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bump quantms-rescoring version - fix bug with quantms-rescoring container permissions #681

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Merged
ypriverol merged 6 commits into from
Mar 3, 2026
+8 −53
Merged

bump quantms-rescoring version - fix bug with quantms-rescoring container permissions #681

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645f7a5
Merge pull request #83 from bigbio/dev
daichengxin Jan 12, 2026
94f5359
Merge pull request #84 from bigbio/dev
daichengxin Jan 20, 2026
6082757
Merge pull request #85 from bigbio/dev
daichengxin Mar 1, 2026
445f78f
fixed bugs
daichengxin Mar 1, 2026
1a4e2cb
Merge pull request #86 from bigbio/dev
daichengxin Mar 3, 2026
dcaeceb
add
daichengxin Mar 3, 2026
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18 changes: 2 additions & 16 deletions modules/local/utils/msrescore_features/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ process MSRESCORE_FEATURES {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.14' :
'ghcr.io/bigbio/quantms-rescoring:0.0.14' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"

input:
tuple val(meta), path(idxml), path(mzml), path(model_weight), val(search_engine)
Expand Down Expand Up @@ -91,20 +91,6 @@ process MSRESCORE_FEATURES {
}

"""
# Fix for UID-less environments (GitHub Actions, OpenShift, etc.)
# where pwd.getpwuid() fails because the running UID has no /etc/passwd entry.
# Python's getpass.getuser() calls getpwuid() only when USER env var is unset.
if [ -w /etc/passwd ]; then
echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
fi
export USER="\${USER:-quantms}"
export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
export LNAME="\${LNAME:-\${USER:-quantms}}"
export USERNAME="\${USERNAME:-\${USER:-quantms}}"
export HOME="\${HOME:-\$PWD}"
export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"

rescoring msrescore2feature \\
--idxml $idxml \\
--mzml $mzml \\
Expand Down
15 changes: 2 additions & 13 deletions modules/local/utils/msrescore_fine_tuning/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ process MSRESCORE_FINE_TUNING {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.14' :
'ghcr.io/bigbio/quantms-rescoring:0.0.14' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"

input:
tuple val(meta), path(idxml), path(mzml), val(groupkey), path(ms2_model_dir)
Expand Down Expand Up @@ -48,17 +48,6 @@ process MSRESCORE_FINE_TUNING {
}

"""
# Fix for UID-less container environments (e.g. GitHub Actions uid 1001)
Comment thread
ypriverol marked this conversation as resolved.
# Python's getpass.getuser() checks USER env var before calling getpwuid()
if [ -w /etc/passwd ]; then
echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
fi
export USER="\${USER:-quantms}"
export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
export HOME="\${HOME:-\$PWD}"
export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"

rescoring transfer_learning \\
--idxml ./ \\
--mzml ./ \\
Expand Down
14 changes: 2 additions & 12 deletions modules/local/utils/psm_clean/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ process PSM_CLEAN {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.13' :
'ghcr.io/bigbio/quantms-rescoring:0.0.13' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"

input:
tuple val(meta), path(idxml), path(mzml)
Expand All @@ -22,16 +22,6 @@ process PSM_CLEAN {
def prefix = task.ext.prefix ?: "${meta.mzml_id}_clean"

"""
# Fix for UID-less container environments (e.g. GitHub Actions uid 1001)
if [ -w /etc/passwd ]; then
echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
fi
export USER="\${USER:-quantms}"
export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
export HOME="\${HOME:-\$PWD}"
export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"

rescoring psm_feature_clean \\
--idxml $idxml \\
--mzml $mzml \\
Expand Down
14 changes: 2 additions & 12 deletions modules/local/utils/spectrum_features/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ process SPECTRUM_FEATURES {
label 'process_low'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.13' :
'ghcr.io/bigbio/quantms-rescoring:0.0.13' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"

input:
tuple val(meta), path(id_file), val(search_engine), path(ms_file)
Expand All @@ -19,16 +19,6 @@ process SPECTRUM_FEATURES {
def prefix = task.ext.prefix ?: "${meta.mzml_id}"

"""
# Fix for UID-less container environments (e.g. GitHub Actions uid 1001)
if [ -w /etc/passwd ]; then
echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
fi
export USER="\${USER:-quantms}"
export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
export HOME="\${HOME:-\$PWD}"
export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"

rescoring spectrum2feature \\
--mzml "${ms_file}" \\
--idxml "${id_file}" \\
Expand Down
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