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stjudecloud
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workflows
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
MIT License
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bumping a docker image necessitates failing CI before merge
#189
a-frantz
opened
1 day ago
2
chore: migrate scrnaseq to external repo
#188
adthrasher
closed
2 days ago
0
ci: tests
#187
a-frantz
closed
1 day ago
2
docs: kraken warning
#186
a-frantz
closed
2 days ago
0
docs: make README clear that command won't work off the shelf
#185
a-frantz
closed
1 week ago
0
feat: add methylation pipelines
#184
adthrasher
opened
2 weeks ago
1
docs: example jsons
#183
a-frantz
closed
2 days ago
2
rework example JSONs
#182
a-frantz
closed
2 days ago
0
fix: remove unused variable and call
#181
adthrasher
closed
1 month ago
1
ci: use public Sprocket action
#180
adthrasher
closed
2 months ago
5
Add a read trimming step to alignment workflows
#179
a-frantz
opened
3 months ago
2
Mem allocations (and other miscellaneous improvements)
#178
a-frantz
closed
3 weeks ago
1
Add intentional pre and post checks for file emptiness
#177
a-frantz
opened
3 months ago
0
feat: wdl-format on everything
#176
a-frantz
closed
2 weeks ago
0
Lint fixes
#175
adthrasher
closed
2 weeks ago
0
chore: add blank CHANGELOGs
#174
a-frantz
closed
4 months ago
0
Clean up various new lints
#173
a-frantz
closed
4 months ago
0
Fragility in workflows around malformed/missing RG records
#172
a-frantz
opened
4 months ago
0
more dynamically allocated mem
#171
a-frantz
opened
4 months ago
0
Tasks that take both pos/name sorted probably need different resources
#170
a-frantz
opened
4 months ago
0
FastQC `prefix` convention is fragile
#169
a-frantz
opened
4 months ago
0
Expose more parameters of tools
#168
a-frantz
opened
4 months ago
1
Better document where GZIP input is required and where it's optional (but recommended)
#167
a-frantz
opened
4 months ago
0
support Single-Ended data
#166
a-frantz
opened
4 months ago
0
feat: use wdl-format on everything
#165
a-frantz
closed
4 months ago
0
Update `outputs` key in `meta` section
#164
adthrasher
closed
4 months ago
0
chore: fix input spacing
#163
adthrasher
closed
4 months ago
2
chore: apply changes for lint
#162
adthrasher
closed
5 months ago
0
chore: SJMotifs -> SpliceJunctionMotifs
#161
a-frantz
closed
5 months ago
0
fix: add lint directives
#160
a-frantz
closed
4 months ago
1
chore: single -> double quotes
#159
adthrasher
closed
6 months ago
0
chore: single -> double quotes
#158
adthrasher
closed
6 months ago
0
chore: single -> double quotes
#157
adthrasher
closed
6 months ago
0
fix: make index optional
#156
adthrasher
closed
6 months ago
0
Picard sort task fails for non-coordinate sorts
#155
adthrasher
closed
6 months ago
0
GATK4 lint warning fixes
#154
adthrasher
closed
6 months ago
0
feat: GATK MarkDuplicatesSpark
#153
adthrasher
closed
6 months ago
1
chore: casing
#152
a-frantz
closed
6 months ago
0
Update star.wdl
#151
adthrasher
closed
6 months ago
0
style: conform to latest lints in wdl crates
#150
a-frantz
closed
6 months ago
0
refactor: Update ReadGroup to force uppercase PL.
#149
adthrasher
closed
6 months ago
0
docs: fix document preamble
#148
adthrasher
closed
6 months ago
0
Reorganize ReadGroup struct
#147
adthrasher
closed
6 months ago
1
DNAseq updates
#146
adthrasher
closed
6 months ago
0
chore: Bump util version
#145
adthrasher
closed
7 months ago
0
Sprocket lint
#144
adthrasher
closed
7 months ago
0
feat: multiqc configs
#143
a-frantz
closed
5 months ago
0
feat(QC): adds optional optical dup marking
#142
a-frantz
closed
7 months ago
0
docs(README): add a bootstrap guide
#141
a-frantz
closed
7 months ago
2
fix(tools/picard): make VALIDATION_STRINGENCY SILENT the default
#140
a-frantz
closed
7 months ago
0
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