quality" for split contigs by taxa
#203
chasemc
closed
2 years ago
4
:art:🐚 Add bash-implementations of Autometa workflows
#202
evanroyrees
closed
2 years ago
0
:art::snake: Add specific parsers for domtblout and tblout for hmmscan output formats
#201
evanroyrees
closed
2 years ago
0
Wrong contigs used when taxonomy aware == true
#200
chasemc
closed
2 years ago
2
Should prodigal be inside of the taxonomy aware if statement?
#199
chasemc
closed
2 years ago
2
Licensing
#198
chasemc
closed
2 years ago
0
:art::green_apple: include other kingdoms as optional emits
#196
evanroyrees
closed
2 years ago
8
:fire::green_apple: Remove duplicate standard slurm profiles
#195
evanroyrees
closed
2 years ago
0
Fix import error in databases.py
#194
evanroyrees
closed
2 years ago
2
Split input fasta file, smartly
#193
chasemc
opened
2 years ago
0
"standard" and "slurm" profiles are referenced twice
#192
chasemc
closed
2 years ago
0
Create GitHub Action for building and publishing docker images
#191
evanroyrees
closed
2 years ago
1
Delete .gitattribute - there is a .gitattributes
#190
chasemc
closed
2 years ago
0
📝 Modify documentation for benchmark.rst
#189
Sidduppal
closed
2 years ago
3
Decide on how output directories should be created/handled
#188
chasemc
closed
2 years ago
1
This should probably be broken up into a subworkflow where `ANALYZE_KMERS` would be
#187
chasemc
closed
2 years ago
3
Add read-based contig coverage instead of spades-based
#186
chasemc
closed
2 years ago
2
Should we include the other kingdoms so they are linked to the output? Some researchers may be interested in some of the other fasta files that could be generated
#185
chasemc
closed
2 years ago
0
Nextflow documentation
#184
chasemc
closed
2 years ago
0
One thing I'm encountering/fixing now on the nfcore/dev branch is that MAKE on Mac doesn't work because 2.7 is the default python. You will need to change the `python` calls to `python3` in the MAKEFILE
#183
chasemc
closed
2 years ago
1
Large data mode
#182
evanroyrees
closed
2 years ago
2
Add nextflow config for testing 2.0
#181
chasemc
closed
3 years ago
0
Upgrade to py3: version 1.0 deprecation of py2.7
#180
evanroyrees
closed
2 years ago
3
Error while installib tsne with conda
#179
Unaimend
closed
3 years ago
15
Large data mode needs more granular checkpointing during clustering
#178
jason-c-kwan
closed
2 years ago
1
Add nf-core licenses to imported modules
#177
chasemc
closed
2 years ago
1
Add densmap embed method and fix binning-summary cluster column bug
#176
evanroyrees
closed
2 years ago
3
Make doc links point to KwanLab repo...
#175
chasemc
closed
2 years ago
1
Binning results Sig-Figs
#174
chasemc
closed
2 years ago
2
Add singularity image url when autometa is on bioconda
#173
chasemc
closed
1 year ago
6
Animations in methods documentation
#172
evanroyrees
opened
3 years ago
8
Create nextflow process to hmmpress marker hmms
#171
chasemc
opened
3 years ago
1
Write pickle files in defined location
#170
chasemc
closed
2 years ago
3
Add nextflow outdir directories to .dockerignore
#169
chasemc
closed
2 years ago
1
unclustered recruitment fails if there are no unclustered bins
#168
chasemc
closed
2 years ago
8
Add a profile for deepthought that everyone in lab can use
#167
chasemc
opened
3 years ago
0
Test if `optional:true` messes up an emit
#166
chasemc
closed
2 years ago
2
Add metagenome name to tags
#165
chasemc
closed
2 years ago
4
Add params.publish_dir_mode
#164
chasemc
closed
2 years ago
3
MultiQC
#163
chasemc
closed
2 years ago
4
Add nextfow test profile
#162
chasemc
opened
3 years ago
0
Split executors and profiles
#161
chasemc
closed
3 years ago
1
Do you think it would be worth changing the I/O behavior here s.t. each input metagenome has its own directory?
#160
chasemc
closed
2 years ago
6
Add nf-core license where necessary
#159
chasemc
closed
2 years ago
4
Nfcore and structuring modules for collaboration
#157
chasemc
closed
2 years ago
39
Only ignore /lib at top level
#156
chasemc
closed
2 years ago
1
Small test datasets to sanity check/attempt to break code
#152
chasemc
opened
3 years ago
6
AUTOMETA:TAXON_ASSIGNMENT:SPLIT_KINGDOMS fails if no bacteria were found
#151
chasemc
closed
2 years ago
1
Simple conda requirements and docker image for nextflow pipeline
#150
chasemc
closed
2 years ago
2
Marker md5 files contain absolute path, should just be file name
#149
chasemc
closed
2 years ago
6
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