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Comment out everything before TCGA SNV caller
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@jaclyn-taroni
jaclyn-taroni committed Apr 3, 2020
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274 changes: 137 additions & 137 deletions .circleci/config.yml
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Expand Up @@ -12,189 +12,189 @@ jobs:
name: Data Download
command: OPENPBTA_URL=https://open-pbta.s3.amazonaws.com/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: 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: 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
# - 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)"
# # 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)"

### MOLECULAR SUBTYPING ###
# ### MOLECULAR SUBTYPING ###

- 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 - HGG
# command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-HGG/run-molecular-subtyping-HGG.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 - 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 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 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 Chordoma
command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-chordoma/run-molecular-subtyping-chordoma.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 - Ependymoma
command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EPN/run-molecular-subtyping-EPN.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 - LGAT
command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-LGAT/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

- run:
name: Molecular Subtyping / Reclassification - EWS
command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EWS/run_reclassification.sh
# - run:
# name: Molecular Subtyping / Reclassification - EWS
# command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EWS/run_reclassification.sh

- 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 - 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)"
# # 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)"

### END MOLECULAR SUBTYPING ###
# ### END MOLECULAR SUBTYPING ###

- run:
name: Collapse RSEM
command: ./scripts/run_in_ci.sh bash analyses/collapse-rnaseq/run-collapse-rnaseq.sh
# - run:
# name: Collapse RSEM
# command: ./scripts/run_in_ci.sh bash analyses/collapse-rnaseq/run-collapse-rnaseq.sh

- run:
name: Immune deconvolution using xCell and MCP-Counter
command: OPENPBTA_DECONV_METHOD="mcp_counter" ./scripts/run_in_ci.sh bash analyses/immune-deconv/run-immune-deconv.sh
# - run:
# name: Immune deconvolution using xCell and MCP-Counter
# command: OPENPBTA_DECONV_METHOD="mcp_counter" ./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 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: 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: 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: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutational-signatures/mutational_signatures.Rmd', clean = TRUE)"
# - run:
# name: Mutational Signatures
# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutational-signatures/mutational_signatures.Rmd', clean = TRUE)"

- 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
command: ./scripts/run_in_ci.sh bash "analyses/copy_number_consensus_call/run_consensus_call.sh"
# - run:
# name: Copy number consensus
# command: ./scripts/run_in_ci.sh bash "analyses/copy_number_consensus_call/run_consensus_call.sh"

- run:
name: Focal CN Preparation
command: ./scripts/run_in_ci.sh bash analyses/focal-cn-file-preparation/run-prepare-cn.sh
# - run:
# name: Focal CN Preparation
# command: ./scripts/run_in_ci.sh bash analyses/focal-cn-file-preparation/run-prepare-cn.sh

- run:
name: Survival analysis
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/survival-analysis/survival-analysis_template.Rmd', params = list(plot_ci = FALSE), clean = TRUE)"
# - run:
# name: Survival analysis
# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/survival-analysis/survival-analysis_template.Rmd', params = list(plot_ci = FALSE), clean = TRUE)"

- run:
name: Comparative RNASeq - generate correlation matrix - rsem-tpm.polya
command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/01-correlation-matrix.py ../../data/pbta-gene-expression-rsem-tpm.polya.rds --clinical-path ../../data/pbta-histologies.tsv --qc-manifest-path ../../data/pbta-mend-qc-manifest.tsv --qc-results-path ../../data/pbta-mend-qc-results.tar.gz --prefix rsem-tpm-polya- --verbose
# - run:
# name: Comparative RNASeq - generate correlation matrix - rsem-tpm.polya
# command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/01-correlation-matrix.py ../../data/pbta-gene-expression-rsem-tpm.polya.rds --clinical-path ../../data/pbta-histologies.tsv --qc-manifest-path ../../data/pbta-mend-qc-manifest.tsv --qc-results-path ../../data/pbta-mend-qc-results.tar.gz --prefix rsem-tpm-polya- --verbose

- run:
name: Comparative RNASeq - generate correlation matrix - rsem-tpm.stranded
command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/01-correlation-matrix.py ../../data/pbta-gene-expression-rsem-tpm.stranded.rds --clinical-path ../../data/pbta-histologies.tsv --qc-manifest-path ../../data/pbta-mend-qc-manifest.tsv --qc-results-path ../../data/pbta-mend-qc-results.tar.gz --prefix rsem-tpm-stranded- --verbose
# - run:
# name: Comparative RNASeq - generate correlation matrix - rsem-tpm.stranded
# command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/01-correlation-matrix.py ../../data/pbta-gene-expression-rsem-tpm.stranded.rds --clinical-path ../../data/pbta-histologies.tsv --qc-manifest-path ../../data/pbta-mend-qc-manifest.tsv --qc-results-path ../../data/pbta-mend-qc-results.tar.gz --prefix rsem-tpm-stranded- --verbose

- run:
name: Comparative RNASeq - generate thresholds and outliers - rsem-tpm.stranded
command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/02-thresholds-and-outliers.py --prefix rsem-tpm-stranded- --results results --verbose
# - run:
# name: Comparative RNASeq - generate thresholds and outliers - rsem-tpm.stranded
# command: ./scripts/run_in_ci.sh python3 analyses/comparative-RNASeq-analysis/02-thresholds-and-outliers.py --prefix rsem-tpm-stranded- --results results --verbose

- run:
name: Process SV file
command: ./scripts/run_in_ci.sh Rscript analyses/sv-analysis/01-process-sv-file.R
# - run:
# name: Process SV file
# command: ./scripts/run_in_ci.sh Rscript analyses/sv-analysis/01-process-sv-file.R

- run:
name: Oncoprint plotting
command: ./scripts/run_in_ci.sh bash "analyses/oncoprint-landscape/run-oncoprint.sh"
# - run:
# name: Oncoprint plotting
# command: ./scripts/run_in_ci.sh bash "analyses/oncoprint-landscape/run-oncoprint.sh"

- run:
name: GISTIC Plots
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/gistic_plot.Rmd', clean = TRUE)"
# - run:
# name: GISTIC Plots
# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/gistic_plot.Rmd', clean = TRUE)"

- run:
name: Gene set enrichment analysis to generate GSVA scores
command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash "analyses/gene-set-enrichment-analysis/run-gsea.sh"
# - run:
# name: Gene set enrichment analysis to generate GSVA scores
# command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash "analyses/gene-set-enrichment-analysis/run-gsea.sh"

- run:
name: Fusion Summary
command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh"
# - run:
# name: Fusion Summary
# command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh"

- run:
name: Add Shatterseek
command: ./scripts/run_in_ci.sh Rscript analyses/sv-analysis/02-shatterseek.R
# - run:
# name: Add Shatterseek
# command: ./scripts/run_in_ci.sh Rscript analyses/sv-analysis/02-shatterseek.R

- run:
name: Telomerase activity
command: ./scripts/run_in_ci.sh bash analyses/telomerase-activity-prediction/RUN-telomerase-activity-prediction.sh
# - run:
# name: Telomerase activity
# command: ./scripts/run_in_ci.sh bash analyses/telomerase-activity-prediction/RUN-telomerase-activity-prediction.sh

- run:
name: GISTIC Results Comparison
command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/compare-gistic/run-compare-gistic.sh
# - run:
# name: GISTIC Results Comparison
# command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/compare-gistic/run-compare-gistic.sh


################################
#### Add your analysis here ####
################################
# ################################
# #### Add your analysis here ####
# ################################

- run:
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: 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
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