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V16 subset files for CircleCI testing #670

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Apr 4, 2020
Merged

V16 subset files for CircleCI testing #670

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8fabc7f
:sparkles: add investigation on the tcga capture kit
yuankunzhu Mar 4, 2020
4ce52c5
:memo: add comments for scripts/intersect-bed-maf.sh
yuankunzhu Mar 4, 2020
bc6bf5d
:art: remove analyses folder name
yuankunzhu Mar 4, 2020
bdc41eb
:memo: add coverage-comparison
yuankunzhu Mar 4, 2020
86faf42
:art: add folder for notebooks
yuankunzhu Mar 4, 2020
b23f4b8
:art: move ipynb to notebooks folder
yuankunzhu Mar 4, 2020
26737d3
:art: remove pbta-tcga-manifest.tsv
yuankunzhu Mar 4, 2020
dc474ba
:memo: add links to notebooks; fix wording
yuankunzhu Mar 4, 2020
add2773
Merge branch 'master' into analyses/tcga-capture-kit-investigation
jashapiro Mar 4, 2020
bd38ba4
Adding coverage for TCGA BED
Mar 4, 2020
01a7ee5
Adding target old and new coverage for TCAG BED
Mar 4, 2020
378dc7a
Merge remote-tracking branch 'upstream/master' into tcga-tmb-qc
yuankunzhu Mar 5, 2020
911a3ba
:sparkles: add gitignore
yuankunzhu Mar 5, 2020
7948f63
:zap: update output file path handle in get-tcga-capture_kit.py
yuankunzhu Mar 5, 2020
8d69525
Adding script for hg19 to Gh38 using CrossMap
Mar 5, 2020
f1addd0
:sparkles: add boxplot.R
yuankunzhu Mar 5, 2020
4ae6dcd
:bug: skip the manifest header
yuankunzhu Mar 5, 2020
5d605c4
:sparkles: add ci for tcga-capture-kit-investigation
yuankunzhu Mar 5, 2020
bd9f5f7
Merge remote-tracking branch 'upstream/master' into tcga-tmb-qc
yuankunzhu Mar 5, 2020
3864b68
Merge branch 'analyses/tcga-capture-kit-investigation' of https://git…
yuankunzhu Mar 5, 2020
aff951a
git pull all changes YUankun submitted on 03-05-2020
Mar 5, 2020
bf32301
Added coverage plot
Mar 5, 2020
09b1aff
Added coverage plot
Mar 5, 2020
8129d96
Added crossmap, fixed run_investigation and moved coverage to /plots
Mar 5, 2020
2a4d6db
Removed CrossMapBED.sh script since all of the commands are in run_in…
Mar 5, 2020
cb12fd3
Changed WORKING_DIR in run-investigation and all other corresponding …
Mar 5, 2020
73fa08e
Changed BED names in intersect-bed-maf.sh
Mar 5, 2020
0530841
Updated READ.md files
Mar 5, 2020
f909a75
Updated READ.md file
Mar 5, 2020
7e65d9e
Update analyses/tcga-capture-kit-investigation/README.md
yuankunzhu Mar 5, 2020
028b479
Update analyses/tcga-capture-kit-investigation/run-investigation.sh
yuankunzhu Mar 5, 2020
8da3c63
Updated READ.md
Mar 5, 2020
8a72920
CHanging coverage file extension from .txt to .tsv
Mar 5, 2020
5635a78
:wastebasket: remove notebooks
yuankunzhu Mar 6, 2020
bc9e423
:pencil: update R script for readme; add links to script;
yuankunzhu Mar 6, 2020
6a585b2
:wrench: update run-investigation.sh to run exsiting scripts
yuankunzhu Mar 6, 2020
52e6bbe
:wrench: update boxplot.R to only output boxplot-all
yuankunzhu Mar 6, 2020
b374755
:wastebasket: remove boxplots for callers
yuankunzhu Mar 6, 2020
0b34516
Resolved conflicts in README.md
Mar 6, 2020
5025aad
Update README.md
yuankunzhu Mar 6, 2020
46e5cd4
Update run-investigation.sh
yuankunzhu Mar 6, 2020
a96758e
Update README.md
tkoganti Mar 6, 2020
074aa69
Merge pull request #2 from tkoganti/Teja_tmbQC
yuankunzhu Mar 6, 2020
86d1ff7
CI files should account for fusion-summary; improve documentation (#604)
jaclyn-taroni Mar 5, 2020
424cf4e
Remove CI logic from fusion-summary; rerun with v15 data (#605)
jaclyn-taroni Mar 6, 2020
f07503d
Merge remote-tracking branch 'upstream/master'
yuankunzhu Mar 10, 2020
41a6f82
Merge remote-tracking branch 'upstream/master'
yuankunzhu Mar 10, 2020
7994035
:wrench: resolve local confilcts
yuankunzhu Mar 11, 2020
e8b3bd1
Merge remote-tracking branch 'upstream/master'
yuankunzhu Mar 20, 2020
a8f5f55
Merge remote-tracking branch 'upstream/master'
yuankunzhu Mar 27, 2020
43b25b5
:memo: update data-files-description.md for v16
Mar 27, 2020
7b0518b
:memo: update release-notes.md for v16
Mar 27, 2020
a06dfe0
:wrench: update download-data.sh for v16
Mar 27, 2020
b62364d
:memo: update files-description and release notes to inclue fusion_su…
Apr 1, 2020
25489a2
add biospecimen RDS
cansavvy Apr 2, 2020
19ca34d
Update create_subset_files.sh to be using v16
cansavvy Apr 2, 2020
3e3f4c8
Merge branch 'master' into v16-ci
cansavvy Apr 2, 2020
c05d027
Merge remote-tracking branch 'upstream/master' into data-release/v16
jaclyn-taroni Apr 3, 2020
278ee54
Account for release-notes.md not being included in md5sum.txt
jaclyn-taroni Apr 3, 2020
2442007
Merge branch 'data-release/v16' into v16-ci
jaclyn-taroni Apr 3, 2020
46fecee
Move release-notes.md cp step after md5sum
jaclyn-taroni Apr 3, 2020
bca7c85
Comment out everything before TCGA SNV caller
jaclyn-taroni Apr 3, 2020
c9675fd
Comment out things downstream of TCGA snv callers
jaclyn-taroni Apr 3, 2020
1d8bc79
Revert "Comment out everything before TCGA SNV caller"
jaclyn-taroni Apr 3, 2020
94e6e25
Comment out TCGA SNV caller in CI
jaclyn-taroni Apr 3, 2020
b23c549
Merge branch 'master' into v16-ci
jaclyn-taroni Apr 3, 2020
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Binary file modified analyses/create-subset-files/biospecimen_ids_for_subset.RDS
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8 changes: 4 additions & 4 deletions analyses/create-subset-files/create_subset_files.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ set -o pipefail

# Set defaults for release and biospecimen file name
BIOSPECIMEN_FILE=${BIOSPECIMEN_FILE:-biospecimen_ids_for_subset.RDS}
RELEASE=${RELEASE:-release-v15-20200228}
RELEASE=${RELEASE:-release-v16-20200320}
NUM_MATCHED=${NUM_MATCHED:-15}

# This option controls whether or not the two larger MAF files are skipped as
Expand Down Expand Up @@ -68,9 +68,6 @@ cp $FULL_DIRECTORY/independent-specimens*.tsv $SUBSET_DIRECTORY
# all bed files
cp $FULL_DIRECTORY/*.bed $SUBSET_DIRECTORY

# the release notes
cp $FULL_DIRECTORY/release-notes.md $SUBSET_DIRECTORY
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Ah, this is why I was missing files. Because the script failed at this step before and the other files after it did not get copied. I ran everything again just in case.


# data file description
cp $FULL_DIRECTORY/data-files-description.md $SUBSET_DIRECTORY

Expand All @@ -91,3 +88,6 @@ cd $SUBSET_DIRECTORY
rm -f md5sum.txt
# create a new md5sum.txt file
md5sum * > md5sum.txt

# the release notes and not included in md5sum.txt
cp $FULL_DIRECTORY/release-notes.md $SUBSET_DIRECTORY
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