diff --git a/.circleci/config.yml b/.circleci/config.yml index b833c4a456..9e41309fd5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -192,29 +192,31 @@ jobs: name: RNA-Seq composition command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/rna-seq-composition/rna-seq-composition.Rmd', clean = TRUE)" - - run: - name: TCGA SNV Caller Analysis - command: ./scripts/run_in_ci.sh bash analyses/snv-callers/run_caller_consensus_analysis-tcga.sh + # - run: + # name: TCGA SNV Caller Analysis + # command: ./scripts/run_in_ci.sh bash analyses/snv-callers/run_caller_consensus_analysis-tcga.sh - run: name: SNV Caller Analysis command: OPENPBTA_VAF_CUTOFF=0.5 ./scripts/run_in_ci.sh bash analyses/snv-callers/run_caller_consensus_analysis-pbta.sh - - run: - name: Tumor mutation burden with TCGA - command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/tmb-compare-tcga/compare-tmb.Rmd', clean = TRUE)" + # - run: + # name: Tumor mutation burden with TCGA + # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/tmb-compare-tcga/compare-tmb.Rmd', clean = TRUE)" - - run: - name: PBTA vs TCGA explore - command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/explore-tcga-pbta.Rmd', clean = TRUE)" + # - run: + # name: PBTA vs TCGA explore + # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/explore-tcga-pbta.Rmd', clean = TRUE)" - - run: - name: Lancet WXS vs WGS test - command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-paired-WXS-WGS.Rmd', clean = TRUE)" + # Retired analysis + # - run: + # name: Lancet WXS vs WGS test + # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-paired-WXS-WGS.Rmd', clean = TRUE)" - - run: - name: Lancet padded vs unpadded test - command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-padded-vs-unpadded.Rmd', clean = TRUE)" + # Retired analysis + # - run: + # name: Lancet padded vs unpadded test + # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-padded-vs-unpadded.Rmd', clean = TRUE)" # This analysis was a side concept question and no longer needs to be run. diff --git a/analyses/create-subset-files/biospecimen_ids_for_subset.RDS b/analyses/create-subset-files/biospecimen_ids_for_subset.RDS index 2849d52a0f..d7101da469 100644 Binary files a/analyses/create-subset-files/biospecimen_ids_for_subset.RDS and b/analyses/create-subset-files/biospecimen_ids_for_subset.RDS differ diff --git a/analyses/create-subset-files/create_subset_files.sh b/analyses/create-subset-files/create_subset_files.sh index d169282e60..e927b7cbbe 100755 --- a/analyses/create-subset-files/create_subset_files.sh +++ b/analyses/create-subset-files/create_subset_files.sh @@ -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 @@ -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 - # data file description cp $FULL_DIRECTORY/data-files-description.md $SUBSET_DIRECTORY @@ -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