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Revert the stream swap after the redirect to .command.out and .command.err #7300

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Revert the stream swap after the redirect to .command.out and .command.err #7300

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a2d1015
Revert the stream swap after the redirect to .command.out and .comman…
tcezard Jul 3, 2026
572280c
Add back 4 spaces
tcezard Jul 16, 2026
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2 changes: 1 addition & 1 deletion modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ nxf_main() {
{{stage_cmd}}

set +e
(set -o pipefail; (nxf_launch | tee {{stdout_file}}) 3>&1 1>&2 2>&3 | tee {{stderr_file}}) &
(set -o pipefail; (nxf_launch | tee {{stdout_file}}) 3>&1 1>&2 2>&3 | tee {{stderr_file}}) 3>&1 1>&2 2>&3 &
pid=$!
wait $pid || nxf_main_ret=$?
{{unstage_cmd}}
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4 changes: 2 additions & 2 deletions modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
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Expand Up @@ -151,7 +151,7 @@ nxf_trace_linux() {
local io_stat0=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
local start_millis=$(nxf_date)
trap 'kill $mem_proc' ERR

@jordeu jordeu Jul 14, 2026

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This change is unnecessary, and it will break a test

@tcezard tcezard Jul 16, 2026

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Added the spaces back

/bin/bash -ue {{folder}}/.command.sh &
local task=$!

Expand Down Expand Up @@ -331,7 +331,7 @@ nxf_main() {
nxf_stage

set +e
(set -o pipefail; (nxf_launch | tee .command.out) 3>&1 1>&2 2>&3 | tee .command.err) &
(set -o pipefail; (nxf_launch | tee .command.out) 3>&1 1>&2 2>&3 | tee .command.err) 3>&1 1>&2 2>&3 &
pid=$!
wait $pid || nxf_main_ret=$?
nxf_unstage
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2 changes: 1 addition & 1 deletion modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,7 @@ nxf_main() {
nxf_stage

set +e
(set -o pipefail; (nxf_launch | tee .command.out) 3>&1 1>&2 2>&3 | tee .command.err) &
(set -o pipefail; (nxf_launch | tee .command.out) 3>&1 1>&2 2>&3 | tee .command.err) 3>&1 1>&2 2>&3 &
pid=$!
wait $pid || nxf_main_ret=$?
nxf_unstage
Expand Down