migrate ci to GitHub actions

.github/workflows/ci.yaml

@@ -0,0 +1,26 @@
+on:
+  push:
+    branches: [main, master, dev]
+  pull_request:
+    branches: [main, master]
+
+name: CI-checks
+
+jobs:
+  CI-checks:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Java
+        uses: actions/setup-java@v1
+        with:
+            java-version: 11.0.4
+
+      - name: Install Nextflow
+        run: curl -fsSL get.nextflow.io | bash && mv nextflow /usr/local/bin
+
+      - name: Run CI checks
+        run: ./ci/ci.sh run && ./ci/ci.sh validate 
+

README.md

@@ -1,7 +1,7 @@
 # sqtlseeker2-nf
 
 [![nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.0-blue.svg)](http://nextflow.io)
-[![Build Status](https://travis-ci.com/guigolab/sqtlseeker2-nf.svg?branch=master)](https://travis-ci.com/guigolab/sqtlseeker2-nf)
+[![CI-checks](https://github.com/guigolab/sqtlseeker2-nf/actions/workflows/ci.yaml/badge.svg)](https://github.com/guigolab/sqtlseeker2-nf/actions/workflows/ci.yaml)
 
 A pipeline for splicing quantitative trait loci (sQTL) mapping.
 

ci/ci.sh

@@ -9,6 +9,7 @@ case "$1" in
     shift
     echo "Running test pipeline..." >&2
     nextflow run . -resume -with-docker --dir ${OUT_DIR} $@
+    md5sum ${OUT_DIR}/*/*/*
     ;;
   validate)
     echo "Validating test results..." >&2

ci/md5s.txt

@@ -1,4 +1,4 @@
-7f8010385e11ea31a6006c500c49258c *ci/groups/tissue1/all-tests.nominal.tsv
-cb6e79a6ec91ae4f0230c6a9c5ea4fa0 *ci/groups/tissue1/sqtls-0.05fdr.nominal.tsv
-2e15a4078124dbcfd98560f3a16bb5af *ci/groups/tissue2/all-tests.nominal.tsv
-c5f627ca7e1f29ccf6d8852e071be638 *ci/groups/tissue2/sqtls-0.05fdr.nominal.tsv
+aa57acbed1d74ea757cf7f1132eae083  ci/groups/tissue1/all-tests.nominal.tsv
+e7c296d0d083a991ae151eac21cc6b03  ci/groups/tissue1/sqtls-0.05fdr.nominal.tsv
+fdc4615294b9ee2bd091b6f36ca1540d  ci/groups/tissue2/all-tests.nominal.tsv
+ec9152800ee2f5ff7bc037dba05c2049  ci/groups/tissue2/sqtls-0.05fdr.nominal.tsv