diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 8127a99..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-services:
-- docker
-install: make docker-login build
-stages:
-- name: test
-- name: publish-release
-  if: branch = main AND type != pull_request
-- name: publish-staging
-  if: branch != main AND type != pull_request
-jobs:
-  include:
-  - stage: test
-    name: Test
-    script:
-    - make validate
-  - stage: publish-staging
-    name: Publish staging image
-    script:
-    - make publish-staging
-  - stage: publish-release
-    name: Publish production image
-    script:
-    - make publish-release
-env:
-  global:
-  - secure: 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
-  - secure: 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
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 4c30824..0000000
--- a/Makefile
+++ /dev/null
@@ -1,39 +0,0 @@
-REPO = gatk4_mutect2_cwl
-
-.PHONY: build build-* init init-*
-init: init-hooks init-secrets
-
-init-hooks:
-	@echo
-	@echo -- Installing Precommit Hooks --
-	pre-commit install
-
-init-secrets:
-	@echo
-	detect-secrets scan --update .secrets.baseline
-	detect-secrets audit .secrets.baseline
-
-.PHONY: build
-build:
-	@echo
-	@echo -- Building dockers --
-	@bash build.sh build
-
-
-.PHONY: publish-staging publish-release
-publish-staging:
-	@echo
-	@bash build.sh publish-staging
-
-publish-release:
-	@echo
-	@bash build.sh publish-release
-
-.PHONY: validate
-validate:
-	@bash build.sh validate
-
-.PHONY: docker-*
-docker-login:
-	@echo
-	docker login -u="${QUAY_USERNAME}" -p="${QUAY_PASSWORD}" quay.io
diff --git a/gatk4-mutect2-calling-cwl/Makefile b/gatk4-mutect2-calling-cwl/Makefile
deleted file mode 100644
index c75b714..0000000
--- a/gatk4-mutect2-calling-cwl/Makefile
+++ /dev/null
@@ -1,72 +0,0 @@
-# quay repo not git repo
-REPO = gatk4-mutect2-calling-cwl
-# TODO: Replace me
-ENTRY_CWL = "gpas_gatk4.2.4.1_mutect2_workflow.cwl"
-
-VERSION := $(shell date -u +"%Y%m%dT%H%MZ")
-COMMIT_HASH:=$(shell git rev-parse HEAD)
-
-DOCKER_REPO := quay.io/ncigdc
-DOCKER_IMAGE_COMMIT := ${DOCKER_REPO}/${REPO}:${COMMIT_HASH}
-DOCKER_IMAGE := ${DOCKER_REPO}/${REPO}:${VERSION}
-
-.PHONY: version version-* name
-name:
-	@echo ${WORKFLOW_NAME}
-
-version:
-	@echo --- VERSION: ${VERSION} ---
-
-version-docker:
-	@echo ${DOCKER_IMAGE_COMMIT}
-	@echo ${DOCKER_IMAGE}
-
-.PHONY: docker-*
-docker-login:
-	@echo
-	docker login -u="${QUAY_USERNAME}" -p="${QUAY_PASSWORD}" quay.io
-
-
-.PHONY: build build-* clean init init-* lint requirements run version
-init: init-pip
-
-init-pip:
-	@echo
-	@echo -- Installing pip packages --
-	pip3 install --no-cache-dir cwltool==1.0.20180306163216
-
-.PHONY: pack pack-%
-pack:
-	@python -m cwltool --pack "${ENTRY_CWL}"
-
-run:
-	@docker run --rm ${DOCKER_IMAGE_COMMIT} pack ENTRY_CWL=/opt/${ENTRY_CWL}
-
-.PHONY: validate validate-*
-validate:
-	@python -m cwltool --validate "${ENTRY_CWL}"
-
-validate-docker:
-	@docker run --rm ${DOCKER_IMAGE_COMMIT} validate ENTRY_CWL=/opt/${ENTRY_CWL}
-
-.PHONY: build build-*
-build: build-docker
-
-build-docker:
-	@echo
-	@echo -- Building docker --
-	docker build .. \
-		--file ./Dockerfile \
-		--build-arg WORKFLOW=${WORKFLOW_NAME} \
-		-t "${DOCKER_IMAGE_COMMIT}"
-
-
-.PHONY: publish publish-release
-publish:
-	docker push ${DOCKER_IMAGE_COMMIT}
-
-publish-staging: publish
-
-publish-release: publish
-	docker tag ${DOCKER_IMAGE_COMMIT} ${DOCKER_IMAGE}
-	docker push ${DOCKER_IMAGE}
\ No newline at end of file
diff --git a/gatk4-mutect2-tumor-only-cwl/Makefile b/gatk4-mutect2-tumor-only-cwl/Makefile
deleted file mode 100644
index 61d8a6c..0000000
--- a/gatk4-mutect2-tumor-only-cwl/Makefile
+++ /dev/null
@@ -1,72 +0,0 @@
-# quay repo not git repo
-REPO = gatk4-mutect2-tumor-only-cwl
-# TODO: Replace me
-ENTRY_CWL = "gpas_gatk4.2.4.1_mutect2_tumor_only_workflow.cwl"
-
-VERSION := $(shell date -u +"%Y%m%dT%H%MZ")
-COMMIT_HASH:=$(shell git rev-parse HEAD)
-
-DOCKER_REPO := quay.io/ncigdc
-DOCKER_IMAGE_COMMIT := ${DOCKER_REPO}/${REPO}:${COMMIT_HASH}
-DOCKER_IMAGE := ${DOCKER_REPO}/${REPO}:${VERSION}
-
-.PHONY: version version-* name
-name:
-	@echo ${WORKFLOW_NAME}
-
-version:
-	@echo --- VERSION: ${VERSION} ---
-
-version-docker:
-	@echo ${DOCKER_IMAGE_COMMIT}
-	@echo ${DOCKER_IMAGE}
-
-.PHONY: docker-*
-docker-login:
-	@echo
-	docker login -u="${QUAY_USERNAME}" -p="${QUAY_PASSWORD}" quay.io
-
-
-.PHONY: build build-* clean init init-* lint requirements run version
-init: init-pip
-
-init-pip:
-	@echo
-	@echo -- Installing pip packages --
-	pip3 install --no-cache-dir cwltool==1.0.20180306163216
-
-.PHONY: pack pack-%
-pack:
-	@python -m cwltool --pack "${ENTRY_CWL}"
-
-run:
-	@docker run --rm ${DOCKER_IMAGE_COMMIT} pack ENTRY_CWL=/opt/${ENTRY_CWL}
-
-.PHONY: validate validate-*
-validate:
-	@python -m cwltool --validate "${ENTRY_CWL}"
-
-validate-docker:
-	@docker run --rm ${DOCKER_IMAGE_COMMIT} validate ENTRY_CWL=/opt/${ENTRY_CWL}
-
-.PHONY: build build-*
-build: build-docker
-
-build-docker:
-	@echo
-	@echo -- Building docker --
-	docker build .. \
-		--file ./Dockerfile \
-		--build-arg WORKFLOW=${WORKFLOW_NAME} \
-		-t "${DOCKER_IMAGE_COMMIT}"
-
-
-.PHONY: publish publish-release
-publish:
-	docker push ${DOCKER_IMAGE_COMMIT}
-
-publish-staging: publish
-
-publish-release: publish
-	docker tag ${DOCKER_IMAGE_COMMIT} ${DOCKER_IMAGE}
-	docker push ${DOCKER_IMAGE}
\ No newline at end of file
diff --git a/gatk4-pon-cwl/Makefile b/gatk4-pon-cwl/Makefile
deleted file mode 100644
index 4ada277..0000000
--- a/gatk4-pon-cwl/Makefile
+++ /dev/null
@@ -1,72 +0,0 @@
-# quay repo not git repo
-REPO = gatk4-pon-cwl
-# TODO: Replace me
-ENTRY_CWL = "gpas_gatk4.2.4.1_mutect2_pon_workflow.cwl"
-
-VERSION := $(shell date -u +"%Y%m%dT%H%MZ")
-COMMIT_HASH:=$(shell git rev-parse HEAD)
-
-DOCKER_REPO := quay.io/ncigdc
-DOCKER_IMAGE_COMMIT := ${DOCKER_REPO}/${REPO}:${COMMIT_HASH}
-DOCKER_IMAGE := ${DOCKER_REPO}/${REPO}:${VERSION}
-
-.PHONY: version version-* name
-name:
-	@echo ${WORKFLOW_NAME}
-
-version:
-	@echo --- VERSION: ${VERSION} ---
-
-version-docker:
-	@echo ${DOCKER_IMAGE_COMMIT}
-	@echo ${DOCKER_IMAGE}
-
-.PHONY: docker-*
-docker-login:
-	@echo
-	docker login -u="${QUAY_USERNAME}" -p="${QUAY_PASSWORD}" quay.io
-
-
-.PHONY: build build-* clean init init-* lint requirements run version
-init: init-pip
-
-init-pip:
-	@echo
-	@echo -- Installing pip packages --
-	pip3 install --no-cache-dir cwltool==1.0.20180306163216
-
-.PHONY: pack pack-%
-pack:
-	@python -m cwltool --pack "${ENTRY_CWL}"
-
-run:
-	@docker run --rm ${DOCKER_IMAGE_COMMIT} pack ENTRY_CWL=/opt/${ENTRY_CWL}
-
-.PHONY: validate validate-*
-validate:
-	@python -m cwltool --validate "${ENTRY_CWL}"
-
-validate-docker:
-	@docker run --rm ${DOCKER_IMAGE_COMMIT} validate ENTRY_CWL=/opt/${ENTRY_CWL}
-
-.PHONY: build build-*
-build: build-docker
-
-build-docker:
-	@echo
-	@echo -- Building docker --
-	docker build .. \
-		--file ./Dockerfile \
-		--build-arg WORKFLOW=${WORKFLOW_NAME} \
-		-t "${DOCKER_IMAGE_COMMIT}"
-
-
-.PHONY: publish publish-release
-publish:
-	docker push ${DOCKER_IMAGE_COMMIT}
-
-publish-staging: publish
-
-publish-release: publish
-	docker tag ${DOCKER_IMAGE_COMMIT} ${DOCKER_IMAGE}
-	docker push ${DOCKER_IMAGE}
\ No newline at end of file