Comment out other steps

jaclyn-taroni · Aug 9, 2021 · e12a34e · e12a34e
1 parent c1a5c8c
commit e12a34e
Showing 1 changed file with 117 additions and 117 deletions.
diff --git 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