add nextflow d30e48d

nextflow/docker/entry.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+#
+# Copyright 2013-2026, Seqera Labs
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+#
+# This script acts as a pass-through container entry point. Its main role
+# is to create a user able to execute docker commands from the container
+# connecting to the host docker socket at runtime.
+#
+# The invoker needs to pass the user ID using the variable NXF_USRMAP.
+# When this variable is defined, it creates a new user in the container
+# with such ID and adds it to the `docker` group, then assigns the docker
+# socket file ownership to that user.
+#
+# Finally it switches the `nextflow` user using the `su` command and
+# executes the original target command line.
+#
+# authors:
+#  Paolo Di Tommaso
+#  Emilio Palumbo
+#
+
+# enable debugging
+[[ "$NXF_DEBUG_ENTRY" ]] && set -x
+
+# wrap cli args with single quote to avoid wildcard expansion
+cli=''; for x in "$@"; do cli+="'$x' "; done
+
+# the NXF_USRMAP hold the user ID in the host environment
+if [[ "$NXF_USRMAP" ]]; then
+# create a `nextflow` user with the provided ID
+groupadd docker
+useradd -u "$NXF_USRMAP" -G docker -s /bin/bash nextflow
+
+# then change the docker socket ownership to `nextflow` user
+# and change the $NXF_HOME ownership to `nextflow` user
+chown nextflow /var/run/docker.sock
+chown -R nextflow /.nextflow
+
+# finally run the target command with `nextflow` user
+su nextflow << EOF
+[[ "$NXF_DEBUG_ENTRY" ]] && set -x
+exec bash -c "$cli"
+EOF
+
+# otherwise just execute the command
+else
+exec bash -c "$cli"
+fi