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jaclyn-taroni
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Oct 30, 2019
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Looks good to me! Thank you!
4 tasks
jaclyn-taroni
added a commit
to cansavvy/OpenPBTA-analysis
that referenced
this pull request
Oct 30, 2019
I'm not sure what went wrong
jaclyn-taroni
pushed a commit
that referenced
this pull request
Oct 30, 2019
* Set up the set up * Add circle CI test and Docker config * Add some more comments * Set up Rprojroot for circle CI test to work better * Fixing Circle CI file. * Change read_tsv to data.table::fread for big file * read in the .gz file * push plot function changes * Fix an error * Add missing package to Dockerfile * Reduce cosmic file to only the brain sample mutations * Update README with changes to cosmic file * re-updated Dockerfile * Ran a linter on set up script * Comment out of date * Get rid of old WGX/WXS bed file set up * Incorporate initial PR suggestions from @jashapiro and @cbethell * Push a working bash script * Add bash script to circle CI * Add usage section in README and change name of script * Add some more comments * Correct a couple things in the README * Get rid of remnant comment * Fix a typo! * Add Usage to the TOC * Add more documentation to the README * Update Circle CI * Push more exact bash script * Fix a couple issues with handling metadata file path * Get rid of dev remnants * Couple changes for readability * Add some things to README and get rid of part of bash that isn't there * Found dumb mistake * Changed [*] to [+] * I mean [*] to a [@] which makes more sense. * Fix some of the overwrite handling * Add template and report script * Add run_eval to bash script * Get rid of dev remnants * Make better handling of strategy that is called but not there * Get rid of dev remnant again * Get rid of stray `\` * File got misplaced * Get rid of cosmic mutations without proper coordinates * Fixed a wrinkle with the COSMIC file * re-run a linter on everything. * Couple more minor touches * Make set up files not run if they are already existing * Fix handling of COSMIC file creation * Incorporate @jashapiro 's suggestions * Add a few more @jashapiro suggestions * Circle CI does not have a kitematic directory. Get rid * Make warning instead of stop * Missing `ggplot2::` * Remove reference files after use to try to reduce memory usage * Make one big mutate * Dumb extra comma * Add VAF_FILTER option and it's circle CI component * get rid of typo * Re-fix Circle CI file * Fix WXS if statement * Fix default Circle CI option * Make indels come last in the barplot * Fix order of barplot graph * Add the comparison notebook * Add initial comparison notebook * Notebook adjustments * Fixed dumb label mix-up problem * Further honing things * Added the other plots except that one combo plot * Add rendered version too * Rough draft of all plots here * Get rid of upsettR's blank plot * Refresh the notebook * Run linter * Change name to reflect the data better * Add to CircleCI and Dockerfile * Try to fix busted CircleCI command * Attempt to fix Dockerfile build problem * Attempt to fix docker build * Some Docker probs fixed * Push latest notebook and Dockerfile * Dockerfile appears to be building right. * Couple more things to finish up Dockerfile adds * development thing was left * Add Template for results discussion * Updates to notebook. Function and etc. * Refresh notebook * Add png saves to each plot * Added options to calculate_vaf_tmb.R script * Add set up for vaf_filter experiment * Push separate notebook for vaf_filter exp * Changes to README * Add more documentation * Push VAF cutoff experiment notebook * Update title of vaf notebook * Update notebook * Fix path problem and also extend no_region option * Fix typo * Added some documentation * Prep consensus mutation file saving * Fix sex chr mislabeling in COSMIC file per @jashapiro 's suggestion * Get rid of regional analysis. Linter the notebooks Add changes to plots * Updated COSMIC file * Streamline this branch * Revert unneeded changes * Clean up README * Add --no_region option to README * Update CircleCI * Get rid of region analysis to save on memory usage * Add documentation about comparison to README * Linter and switch to rds * Upload results * refresh notebook and results * Updated notebook * Change name of bash script and make it run the notebook too * Update README * column problem *should* be fixed * Push refreshed notebook and results * Add a bit more info in the README * attempt to fix CircleCI's lack of grid package * Add grid to Dockerfile explicitly * Made some things a tad less janky * Push refreshed notebook. Get rid of grid install from Dockerfile * Try older version of UpSetR for shiggles * Get rid of `library(grid)` so we know if the version of UpSetR has it fixed * Test CRAN installation fo UpSetR * beginning to reformulate script organization for consensus file creation * Push reorganized scripts and notebooks * renaming and reorganzing and styling * suppressWarnings for coercing variables. We expect that * get rid of some development remnants * Streamline the PR * Get rid of dummy file * Streamline even more * Get rid of superfluous pound signs * Actually add merge callers script * get rid of outdated source(functions) command * Make --overwrite actually functional * re-run linter after those adds * Get rid of outdated `-w` * Fix example * Found an outdated comment * Address the outdated comments spotted by @jaclyn-taroni * Make sure #190 changes are included I'm not sure what went wrong
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Purpose/implementation
data release updates for v6
aliquot_id
andsample_id
addedbroad_composition
tocell line
for WGS samples denoted as Cell lineBS_4M0ZMCDC
with wrong age at diagnosiscohort
column for CBTTC or PNOC003 samplescomposition
were changed toSolid Tumor
primary_site
were changed toPeripheral Whole Blood
age_at_diagnosis
to earliest age reported (same age used in OS calculations)OS_days
andOS_status
based on updated clinical datacancer_predispositions
informationseq_center
(could not add seq_instrument at this time due to multiple entries for BS_IDs)Diagnosis
andInitial CNS Tumor
fortumor_descriptor
fieldRelapse
sample toProgressive
(DIPG sample truly progressive, not relapse)normal_fraction
andtumor_fraction
)glioma_brain_region
for low- and high-grade gliomas
Issue/Caveats
Directions for reviewers
changed on release notes and download script.
pbta-cnv-cnvkit.seg.gz
pbta-histologies.tsv
pbta-snv-lancet.vep.maf.gz
pbta-snv-mutect2.vep.maf.gz
pbta-snv-strelka2.vep.maf.gz
pbta-snv-vardict.vep.maf.gz
pbta-sv-manta.tsv.gz
StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
StrexomeLite_hg38_liftover_100bp_padded.bed
pbta-sv-lumpy.tsv.gz
pbta-cnv-controlfreec.seg.gz
Results
Docker and continuous integration