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ctmrbio
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stag-mwc
StaG Metagenomic Workflow Collaboration
https://stag-mwc.readthedocs.org
MIT License
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Merge dev (0.7.1)
#224
boulund
opened
2 weeks ago
0
Parameterize container images
#223
boulund
closed
5 months ago
0
Bring dev in sync with master
#222
boulund
closed
7 months ago
0
Error in Bowtie2 and kraken2 db
#221
mksherwani
closed
9 months ago
2
Release v0.7
#220
boulund
closed
1 year ago
0
Improve host removal
#219
boulund
closed
1 year ago
0
Include text file summarizing versions of all tools used, database versions, and StaG verison
#218
boulund
opened
1 year ago
0
StaG v6.1
#217
boulund
closed
1 year ago
0
Drop amr-related tools
#216
boulund
closed
1 year ago
0
Version 0.6.1
#215
boulund
closed
1 year ago
0
Use resources.tmpdir instead of custom solution
#214
boulund
closed
1 year ago
1
Make HUMAnN rules use resources.tmpdir directive instead of params.tmpdir
#213
boulund
closed
1 year ago
1
KrakenUniq: Use fuse.sh instead of reformat.sh
#212
boulund
closed
1 year ago
0
Make BAM files from mappers temporary
#211
boulund
closed
1 year ago
0
KrakenUniq does not work when skipping host removal (host_removal: False)
#210
boulund
closed
1 year ago
1
Merge reads to avoid feeding krakenuniq symlinks when skipping host removal
#209
boulund
closed
1 year ago
0
First outline draft of new assembly+binning workflow
#208
boulund
closed
1 year ago
2
New assembly+binning workflow
#207
boulund
closed
1 year ago
1
Merge 0.6.0
#206
boulund
closed
1 year ago
0
Reorganize repo to conform to Snakemake best practices
#205
boulund
closed
1 year ago
2
Add Kaiju Krona HTML to report
#204
boulund
closed
1 year ago
0
New gandalf profile
#203
boulund
closed
1 year ago
0
Amount of CPUs/threads for rules running in Slurm is incorrect
#202
boulund
closed
1 year ago
1
Add feature to disable metaphlan heatmap plot
#201
boulund
closed
1 year ago
1
Release 0.5.1
#200
boulund
closed
1 year ago
1
Update AMR++ to v3
#199
boulund
closed
1 year ago
1
KrakenUniq not working with Singularity
#198
boulund
closed
1 year ago
1
Enable remote sources over HTTP/HTTPS
#197
boulund
closed
1 year ago
0
Enable automatic download of test data
#196
boulund
closed
1 year ago
1
Add rule to automatically download test data
#195
boulund
closed
1 year ago
2
Make Snakemake report generation more robust and reliable
#194
boulund
closed
1 year ago
0
Cannot generate report with --use-singularity
#193
boulund
closed
1 year ago
1
Remove db download rules
#192
boulund
closed
1 year ago
0
KrakenUniq module: add Krona, mpa-style output, area plot
#191
boulund
closed
1 year ago
1
Make krona optional, change to mpa4 biocontainer
#190
boulund
closed
1 year ago
0
Bump minimum required Snakemake version
#189
boulund
closed
1 year ago
1
Add samplesheet input option
#188
boulund
closed
1 year ago
1
Remove outdated DB download rules
#187
boulund
closed
1 year ago
0
Make StaG-mwc Snakemake workflow standards compliant
#186
boulund
closed
1 year ago
3
Fix broken reference to StaG logo in reports
#185
boulund
closed
1 year ago
1
make krona plots optional
#184
luhugerth
closed
1 year ago
2
Add KrakenUniq
#183
boulund
closed
1 year ago
2
Update MetaPhlAn to version 4.0.0
#182
boulund
closed
2 years ago
0
Update Snakefile
#181
MaeSei
closed
2 years ago
0
Update to mpa4 and humann 3.5
#180
boulund
closed
2 years ago
0
Make essential parts of MetaWRAP run in StaG
#179
boulund
closed
1 year ago
0
keep_kreport broken in host_removal
#178
boulund
closed
2 years ago
1
Use GHCR for Singularity
#177
boulund
closed
2 years ago
1
Next release (0.5.0)
#176
boulund
closed
2 years ago
0
Limit gandalf slurm jobs to one node
#175
boulund
closed
2 years ago
1
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