From c1a5c8ca406da6fc575278ca2868f01edae610cf Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni Date: Mon, 9 Aug 2021 16:18:27 -0400 Subject: [PATCH 1/3] Try using the consensus seg in the download file --- .../focal-cn-file-preparation/02-add-ploidy-consensus.Rmd | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd index 7dc1733e25..86c26c789f 100644 --- a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd +++ b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd @@ -41,9 +41,7 @@ if(!dir.exists(output_dir)) { ``` ```{r} -# TODO: the consensus SEG file is not currently in the data download -- when it -# gets included we will have to change the file path here -consensus_seg_file <- file.path("..", "copy_number_consensus_call", "results", +consensus_seg_file <- file.path("..", "..", "data", "pbta-cnv-consensus.seg.gz") histologies_file <- file.path("..", "..", "data", "pbta-histologies.tsv") From e12a34e441e0580636f0d711cf2c9b4d22f5768e Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni Date: Mon, 9 Aug 2021 16:19:16 -0400 Subject: [PATCH 2/3] Comment out other steps --- .circleci/config.yml | 234 +++++++++++++++++++++---------------------- 1 file changed, 117 insertions(+), 117 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index fb87b3fba1..c45197c577 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -12,157 +12,157 @@ jobs: name: Data Download command: OPENPBTA_URL=https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/data OPENPBTA_RELEASE=testing ./scripts/run_in_ci.sh bash download-data.sh - - run: - name: List Data Directory Contents - command: ./scripts/run_in_ci.sh ls data/testing +# - run: +# name: List Data Directory Contents +# command: ./scripts/run_in_ci.sh ls data/testing - - run: - name: Check python packages - command: ./scripts/run_in_ci.sh bash scripts/check-python.sh +# - run: +# name: Check python packages +# command: ./scripts/run_in_ci.sh bash scripts/check-python.sh - - run: - name: High level histology grouping for plot labels - command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('figures/mapping-histology-labels.Rmd', clean = TRUE)" +# - run: +# name: High level histology grouping for plot labels +# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('figures/mapping-histology-labels.Rmd', clean = TRUE)" - - run: - name: Sample Distribution Analyses - command: ./scripts/run_in_ci.sh bash "analyses/sample-distribution-analysis/run-sample-distribution.sh" +# - run: +# name: Sample Distribution Analyses +# command: ./scripts/run_in_ci.sh bash "analyses/sample-distribution-analysis/run-sample-distribution.sh" + +# - run: +# name: Sample Distribution Figure +# command: ./scripts/run_in_ci.sh Rscript figures/scripts/fig1-sample-distribution.R + +# - run: +# name: Transcriptome dimensionality reduction +# command: ./scripts/run_in_ci.sh ./analyses/transcriptomic-dimension-reduction/ci-dimension-reduction-plots.sh + +# # The analysis no longer needs to be tested as it has been retired and is better covered by 'SNV Caller Analysis' below. +# #- run: +# # name: Mutect2 vs Strelka2 +# # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutect2-vs-strelka2/01-set-up.Rmd', clean = TRUE); +# # rmarkdown::render('analyses/mutect2-vs-strelka2/02-analyze-concordance.Rmd', clean = TRUE)" - - run: - name: Sample Distribution Figure - command: ./scripts/run_in_ci.sh Rscript figures/scripts/fig1-sample-distribution.R +# ### MOLECULAR SUBTYPING ### - - run: - name: Transcriptome dimensionality reduction - command: ./scripts/run_in_ci.sh ./analyses/transcriptomic-dimension-reduction/ci-dimension-reduction-plots.sh +# - run: +# name: Molecular Subtyping - HGG +# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-HGG/run-molecular-subtyping-HGG.sh - # The analysis no longer needs to be tested as it has been retired and is better covered by 'SNV Caller Analysis' below. - #- run: - # name: Mutect2 vs Strelka2 - # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutect2-vs-strelka2/01-set-up.Rmd', clean = TRUE); - # rmarkdown::render('analyses/mutect2-vs-strelka2/02-analyze-concordance.Rmd', clean = TRUE)" +# - run: +# name: Molecular subtyping - Non-MB/Non-ATRT Embryonal tumors +# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-embryonal/run-embryonal-subtyping.sh - ### MOLECULAR SUBTYPING ### +# - run: +# name: Molecular Subtyping and Plotting - ATRT +# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-ATRT/run-molecular-subtyping-ATRT.sh - - run: - name: Molecular Subtyping - HGG - command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-HGG/run-molecular-subtyping-HGG.sh +# - run: +# name: Molecular subtyping Chordoma +# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-chordoma/run-molecular-subtyping-chordoma.sh - - run: - name: Molecular subtyping - Non-MB/Non-ATRT Embryonal tumors - command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-embryonal/run-embryonal-subtyping.sh +# - run: +# name: Molecular subtyping - Ependymoma +# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EPN/run-molecular-subtyping-EPN.sh - - run: - name: Molecular Subtyping and Plotting - ATRT - command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-ATRT/run-molecular-subtyping-ATRT.sh +# - run: +# name: Molecular Subtyping - LGAT +# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-LGAT/run_subtyping.sh - - run: - name: Molecular subtyping Chordoma - command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-chordoma/run-molecular-subtyping-chordoma.sh +# - run: +# name: Molecular Subtyping - EWS +# command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EWS/run_subtyping.sh - - run: - name: Molecular subtyping - Ependymoma - command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EPN/run-molecular-subtyping-EPN.sh +# - run: +# name: Molecular Subtyping Neurocytoma +# command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-neurocytoma/run_subtyping.sh - - run: - name: Molecular Subtyping - LGAT - command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-LGAT/run_subtyping.sh +# # Commenting this out for now; the code is expected to change +# # - run: +# # name: Molecular Subtyping - Compile and incorporate pathology feedback +# # command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-pathology/run-subtyping-aggregation.sh - - run: - name: Molecular Subtyping - EWS - command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EWS/run_subtyping.sh +# - run: +# name: Molecular Subtyping - MB +# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-MB/run-molecular-subtyping-mb.sh - - run: - name: Molecular Subtyping Neurocytoma - command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-neurocytoma/run_subtyping.sh +# - run: +# name: Molecular Subtyping - CRANIO +# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-CRANIO/run-molecular-subtyping-cranio.sh - # Commenting this out for now; the code is expected to change - # - run: - # name: Molecular Subtyping - Compile and incorporate pathology feedback - # command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-pathology/run-subtyping-aggregation.sh +# - run: +# name: Molecular Subtyping - INTEGRATE to BASE histology +# command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-integrate/run-subtyping-integrate.sh - - run: - name: Molecular Subtyping - MB - command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-MB/run-molecular-subtyping-mb.sh +# # Deprecated - these results do not include germline calls and therefore are insufficient by subtyping +# # - run: +# # name: SHH TP53 Molecular Subtyping +# # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/molecular-subtyping-SHH-tp53/SHH-tp53-molecular-subtyping-data-prep.Rmd', clean = TRUE)" - - run: - name: Molecular Subtyping - CRANIO - command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-CRANIO/run-molecular-subtyping-cranio.sh +# ### END MOLECULAR SUBTYPING ### - - run: - name: Molecular Subtyping - INTEGRATE to BASE histology - command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-integrate/run-subtyping-integrate.sh +# - run: +# name: Collapse RSEM +# command: ./scripts/run_in_ci.sh bash analyses/collapse-rnaseq/run-collapse-rnaseq.sh - # Deprecated - these results do not include germline calls and therefore are insufficient by subtyping - # - run: - # name: SHH TP53 Molecular Subtyping - # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/molecular-subtyping-SHH-tp53/SHH-tp53-molecular-subtyping-data-prep.Rmd', clean = TRUE)" +# - run: +# name: Fusion Summary +# command: ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh" - ### END MOLECULAR SUBTYPING ### +# - run: +# name: Immune deconvolution using immunedeconv, uses xCell by default +# command: ./scripts/run_in_ci.sh bash analyses/immune-deconv/run-immune-deconv.sh - - run: - name: Collapse RSEM - command: ./scripts/run_in_ci.sh bash analyses/collapse-rnaseq/run-collapse-rnaseq.sh +# - run: +# name: Fusion standardization and annotation for STARfusion and Arriba with polya and stranded data and creates recurrent fusion list +# command: ./scripts/run_in_ci.sh bash "analyses/fusion_filtering/run_fusion_merged.sh" - - run: - name: Fusion Summary - command: ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh" +# - run: +# name: Fusion standardization and annotation for STARFusio and Arriba for base subtyping +# command: OPENPBTA_BASE_SUBTYPING=1 ./scripts/run_in_ci.sh bash "analyses/fusion_filtering/run_fusion_merged.sh" - - run: - name: Immune deconvolution using immunedeconv, uses xCell by default - command: ./scripts/run_in_ci.sh bash analyses/immune-deconv/run-immune-deconv.sh - - - run: - name: Fusion standardization and annotation for STARfusion and Arriba with polya and stranded data and creates recurrent fusion list - command: ./scripts/run_in_ci.sh bash "analyses/fusion_filtering/run_fusion_merged.sh" - - - run: - name: Fusion standardization and annotation for STARFusio and Arriba for base subtyping - command: OPENPBTA_BASE_SUBTYPING=1 ./scripts/run_in_ci.sh bash "analyses/fusion_filtering/run_fusion_merged.sh" - - - run: - name: Sex prediction from RNA-seq - Clean data-train elasticnet-evaluate model - command: OPENPBTA_PERCENT=0 ./scripts/run_in_ci.sh bash analyses/sex-prediction-from-RNASeq/run-sex-prediction-from-RNASeq.sh +# - run: +# name: Sex prediction from RNA-seq - Clean data-train elasticnet-evaluate model +# command: OPENPBTA_PERCENT=0 ./scripts/run_in_ci.sh bash analyses/sex-prediction-from-RNASeq/run-sex-prediction-from-RNASeq.sh - # Deprecated: this comparison is no longer needed after separating Poly-A and stranded. - # - run: - # name: Selection Strategy Comparison - # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/selection-strategy-comparison/01-selection-strategies.rmd', params = list(neighbors = 2), clean = TRUE)" +# # Deprecated: this comparison is no longer needed after separating Poly-A and stranded. +# # - run: +# # name: Selection Strategy Comparison +# # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/selection-strategy-comparison/01-selection-strategies.rmd', params = list(neighbors = 2), clean = TRUE)" - - run: - name: TP53 NF1 classifier run - command: OPENPBTA_POLYAPLOT=0 ./scripts/run_in_ci.sh bash "analyses/tp53_nf1_score/run_classifier.sh" +# - run: +# name: TP53 NF1 classifier run +# command: OPENPBTA_POLYAPLOT=0 ./scripts/run_in_ci.sh bash "analyses/tp53_nf1_score/run_classifier.sh" -# This is deprecated -# - run: -# name: ssGSEA Analysis -# command: OPENPBTA_ANOVAPVALUE=0.25 OPENPBTA_TUKEYPVALUE=0.50 OPENPBTA_PERCKEEP=0.50 ./scripts/run_in_ci.sh bash analyses/ssgsea-hallmark/run-ssgsea-hallmark.sh +# # This is deprecated +# # - run: +# # name: ssGSEA Analysis +# # command: OPENPBTA_ANOVAPVALUE=0.25 OPENPBTA_TUKEYPVALUE=0.50 OPENPBTA_PERCKEEP=0.50 ./scripts/run_in_ci.sh bash analyses/ssgsea-hallmark/run-ssgsea-hallmark.sh -# The second method - ControlFREEC - was not included as of v6, so the comparison can no longer be performed -# - run: -# name: CNV Caller Comparison -# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-comparison/01-cnv-comparison-plotting.Rmd', clean = TRUE)" +# # The second method - ControlFREEC - was not included as of v6, so the comparison can no longer be performed +# # - run: +# # name: CNV Caller Comparison +# # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-comparison/01-cnv-comparison-plotting.Rmd', clean = TRUE)" - - run: - name: Independent samples - command: ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh +# - run: +# name: Independent samples +# command: ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh - - run: - name: Independent sample for base subtyping - command: OPENPBTA_BASE_SUBTYPING=1 ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh +# - run: +# name: Independent sample for base subtyping +# command: OPENPBTA_BASE_SUBTYPING=1 ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh - - run: - name: Interaction plot - command: OPENPBTA_ALL=0 ./scripts/run_in_ci.sh bash analyses/interaction-plots/01-create-interaction-plots.sh +# - run: +# name: Interaction plot +# command: OPENPBTA_ALL=0 ./scripts/run_in_ci.sh bash analyses/interaction-plots/01-create-interaction-plots.sh - - run: - name: Mutational Signatures - command: OPENPBTA_QUICK_MUTSIGS=1 ./scripts/run_in_ci.sh bash analyses/mutational-signatures/run_mutational_signatures.sh +# - run: +# name: Mutational Signatures +# command: OPENPBTA_QUICK_MUTSIGS=1 ./scripts/run_in_ci.sh bash analyses/mutational-signatures/run_mutational_signatures.sh -# - run: -# name: Chromosomal instability breakpoints -# command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/chromosomal-instability/run_breakpoint_analysis.sh +# # - run: +# # name: Chromosomal instability breakpoints +# # command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/chromosomal-instability/run_breakpoint_analysis.sh - run: name: Copy number consensus From 9f1160a6e6edf4ced189bc8c8bc1ccef5297c50e Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni Date: Mon, 9 Aug 2021 16:19:16 -0400 Subject: [PATCH 3/3] Revert "Comment out other steps" This reverts commit e12a34e441e0580636f0d711cf2c9b4d22f5768e. --- .circleci/config.yml | 234 +++++++++++++++++++++---------------------- 1 file changed, 117 insertions(+), 117 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index c45197c577..fb87b3fba1 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -12,157 +12,157 @@ jobs: name: Data Download command: OPENPBTA_URL=https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/data OPENPBTA_RELEASE=testing ./scripts/run_in_ci.sh bash download-data.sh -# - run: -# name: List Data Directory Contents -# command: ./scripts/run_in_ci.sh ls data/testing + - run: + name: List Data Directory Contents + command: ./scripts/run_in_ci.sh ls data/testing -# - run: -# name: Check python packages -# command: ./scripts/run_in_ci.sh bash scripts/check-python.sh + - run: + name: Check python packages + command: ./scripts/run_in_ci.sh bash scripts/check-python.sh -# - run: -# name: High level histology grouping for plot labels -# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('figures/mapping-histology-labels.Rmd', clean = TRUE)" + - run: + name: High level histology grouping for plot labels + command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('figures/mapping-histology-labels.Rmd', clean = TRUE)" -# - run: -# name: Sample Distribution Analyses -# command: ./scripts/run_in_ci.sh bash "analyses/sample-distribution-analysis/run-sample-distribution.sh" - -# - run: -# name: Sample Distribution Figure -# command: ./scripts/run_in_ci.sh Rscript figures/scripts/fig1-sample-distribution.R - -# - run: -# name: Transcriptome dimensionality reduction -# command: ./scripts/run_in_ci.sh ./analyses/transcriptomic-dimension-reduction/ci-dimension-reduction-plots.sh - -# # The analysis no longer needs to be tested as it has been retired and is better covered by 'SNV Caller Analysis' below. -# #- run: -# # name: Mutect2 vs Strelka2 -# # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutect2-vs-strelka2/01-set-up.Rmd', clean = TRUE); -# # rmarkdown::render('analyses/mutect2-vs-strelka2/02-analyze-concordance.Rmd', clean = TRUE)" + - run: + name: Sample Distribution Analyses + command: ./scripts/run_in_ci.sh bash "analyses/sample-distribution-analysis/run-sample-distribution.sh" -# ### MOLECULAR SUBTYPING ### + - run: + name: Sample Distribution Figure + command: ./scripts/run_in_ci.sh Rscript figures/scripts/fig1-sample-distribution.R -# - run: -# name: Molecular Subtyping - HGG -# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-HGG/run-molecular-subtyping-HGG.sh + - run: + name: Transcriptome dimensionality reduction + command: ./scripts/run_in_ci.sh ./analyses/transcriptomic-dimension-reduction/ci-dimension-reduction-plots.sh -# - run: -# name: Molecular subtyping - Non-MB/Non-ATRT Embryonal tumors -# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-embryonal/run-embryonal-subtyping.sh + # The analysis no longer needs to be tested as it has been retired and is better covered by 'SNV Caller Analysis' below. + #- run: + # name: Mutect2 vs Strelka2 + # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutect2-vs-strelka2/01-set-up.Rmd', clean = TRUE); + # rmarkdown::render('analyses/mutect2-vs-strelka2/02-analyze-concordance.Rmd', clean = TRUE)" -# - run: -# name: Molecular Subtyping and Plotting - ATRT -# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-ATRT/run-molecular-subtyping-ATRT.sh + ### MOLECULAR SUBTYPING ### -# - run: -# name: Molecular subtyping Chordoma -# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-chordoma/run-molecular-subtyping-chordoma.sh + - run: + name: Molecular Subtyping - HGG + command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-HGG/run-molecular-subtyping-HGG.sh -# - run: -# name: Molecular subtyping - Ependymoma -# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EPN/run-molecular-subtyping-EPN.sh + - run: + name: Molecular subtyping - Non-MB/Non-ATRT Embryonal tumors + command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-embryonal/run-embryonal-subtyping.sh -# - run: -# name: Molecular Subtyping - LGAT -# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-LGAT/run_subtyping.sh + - run: + name: Molecular Subtyping and Plotting - ATRT + command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-ATRT/run-molecular-subtyping-ATRT.sh -# - run: -# name: Molecular Subtyping - EWS -# command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EWS/run_subtyping.sh + - run: + name: Molecular subtyping Chordoma + command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-chordoma/run-molecular-subtyping-chordoma.sh -# - run: -# name: Molecular Subtyping Neurocytoma -# command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-neurocytoma/run_subtyping.sh + - run: + name: Molecular subtyping - Ependymoma + command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EPN/run-molecular-subtyping-EPN.sh -# # Commenting this out for now; the code is expected to change -# # - run: -# # name: Molecular Subtyping - Compile and incorporate pathology feedback -# # command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-pathology/run-subtyping-aggregation.sh + - run: + name: Molecular Subtyping - LGAT + command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-LGAT/run_subtyping.sh -# - run: -# name: Molecular Subtyping - MB -# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-MB/run-molecular-subtyping-mb.sh + - run: + name: Molecular Subtyping - EWS + command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EWS/run_subtyping.sh -# - run: -# name: Molecular Subtyping - CRANIO -# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-CRANIO/run-molecular-subtyping-cranio.sh + - run: + name: Molecular Subtyping Neurocytoma + command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-neurocytoma/run_subtyping.sh -# - run: -# name: Molecular Subtyping - INTEGRATE to BASE histology -# command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-integrate/run-subtyping-integrate.sh + # Commenting this out for now; the code is expected to change + # - run: + # name: Molecular Subtyping - Compile and incorporate pathology feedback + # command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-pathology/run-subtyping-aggregation.sh -# # Deprecated - these results do not include germline calls and therefore are insufficient by subtyping -# # - run: -# # name: SHH TP53 Molecular Subtyping -# # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/molecular-subtyping-SHH-tp53/SHH-tp53-molecular-subtyping-data-prep.Rmd', clean = TRUE)" + - run: + name: Molecular Subtyping - MB + command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-MB/run-molecular-subtyping-mb.sh -# ### END MOLECULAR SUBTYPING ### + - run: + name: Molecular Subtyping - CRANIO + command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-CRANIO/run-molecular-subtyping-cranio.sh -# - run: -# name: Collapse RSEM -# command: ./scripts/run_in_ci.sh bash analyses/collapse-rnaseq/run-collapse-rnaseq.sh + - run: + name: Molecular Subtyping - INTEGRATE to BASE histology + command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-integrate/run-subtyping-integrate.sh -# - run: -# name: Fusion Summary -# command: ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh" + # Deprecated - these results do not include germline calls and therefore are insufficient by subtyping + # - run: + # name: SHH TP53 Molecular Subtyping + # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/molecular-subtyping-SHH-tp53/SHH-tp53-molecular-subtyping-data-prep.Rmd', clean = TRUE)" -# - run: -# name: Immune deconvolution using immunedeconv, uses xCell by default -# command: ./scripts/run_in_ci.sh bash analyses/immune-deconv/run-immune-deconv.sh + ### END MOLECULAR SUBTYPING ### -# - run: -# name: Fusion standardization and annotation for STARfusion and Arriba with polya and stranded data and creates recurrent fusion list -# command: ./scripts/run_in_ci.sh bash "analyses/fusion_filtering/run_fusion_merged.sh" + - run: + name: Collapse RSEM + command: ./scripts/run_in_ci.sh bash analyses/collapse-rnaseq/run-collapse-rnaseq.sh -# - run: -# name: Fusion standardization and annotation for STARFusio and Arriba for base subtyping -# command: OPENPBTA_BASE_SUBTYPING=1 ./scripts/run_in_ci.sh bash "analyses/fusion_filtering/run_fusion_merged.sh" + - run: + name: Fusion Summary + command: ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh" -# - run: -# name: Sex prediction from RNA-seq - Clean data-train elasticnet-evaluate model -# command: OPENPBTA_PERCENT=0 ./scripts/run_in_ci.sh bash analyses/sex-prediction-from-RNASeq/run-sex-prediction-from-RNASeq.sh + - run: + name: Immune deconvolution using immunedeconv, uses xCell by default + command: ./scripts/run_in_ci.sh bash analyses/immune-deconv/run-immune-deconv.sh + + - run: + name: Fusion standardization and annotation for STARfusion and Arriba with polya and stranded data and creates recurrent fusion list + command: ./scripts/run_in_ci.sh bash "analyses/fusion_filtering/run_fusion_merged.sh" + + - run: + name: Fusion standardization and annotation for STARFusio and Arriba for base subtyping + command: OPENPBTA_BASE_SUBTYPING=1 ./scripts/run_in_ci.sh bash "analyses/fusion_filtering/run_fusion_merged.sh" + + - run: + name: Sex prediction from RNA-seq - Clean data-train elasticnet-evaluate model + command: OPENPBTA_PERCENT=0 ./scripts/run_in_ci.sh bash analyses/sex-prediction-from-RNASeq/run-sex-prediction-from-RNASeq.sh -# # Deprecated: this comparison is no longer needed after separating Poly-A and stranded. -# # - run: -# # name: Selection Strategy Comparison -# # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/selection-strategy-comparison/01-selection-strategies.rmd', params = list(neighbors = 2), clean = TRUE)" + # Deprecated: this comparison is no longer needed after separating Poly-A and stranded. + # - run: + # name: Selection Strategy Comparison + # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/selection-strategy-comparison/01-selection-strategies.rmd', params = list(neighbors = 2), clean = TRUE)" -# - run: -# name: TP53 NF1 classifier run -# command: OPENPBTA_POLYAPLOT=0 ./scripts/run_in_ci.sh bash "analyses/tp53_nf1_score/run_classifier.sh" + - run: + name: TP53 NF1 classifier run + command: OPENPBTA_POLYAPLOT=0 ./scripts/run_in_ci.sh bash "analyses/tp53_nf1_score/run_classifier.sh" -# # This is deprecated -# # - run: -# # name: ssGSEA Analysis -# # command: OPENPBTA_ANOVAPVALUE=0.25 OPENPBTA_TUKEYPVALUE=0.50 OPENPBTA_PERCKEEP=0.50 ./scripts/run_in_ci.sh bash analyses/ssgsea-hallmark/run-ssgsea-hallmark.sh +# This is deprecated +# - run: +# name: ssGSEA Analysis +# command: OPENPBTA_ANOVAPVALUE=0.25 OPENPBTA_TUKEYPVALUE=0.50 OPENPBTA_PERCKEEP=0.50 ./scripts/run_in_ci.sh bash analyses/ssgsea-hallmark/run-ssgsea-hallmark.sh -# # The second method - ControlFREEC - was not included as of v6, so the comparison can no longer be performed -# # - run: -# # name: CNV Caller Comparison -# # command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-comparison/01-cnv-comparison-plotting.Rmd', clean = TRUE)" +# The second method - ControlFREEC - was not included as of v6, so the comparison can no longer be performed +# - run: +# name: CNV Caller Comparison +# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-comparison/01-cnv-comparison-plotting.Rmd', clean = TRUE)" -# - run: -# name: Independent samples -# command: ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh + - run: + name: Independent samples + command: ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh -# - run: -# name: Independent sample for base subtyping -# command: OPENPBTA_BASE_SUBTYPING=1 ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh + - run: + name: Independent sample for base subtyping + command: OPENPBTA_BASE_SUBTYPING=1 ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh -# - run: -# name: Interaction plot -# command: OPENPBTA_ALL=0 ./scripts/run_in_ci.sh bash analyses/interaction-plots/01-create-interaction-plots.sh + - run: + name: Interaction plot + command: OPENPBTA_ALL=0 ./scripts/run_in_ci.sh bash analyses/interaction-plots/01-create-interaction-plots.sh -# - run: -# name: Mutational Signatures -# command: OPENPBTA_QUICK_MUTSIGS=1 ./scripts/run_in_ci.sh bash analyses/mutational-signatures/run_mutational_signatures.sh + - run: + name: Mutational Signatures + command: OPENPBTA_QUICK_MUTSIGS=1 ./scripts/run_in_ci.sh bash analyses/mutational-signatures/run_mutational_signatures.sh -# # - run: -# # name: Chromosomal instability breakpoints -# # command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/chromosomal-instability/run_breakpoint_analysis.sh +# - run: +# name: Chromosomal instability breakpoints +# command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/chromosomal-instability/run_breakpoint_analysis.sh - run: name: Copy number consensus