diff --git a/.circ b/.circ
deleted file mode 100755
index c11337f..0000000
--- a/.circ
+++ /dev/null
@@ -1,154 +0,0 @@
-# Print usage information
-_ci_usage() {
-	cat <<-MSG
-		Run CI tests
-
-		Commands:
-		run          run the pipeline in '\$CI_DIR'
-		check        compute checksums and validate results
-		clean        remove the temporary directory used for vaildation
-
-		Notes:
-		If '\$CI_DIR' is in the Nextflow asset folder the pipeline is run using the GitHub repository
-		to allow to change revision from the comand line, e.g.:
-
-		CI_DIR=~/.nextflow/assets/guigolab/grape-nf ci test -r v0.4.1
-	MSG
-}
-
-# Get canonical path of either a directory or a file
-_ci_canonicalize_path() {
-    if [ -d "$1" ]; then
-        _ci_canonicalize_dir_path "$1"
-    else
-        _ci_canonicalize_file_path "$1"
-    fi
-}
-
-# Get canonical path of a directory
-_ci_canonicalize_dir_path() {
-    (cd "$1" 2>/dev/null && pwd -P)
-}
-
-# Get canonical path of a file
-_ci_canonicalize_file_path() {
-    local dir file
-    dir=$(dirname -- "$1")
-    file=$(basename -- "$1")
-    (cd "$dir" 2>/dev/null && printf '%s/%s\n' "$(pwd -P)" "$file")
-}
-
-# Check that Nextflow is installed and download it to the current
-# folder otherwise
-_ci_setup_nxf() {
-	if ! nextflow &>/dev/null; then
-		export PATH=$PWD:$PATH
-		if [ ! -x nextflow ]; then
-			curl -fsSL get.nextflow.io | bash && chmod +x nextflow
-		fi
-	fi
-}
-
-# Get the content of a BAM file for checksum
-_ci_normalize_bam() {
-	docker run --rm -v $CI_DIR:$CI_DIR -v $1:$1 -w $PWD grapenf/samtools:1.3.1 bash -c "samtools view -h $2 | grep -v '@CO\|@PG' | LC_ALL=C sort > $(basename $2) 2>/dev/null"
-}
-
-# Get file to the CI output directory either by creating a symlink
-# or normalizing a BAM file
-_ci_get_file() {
-	local baseDir=$1
-	local filename=$2
-	case "$filename" in
-		*.bam)
-			_ci_normalize_bam "$baseDir" "$filename" ;;
-		*.bed|*.bw|*.results|*.json|*.g[tf]f)
-			ln -fs "$filename";;
-		*)
-			echo "'${filename##*.}' extension not supported";;
-	esac
-}
-
-# Get current script being sourced
-_ci_get_script_dir() {
-	local CI_SCRIPT="$1"
-	if [ ! -z "$BASH_SOURCE" ]
-	then
-		CI_SCRIPT=${BASH_SOURCE[0]}
-	fi
-	echo $(_ci_canonicalize_path $(dirname ${CI_SCRIPT}))
-}
-
-# Run the pipeline for CI
-_ci_run() {
-	local WF=${CI_DIR}
-	if [[ "$CI_DIR" =~ "$HOME/.nextflow/asset" ]]; then
-		local ORG=$(basename $(dirname $CI_DIR))
-		local REPO=$(basename $CI_DIR)
-		WF="${ORG}/${REPO}"
-	fi
-	_ci_setup_nxf && nextflow run ${WF} -profile $CI_PROFILE "${CI_RUNOPTS[@]}" "$@"
-}
-
-# Check pipeline results for CI
-_ci_check() {
-	(mkdir -p $CI_OUTDIR && cd $CI_OUTDIR
-	echo $CI_PROFILE > .ci_profile
-	cut -f 3 ../pipeline.db | while read f
-	do
-		_ci_get_file $(_ci_canonicalize_path ..) $f
-	done
-	md5sum -c ${CI_DIR}/data/$CI_PROFILE.md5)
-}
-
-# Cleanup CI result directory
-_ci_clean() {
-	rm --interactive=never -r $CI_OUTDIR
-}
-
-# Perform a ful CI test
-_ci_test() {
-	# Define colors
-	local RED="\033[1;31m"
-	local GREEN="\033[1;32m"
-	local YELLOW="\033[1;33m"
-	local BLUE="\033[1;34m"
-	local NORMAL="\033[0m"
-
-	echo -e "==$YELLOW Running with profile -> $BLUE${CI_PROFILE}$NORMAL" \
-	&& _ci_run "$@" \
-	&& echo -e "==$YELLOW Compute MD5 checksums$NORMAL" \
-	&& _ci_check \
-	&& echo -e "==$GREEN SUCCESS$NORMAL" \
-	&& echo -e "==$YELLOW Cleaning up$NORMAL" \
-	&& _ci_clean \
-	&& echo -e "==$YELLOW DONE$NORMAL" && exit 0 \
-	|| echo -e "==$RED FAILED$NORMAL" && exit 1
-}
-
-# Main command
-ci() {
-	case $1 in
-		run)
-			shift
-			(_ci_run "$@");;
-		check)
-			shift
-			(_ci_check);;
-		clean)
-			shift
-			(_ci_clean);;
-		test)
-			shift
-			(_ci_test "$@");;
-		*)
-			_ci_usage;;
-	esac
-}
-
-# Define CI environment variables
-CI_DIR=${CI_DIR-"$(_ci_get_script_dir $0)"}
-CI_LOG=${CI_LOG-"pipeline-ci.log"}
-CI_PROFILE=${CI_PROFILE-"starrsem"}
-CI_OUTDIR=${CI_OUTDIR-"checksum"}
-CI_RUNOPTS=("-process.errorStrategy=terminate" "-with-docker" "-ansi-log" "false" "--rsemCalcCI")
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 409736a..35de279 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -5,7 +5,6 @@ on:
     branches:
       - master
       - dev
-      - test-refactor
   pull_request:
     branches:
       - master