broadinstitute gdctools issues

broadinstitute / gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons

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issues

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Clinical dicing update

#89 dheiman closed 6 years ago
1
loadfiles need to contain unadulterated case id

#88 noblem opened 6 years ago
0
Merge CPTAC support code into master branch

#87 noblem closed 6 years ago
0
annotation_table enhancement: stop using Firehose_annotation column name

#86 noblem opened 6 years ago
0
findPython.sh should prioritize an activated virtual environment over all else

#85 dheiman closed 6 years ago
1
gdc_report should tolerate missing filter file

#84 noblem opened 6 years ago
0
need to cross-check samples for consistency

#83 noblem opened 6 years ago
1
Support new V2 segfile, and externalize test data for simpler/faster builds

#82 noblem closed 6 years ago
0
simplify & rationalize dicing of [new] data types

#81 noblem opened 6 years ago
0
change when ingestor syncs data & writes VERSION to cloud

#80 noblem opened 6 years ago
0
regression tests need to be less dependent upon content of data at GDC

#79 noblem opened 6 years ago
0
sample reports should be segregated by "program" name

#78 noblem opened 6 years ago
1
logfiles should be segregated by "program" name

#77 noblem opened 6 years ago
1
problem dicing latest CN data (from 2018_06_13)

#76 noblem closed 6 years ago
1
Failed to mirror TCGA-BRCA

#75 buchanae closed 6 years ago
2
exclude tests directory when doing pip install

#74 noblem opened 6 years ago
1
Improve config file to support exclusion of data types during mirror

#73 noblem opened 6 years ago
0
generalize sample reports

#72 noblem opened 6 years ago
1
Pull in master v0.2.6.7: ensuring that config and reference files are installed; updat…

#71 noblem closed 6 years ago
0
major bug: reference files not installed

#70 noblem closed 6 years ago
1
RFE: small tweaks to summarization

#69 noblem opened 6 years ago
0
New maf datatypes need to be recognized

#68 gsaksena opened 7 years ago
3
Gsaksena mmd2

#67 gsaksena opened 7 years ago
15
gdc_loadfile v0.3.5

#66 dheiman closed 7 years ago
1
gdac_loadfile allowed FFPE samples into a -TP sampleset

#65 gsaksena closed 7 years ago
5
BUG: multiple versions of clustering algorithms showing up in reports

#64 noblem closed 7 years ago
0
RFE: tools should be more stringent about when nothing needs to be done

#63 noblem opened 7 years ago
0
RFE: facilitate operation of downstream tools in offline mode

#62 noblem opened 7 years ago
0
Loadfile format

#61 noblem closed 7 years ago
0
python3 test failing, due to code from methylation branch

#60 noblem closed 6 years ago
1
Replicates test

#59 noblem closed 7 years ago
0
Some tools do not return proper exit code to invocation context (e.g. shell)

#58 noblem closed 7 years ago
1
gdc_loadfile does not observe or respect datestamps properly

#57 noblem closed 7 years ago
2
Cohorts include program name consistently (program-project)

#56 dheiman closed 7 years ago
0
Scrub code to remove TCGA specificity

#55 noblem opened 7 years ago
2
sample counts table needs to include project in cohort name

#54 noblem closed 7 years ago
2
gdc_mirror reports success even when some downloads fail

#53 gsaksena opened 7 years ago
3
gdc_loadfile is not preserving file paths

#52 dheiman closed 7 years ago
2
RFE: enable use of FORMAT argument in gdc_loadfile

#51 dheiman closed 7 years ago
1
docs need to be explicit about how configuration works: cli flags, config files, defaults ...

#50 noblem closed 7 years ago
1
fragility: gdc_report looks for config/blacklist.tsv (per tcga.cfg) ...

#49 noblem opened 7 years ago
0
gdc_loadfile sometimes does nothing

#48 gsaksena closed 7 years ago
2
behavior surprise when gdc_dice follows multiple gdc_mirror calls

#47 gsaksena opened 7 years ago
9
fix edge cases in config file handling

#46 noblem closed 7 years ago
3
New types of SNV data at GDC: needs scrutiny

#45 noblem closed 7 years ago
2
soft timeout when mirroring methylation data

#44 gsaksena opened 7 years ago
0
BUG: update gdac_ingestor to reflect latest incarnation of GDCtools

#43 noblem closed 7 years ago
1
possible bug in diced_file_comparator

#42 cbirger closed 7 years ago
2
Gsaksena methyl

#41 gsaksena closed 7 years ago
4
dicer does not handle failures appropriately

#40 noblem opened 7 years ago
0