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ypriverolypriverol
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Merge branch 'dev' into upt_schema
2 parents cba2229 + 87d51ac commit 9276986

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4 files changed

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-53
lines changed

4 files changed

+8
-53
lines changed

‎modules/local/utils/msrescore_features/main.nf‎

Lines changed: 2 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@ process MSRESCORE_FEATURES {
33
label 'process_high'
44

55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
6-
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.14' :
7-
'ghcr.io/bigbio/quantms-rescoring:0.0.14' }"
6+
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
7+
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"
88

99
input:
1010
tuple val(meta), path(idxml), path(mzml), path(model_weight), val(search_engine)
@@ -91,20 +91,6 @@ process MSRESCORE_FEATURES {
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}
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9393
"""
94-
# Fix for UID-less environments (GitHub Actions, OpenShift, etc.)
95-
# where pwd.getpwuid() fails because the running UID has no /etc/passwd entry.
96-
# Python's getpass.getuser() calls getpwuid() only when USER env var is unset.
97-
if [ -w /etc/passwd ]; then
98-
echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
99-
fi
100-
export USER="\${USER:-quantms}"
101-
export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
102-
export LNAME="\${LNAME:-\${USER:-quantms}}"
103-
export USERNAME="\${USERNAME:-\${USER:-quantms}}"
104-
export HOME="\${HOME:-\$PWD}"
105-
export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
106-
mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"
107-
10894
rescoring msrescore2feature \\
10995
--idxml $idxml \\
11096
--mzml $mzml \\

‎modules/local/utils/msrescore_fine_tuning/main.nf‎

Lines changed: 2 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@ process MSRESCORE_FINE_TUNING {
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label 'process_high'
44

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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
6-
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.14' :
7-
'ghcr.io/bigbio/quantms-rescoring:0.0.14' }"
6+
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
7+
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"
88

99
input:
1010
tuple val(meta), path(idxml), path(mzml), val(groupkey), path(ms2_model_dir)
@@ -48,17 +48,6 @@ process MSRESCORE_FINE_TUNING {
4848
}
4949

5050
"""
51-
# Fix for UID-less container environments (e.g. GitHub Actions uid 1001)
52-
# Python's getpass.getuser() checks USER env var before calling getpwuid()
53-
if [ -w /etc/passwd ]; then
54-
echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
55-
fi
56-
export USER="\${USER:-quantms}"
57-
export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
58-
export HOME="\${HOME:-\$PWD}"
59-
export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
60-
mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"
61-
6251
rescoring transfer_learning \\
6352
--idxml ./ \\
6453
--mzml ./ \\

‎modules/local/utils/psm_clean/main.nf‎

Lines changed: 2 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@ process PSM_CLEAN {
33
label 'process_high'
44

55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
6-
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.13' :
7-
'ghcr.io/bigbio/quantms-rescoring:0.0.13' }"
6+
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
7+
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"
88

99
input:
1010
tuple val(meta), path(idxml), path(mzml)
@@ -22,16 +22,6 @@ process PSM_CLEAN {
2222
def prefix = task.ext.prefix ?: "${meta.mzml_id}_clean"
2323

2424
"""
25-
# Fix for UID-less container environments (e.g. GitHub Actions uid 1001)
26-
if [ -w /etc/passwd ]; then
27-
echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
28-
fi
29-
export USER="\${USER:-quantms}"
30-
export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
31-
export HOME="\${HOME:-\$PWD}"
32-
export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
33-
mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"
34-
3525
rescoring psm_feature_clean \\
3626
--idxml $idxml \\
3727
--mzml $mzml \\

‎modules/local/utils/spectrum_features/main.nf‎

Lines changed: 2 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@ process SPECTRUM_FEATURES {
33
label 'process_low'
44

55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
6-
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.13' :
7-
'ghcr.io/bigbio/quantms-rescoring:0.0.13' }"
6+
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.15' :
7+
'ghcr.io/bigbio/quantms-rescoring:0.0.15' }"
88

99
input:
1010
tuple val(meta), path(id_file), val(search_engine), path(ms_file)
@@ -19,16 +19,6 @@ process SPECTRUM_FEATURES {
1919
def prefix = task.ext.prefix ?: "${meta.mzml_id}"
2020

2121
"""
22-
# Fix for UID-less container environments (e.g. GitHub Actions uid 1001)
23-
if [ -w /etc/passwd ]; then
24-
echo "\${USER:-quantms}:x:\$(id -u):\$(id -g):\${USER:-quantms} user:/tmp:/bin/bash" >> /etc/passwd
25-
fi
26-
export USER="\${USER:-quantms}"
27-
export LOGNAME="\${LOGNAME:-\${USER:-quantms}}"
28-
export HOME="\${HOME:-\$PWD}"
29-
export TORCHINDUCTOR_CACHE_DIR="\${TORCHINDUCTOR_CACHE_DIR:-\$PWD/.torchinductor_cache}"
30-
mkdir -p "\$TORCHINDUCTOR_CACHE_DIR"
31-
3222
rescoring spectrum2feature \\
3323
--mzml "${ms_file}" \\
3424
--idxml "${id_file}" \\

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