OPC action: make base and top docker file, only build and push the top image #119

Workflow file for this run

.github/workflows/run_analysis.yml at 7d93778

	name: Analysis

	on:
	pull_request:

	jobs:
	consensus_cn_manta:
	name: Run Analysis - Consensus CN Manta
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: free disk space
	run: \|
	echo "Disk usage before cleanup:" && df -h
	# Remove swap
	sudo swapoff -a \|\| true
	sudo rm -f /swapfile \|\| true
	# Remove pre-installed tools and caches
	sudo rm -rf /usr/share/dotnet \|\| true
	sudo rm -rf /opt/ghc \|\| true
	sudo rm -rf /usr/local/share/boost \|\| true
	sudo rm -rf "$AGENT_TOOLSDIRECTORY" \|\| true
	# Clean apt cache
	sudo apt-get clean \|\| true
	# Docker cleanup
	docker system prune -af \|\| true
	echo "Disk usage after cleanup:" && df -h
	- name: Download Data for Consensus CN Manta
	uses: docker://pgc-images.sbgenomics.com/rokita-lab/openpedcanverse:latest
	with:
	entrypoint: ./download-data.sh
	env:
	OPENPEDCAN_URL: https://s3.amazonaws.com/bti-openaccess-us-east-1-prd-opc
	OPENPEDCAN_RELEASE: testing
	- name: Run Consensus CN Manta
	uses: docker://pgc-images.sbgenomics.com/rokita-lab/openpedcanverse:latest
	with:
	entrypoint: ./analyses/copy_number_consensus_call_manta/run_consensus_call.sh

	consensus_cn:
	name: Run Analysis - Consensus CN
	needs: consensus_cn_manta
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: free disk space
	run: \|
	echo "Disk usage before cleanup:" && df -h
	# Remove swap
	sudo swapoff -a \|\| true
	sudo rm -f /swapfile \|\| true
	# Remove pre-installed tools and caches
	sudo rm -rf /usr/share/dotnet \|\| true
	sudo rm -rf /opt/ghc \|\| true
	sudo rm -rf /usr/local/share/boost \|\| true
	sudo rm -rf "$AGENT_TOOLSDIRECTORY" \|\| true
	# Clean apt cache
	sudo apt-get clean \|\| true
	# Docker cleanup
	docker system prune -af \|\| true
	echo "Disk usage after cleanup:" && df -h
	- name: Download Data for Consensus CN
	uses: docker://pgc-images.sbgenomics.com/rokita-lab/openpedcanverse:latest
	with:
	entrypoint: ./download-data.sh
	env:
	OPENPEDCAN_URL: https://s3.amazonaws.com/bti-openaccess-us-east-1-prd-opc
	OPENPEDCAN_RELEASE: testing
	- name: Run Consensus CN
	uses: docker://pgc-images.sbgenomics.com/rokita-lab/openpedcanverse:latest
	with:
	entrypoint: ./analyses/copy_number_consensus_call/run_consensus_call.sh

	run_analysis:
	name: Run Analysis
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	include:
	# Molecular subtyping modules
	- name: Molecular Subtyping - MB
	entrypoint: molecular-subtyping-MB/run-molecular-subtyping-mb.sh
	openpbta_subset: 0

	- name: Molecular Subtyping - CRANIO
	entrypoint: molecular-subtyping-CRANIO/run-molecular-subtyping-cranio.sh
	openpbta_subset: 0

	- name: Molecular Subtyping - EPN
	entrypoint: molecular-subtyping-EPN/run-molecular-subtyping-EPN.sh

	- name: Molecular Subtyping - EMBRYONAL
	entrypoint: molecular-subtyping-embryonal/run-embryonal-subtyping.sh
	openpbta_testing: 1

	- name: Molecular Subtyping - CHORDOMA
	entrypoint: molecular-subtyping-chordoma/run-molecular-subtyping-chordoma.sh
	openpbta_subset: 0

	- name: Molecular Subtyping - EWS
	entrypoint: molecular-subtyping-EWS/run_subtyping.sh

	- name: Molecular Subtyping - NEUROCYTOMA
	entrypoint: molecular-subtyping-neurocytoma/run_subtyping.sh

	- name: Molecular Subtyping - HGG
	entrypoint: molecular-subtyping-HGG/run-molecular-subtyping-HGG.sh

	- name: Molecular Subtyping - LGG
	entrypoint: molecular-subtyping-LGAT/run_subtyping.sh
	openpbta_subset: 0

	- name: Molecular Subtyping - ATRT
	entrypoint: molecular-subtyping-ATRT/run-molecular-subtyping-ATRT.sh

	- name: Molecular Subtyping - PB
	entrypoint: molecular-subtyping-PB/run-molecular-subtyping-PB.sh
	openpbta_subset: 0

	- name: Molecular Subtyping - NBL
	entrypoint: molecular-subtyping-NBL/run-molecular-subtyping-NBL.sh

	- name: Molecular Subtyping - PATHOLOGY/COMPILE
	entrypoint: molecular-subtyping-pathology/run-subtyping-aggregation.sh
	openpbta_testing: 1

	- name: Molecular Subtyping - INTEGRATE (+ add cancer groups)
	entrypoint: molecular-subtyping-integrate/run-subtyping-integrate.sh


	# Analysis modules
	- name: Independent Specimens
	entrypoint: independent-samples/run-independent-samples.sh

	- name: Independent Specimens pre-release
	entrypoint: independent-samples/run-independent-samples.sh
	run_for_subtyping: 1

	- name: Gene set enrichment
	entrypoint: gene-set-enrichment-analysis/run-gsea.sh
	run_for_subtyping: 1
	openpbta_testing: 1

	- name: TP53/NF1 scores
	entrypoint: tp53_nf1_score/run_classifier.sh
	openpedcan_polya_strand: 0

	- name: Fusion filtering
	entrypoint: fusion_filtering/run_fusion_merged.sh

	- name: Fusion summary
	entrypoint: fusion-summary/run-new-analysis.sh
	openpbta_subset: 0

	- name: Consensus CN Manta
	entrypoint: copy_number_consensus_call_manta/run_consensus_call.sh

	- name: Consensus CN
	entrypoint: copy_number_consensus_call/run_consensus_call.sh

	- name: Consensus CN annotation
	entrypoint: focal-cn-file-preparation/run-prepare-cn.sh
	openpbta_testing: 1

	- name: TMB calculation
	entrypoint: tmb-calculation/run_tmb_calculation.sh

	- name: Mutational signatures
	entrypoint: mutational-signatures/run_mutational_signatures.sh
	openpbta_testing: 1

	- name: Immune Deconvolution
	entrypoint: immune-deconv/run-immune-deconv.sh

	#- name: EFO/MONDO annotation
	# entrypoint: efo-mondo-mapping/run_search_and_qc.sh

	#- name: ENSEMBL Gene matching
	# entrypoint: gene_match/run-gene-mapping.sh

	#- name: Update table annotation data
	# entrypoint: long-format-table-utils/run-update-long-format-table-utils.sh

	#- name: RNA-Seq Expression Summary stats
	# entrypoint: rna-seq-expression-summary-stats/run-rna-seq-expression-summary-stats.sh

	# MTP-specific modules
	#- name: Fusion frequency tables
	# entrypoint: fusion-frequencies/run-frequencies.sh

	#- name: SNV frequency tables
	# entrypoint: snv-frequencies/run-snv-frequencies.sh

	#- name: CNV frequency tables
	# entrypoint: cnv-frequencies/run-cnv-frequencies-analysis.sh

	#- name: RNA-Seq batch correction
	# entrypoint: rnaseq-batch-correct/run_ruvseq.sh

	steps:
	- uses: actions/checkout@v4
	- name: free disk space
	run: \|
	echo "Disk usage before cleanup:" && df -h
	# Remove swap
	sudo swapoff -a \|\| true
	sudo rm -f /swapfile \|\| true
	# Remove pre-installed tools and caches
	sudo rm -rf /usr/share/dotnet \|\| true
	sudo rm -rf /opt/ghc \|\| true
	sudo rm -rf /usr/local/share/boost \|\| true
	sudo rm -rf "$AGENT_TOOLSDIRECTORY" \|\| true
	# Clean apt cache
	sudo apt-get clean \|\| true
	# Docker cleanup
	docker system prune -af \|\| true
	echo "Disk usage after cleanup:" && df -h
	- name: Download Data
	uses: docker://pgc-images.sbgenomics.com/rokita-lab/openpedcanverse:latest
	with:
	entrypoint: ./download-data.sh
	env:
	OPENPEDCAN_URL: https://s3.amazonaws.com/bti-openaccess-us-east-1-prd-opc
	OPENPEDCAN_RELEASE: testing

	- name: Run Analysis
	uses: docker://pgc-images.sbgenomics.com/rokita-lab/openpedcanverse:latest
	with:
	entrypoint: analyses/${{ matrix.entrypoint }}
	env:
	OPENPBTA_SUBSET: ${{ matrix.openpbta_subset }}
	OPENPBTA_TESTING: ${{ matrix.openpbta_testing }}
	RUN_FOR_SUBTYPING: ${{ matrix.run_for_subtyping }}
	OPENPEDCAN_POLYA_STRAND: ${{ matrix.openpedcan_polya_strand }}

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OPC action: make base and top docker file, only build and push the top image #119

Workflow file

OPC action: make base and top docker file, only build and push the top image #119

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Workflow file for this run