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TheJacksonLaboratory
/
splicing-pipelines-nf
Repository for the Anczukow-Lab splicing pipeline
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Fixes env gtex issue #290
#294
Vlad-Dembrovskyi
closed
2 years ago
0
Updates ch_gtex_gen3_ids items #289
#293
Vlad-Dembrovskyi
closed
2 years ago
1
Updates GEN3-DRS manifest file parsing
#292
cgpu
closed
2 years ago
1
Updates GEN3-DRS manifest file parsing
#291
cgpu
closed
2 years ago
0
FIX Gen3-DRS ENV issue
#290
Vlad-Dembrovskyi
closed
2 years ago
0
'GEN3-DRS' is potentially outdated and not working
#289
angarb
closed
2 years ago
1
Remove requirement to provide reference fasta for Gen3-DRS download option
#288
Vlad-Dembrovskyi
closed
2 years ago
2
Simplify the Gen3-DRS download option
#287
Vlad-Dembrovskyi
closed
2 years ago
4
Remove GTEX download option as obsolete
#286
Vlad-Dembrovskyi
closed
2 years ago
0
(Low prio) Compress BAMs to CRAMs for storage
#285
Vlad-Dembrovskyi
closed
2 years ago
2
Makes saving of unmapped files optional, cleanup true by default
#284
Vlad-Dembrovskyi
closed
2 years ago
1
[DEL 3039] Implement ftp download for SRA accessions (#2)
#283
Vlad-Dembrovskyi
closed
2 years ago
1
Using new STAR index fails on CloudOS GCP env
#282
Vlad-Dembrovskyi
closed
2 years ago
1
Fixes containers and parametrizes options in google.config
#281
Vlad-Dembrovskyi
closed
2 years ago
0
Add an optional step to generate star index with pipeline
#280
Vlad-Dembrovskyi
opened
2 years ago
0
Implement a solution to get SRA samples from ENA via ftp
#279
Vlad-Dembrovskyi
closed
2 years ago
1
Add to docs that you can use SRA ftp links with default input csv
#278
Vlad-Dembrovskyi
closed
2 years ago
1
test if sra config creation works on other machine for singularity
#277
Vlad-Dembrovskyi
opened
2 years ago
0
Fix strType issue when stranded=false
#276
Vlad-Dembrovskyi
closed
2 years ago
1
Save only compresses gtf files in stringtie_merge process
#275
Vlad-Dembrovskyi
closed
2 years ago
1
Parametrize output of STAR "Unmapped" file
#274
Vlad-Dembrovskyi
closed
2 years ago
0
Research - if we can save only compressed bams from star into results
#273
Vlad-Dembrovskyi
closed
2 years ago
4
Remove the non-dated multiqc from the results
#272
Vlad-Dembrovskyi
opened
2 years ago
0
Add a CI tests to cover rMATS and the second half of the pipeline
#271
Vlad-Dembrovskyi
opened
2 years ago
0
Add a CI test that would cover paired_rMATS
#270
Vlad-Dembrovskyi
opened
2 years ago
0
Add documentation on paired_rMATS
#269
Vlad-Dembrovskyi
opened
2 years ago
0
Explore alternative ways to get public SRA samples (without SRA toolkit)
#268
Vlad-Dembrovskyi
closed
2 years ago
1
Parametrize error strategy (clean pr)
#267
Vlad-Dembrovskyi
closed
2 years ago
1
Fix saving files (#263)
#266
Vlad-Dembrovskyi
closed
2 years ago
0
Parametrize error strategy
#265
Vlad-Dembrovskyi
closed
2 years ago
1
Adds xstag strType parameter (clean pr)
#264
Vlad-Dembrovskyi
closed
2 years ago
1
Fix saving files
#263
Vlad-Dembrovskyi
closed
2 years ago
1
CI test can't pull singularity image for download_reads container
#262
Vlad-Dembrovskyi
opened
2 years ago
0
Adds xstag strType parameter
#261
Vlad-Dembrovskyi
closed
2 years ago
5
No paired-end CI test currently added in Github actions tests
#260
cgpu
opened
2 years ago
1
Consider limiting CI to 2 SRR ids in the input reads.csv
#259
cgpu
opened
2 years ago
0
Fast-fail strategy in CI does not allow us to gather information for debugging
#258
cgpu
closed
2 years ago
0
Add tree view of results as last step of CI
#257
cgpu
closed
2 years ago
0
.bw files are duplicated in the results folder
#256
cgpu
closed
2 years ago
0
Documentation: reads.csv
#255
angarb
closed
2 years ago
1
debug ci tests dev
#254
Vlad-Dembrovskyi
opened
2 years ago
0
Adds sra test
#253
Vlad-Dembrovskyi
closed
2 years ago
3
Add small SRA dataset to CI [SRR15346687]
#252
cgpu
closed
2 years ago
0
Implements .command.* save in results/
#251
cgpu
closed
2 years ago
1
Implements .command.* save in results/
#250
cgpu
closed
2 years ago
1
Bump Samtools version
#249
Vlad-Dembrovskyi
closed
2 years ago
0
Updates all tools and moves docker containers to anczukowlab repo
#248
Vlad-Dembrovskyi
closed
2 years ago
2
cacheDir = "/projects/anczukow-lab/.singularity_cache/" is problematic
#247
angarb
closed
2 years ago
0
--outdir param does not overwrite the main.pbs
#246
angarb
closed
2 years ago
0
Pipeline release v2.0
#245
Vlad-Dembrovskyi
closed
2 years ago
3
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