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APPS-1511, APPS-1566 Simplify nextflow pipeline applet subjob inputs #917

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APPS-1511, APPS-1566 Simplify nextflow pipeline applet subjob inputs #917

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6eb7c9d
wip: use nxf_dx_upload and simplify subjob inputs
YuxinShi0423 Jan 17, 2023
62837a8
revert export nxf_dx_upload
YuxinShi0423 Jan 19, 2023
7c40649
Merge branch 'master' into APPS-1511-simplify-subjob-inputs
YuxinShi0423 Jan 24, 2023
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16 changes: 11 additions & 5 deletions src/python/dxpy/templating/templates/nextflow/src/nextflow.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -103,9 +103,7 @@ on_exit() {
# wrap cache folder and upload cache.tar
if [[ -n "$(ls -A .nextflow)" ]]; then
tar -cf cache.tar .nextflow

CACHE_ID=$(dx upload "cache.tar" --path "$DX_CACHEDIR/$NXF_UUID/cache.tar" --no-progress --brief --wait -p -r) &&
echo "Upload cache of current session as file: $CACHE_ID" &&
nxf_dx_upload "cache.tar" "$DX_CACHEDIR/$NXF_UUID" &&
rm -f cache.tar ||
echo "Failed to upload cache of current session $NXF_UUID"
else
Expand Down Expand Up @@ -422,10 +420,17 @@ main() {
exit $ret
}

nxf_dx_upload() {
local name=$1
local target=${2%/}
escape_name="${name//:/\\:}"
dx upload "$name" --path "$target/$escape_name" --no-progress --brief --wait -p -r | (echo -n "Upload $name to $target/$escape_name: " && cat) || true
}

nf_task_exit() {
ret=$?
if [ -f .command.log ]; then
dx upload .command.log --path "${cmd_log_file}" --brief --wait --no-progress || true
nxf_dx_upload .command.log "$TASK_WORKDIR"
else
>&2 echo "Missing Nextflow .command.log file"
fi
Expand Down Expand Up @@ -453,8 +458,9 @@ nf_task_entry() {
fi
# capture the exit code
trap nf_task_exit EXIT

# remove the line in .command.run to disable printing env vars if debugging is on
dx cat "${cmd_launcher_file}" | sed 's/\[\[ $NXF_DEBUG > 0 ]] && nxf_env//' > .command.run
dx cat "${TASK_WORKDIR}/.command.run" | sed 's/\[\[ $NXF_DEBUG > 0 ]] && nxf_env//' > .command.run
set +e
# enable debugging mode
[[ $NXF_DEBUG ]] && set -x
Expand Down