ci: add GitLab CI config

.gitlab-ci.yml

+default:
+  tags:
+    - shell
+
+workflow:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+
+test:
+  rules:
+    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+  script:
+    - export IMAGE="${DOCKER_ORG}/${DOCKER_REPO}:latest"
+    - docker build -t $IMAGE .
+    - docker run --rm $IMAGE tests/test.sh
+
+test_and_publish:
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+  script:
+    - export VERSION=$(grep 'version <-' ascii_alignment_pileup.R | cut -f2 -d'"')
+    - export IMAGE="${DOCKER_ORG}/${DOCKER_REPO}"
+    - |
+      docker build \
+      -t ${IMAGE}:${VERSION} \
+      --build-arg version=$VERSION \
+      .
+    - docker run --rm ${IMAGE}:${VERSION} tests/test.sh
+    - echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
+    - docker tag ${IMAGE}:${VERSION} ${IMAGE}:latest
+    - docker push ${IMAGE}:${VERSION}
+    - docker push ${IMAGE}:latest

Dockerfile

 ##### BASE #####
 FROM rocker/r-ver:4.2.1
 
+##### BUILD ARGUMENTS #####
+ARG version=unknown
+
 ##### METADATA #####
 MAINTAINER zavolab-biozentrum@unibas.ch
 LABEL base.image="rocker/r-ver:4.2.1"
 LABEL version="1"
 LABEL software="ascii_alignment_pileup.R"
-LABEL software.version="1.0.1"
+LABEL software.version=$version
 LABEL software.description="Generates an ASCII-style pileup of read alignments in one or more BAM files against one or more regions specified in a BED file"
 LABEL software.website="https://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup"
 LABEL software.documentation="https://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup"
@@ -64,4 +67,3 @@ WORKDIR ${WORKDIR}
 RUN chown -R ${USER}:${GROUP} ${WORKDIR} \
   && chmod 700 ${WORKDIR}
 USER ${USER}
-

ascii_alignment_pileup.R

@@ -29,10 +29,11 @@ against one or more regions specified in a BED file.\n"
 author <- "Author: Alexander Kanitz"
 affiliation <- "Affiliation: Biozentrum, University of Basel"
 email <- "Email: alexander.kanitz@alumni.ethz.ch"
-version <- "Version: 1.0.2"
+version <- "1.1.0"
+version_formatted <- paste("Version:", version, sep=" ")
 requirements <- c("optparse", "rtracklayer", "GenomicAlignments", "tools")
 requirements_txt <- paste("Requires:", paste(requirements, collapse=", "), sep=" ")
-msg <- paste(description, author, affiliation, email, version, requirements_txt, sep="\n")
+msg <- paste(description, author, affiliation, email, version_formatted, requirements_txt, sep="\n")
 notes <- "Notes:
 - For the input queries, consider the `--maximum-region-width` parameter, which
   is provided for safety. While it is possible to increase it, wide regions may

tests/expected_output.md5

+6b5a66981bd83329219002897be393a6  test.test-mir.min.1.pileup.tab

tests/test.sh

+#!/usr/bin/env bash
+
+# Tear down test environment
+cleanup () {
+    rc=$?
+    rm "test.test-mir.min.1.pileup.tab"
+    cd $user_dir
+    echo "Exit status: $rc"
+}
+trap cleanup EXIT
+
+# Set up test environment
+set -eo pipefail  # ensures that script exits at first command that exits with non-zero status
+set -u  # ensures that script exits when unset variables are used
+set -x  # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+ascii_alignment_pileup.R \
+  --verbose \
+  --reference="test_files/test.fa.gz" \
+  --annotations="test_files/test.gff" \
+  --output-directory="$PWD" \
+  "test_files/test.bed" \
+  "test_files/test.bam"
+
+# Check md5 sum of output file
+md5sum --check "expected_output.md5"