nextflow.executor.command-env.txt Maven / Gradle / Ivy

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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner

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##
##  Copyright 2013-2023, 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.

# capture process environment
set +u
set +e
cd "$NXF_TASK_WORKDIR"

## SYNTAX:
##   catch STDOUT_VARIABLE STDERR_VARIABLE COMMAND [ARG1[ ARG2[ ...[ ARGN]]]]
##
## See solution 7 at https://stackoverflow.com/a/59592881/395921
##
nxf_eval_cmd() {
    {
        IFS=$'\n' read -r -d '' "${1}";
        IFS=$'\n' read -r -d '' "${2}";
        (IFS=$'\n' read -r -d '' _ERRNO_; return ${_ERRNO_});
    } < <((printf '\0%s\0%d\0' "$(((({ shift 2; "${@}"; echo "${?}" 1>&3-; } | tr -d '\0' 1>&4-) 4>&2- 2>&1- | tr -d '\0' 1>&4-) 3>&1- | exit "$(cat)") 4>&1-)" "${?}" 1>&2) 2>&1)
}

## reset/create command env file
echo '' > {{env_file}}