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Skyline logging #16

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merged 3 commits into from
Sep 11, 2024
Merged

Skyline logging #16

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934463a
Add memstamp to all skyline log output.
ajmaurais Sep 9, 2024
59375e4
Write to stdout and stderr instead of log in all Skyline processes.
ajmaurais Sep 9, 2024
28174b9
Create run_details_file before it needs to be uploaded.
ajmaurais Sep 9, 2024
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13 changes: 6 additions & 7 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,12 @@ workflow {
all_mzml_ch = wide_mzml_ch
}

// save details about this run
input_files = all_mzml_ch.map{ it -> ['Spectra File', it.baseName] }
version_files = Channel.empty()
save_run_details(input_files.collect(), version_files.collect())
run_details_file = save_run_details.out.run_details

// if requested, upload mzMLs to panorama
if(params.panorama.upload) {

Expand All @@ -124,13 +130,6 @@ workflow {
)
}


// save details about this run
input_files = all_mzml_ch.map{ it -> ['Spectra File', it.baseName] }
version_files = Channel.empty()
save_run_details(input_files.collect(), version_files.collect())
run_details_file = save_run_details.out.run_details

return
}

Expand Down
39 changes: 21 additions & 18 deletions modules/skyline.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -17,22 +17,23 @@ process SKYLINE_ADD_LIB {

output:
path("results.sky.zip"), emit: skyline_zipfile
path("skyline_add_library.log"), emit: log
path("skyline_add_library.stdout"), emit: stdout
path("skyline_add_library.stderr"), emit: stderr
path("pwiz_versions.txt"), emit: version

shell:
'''
unzip !{skyline_template_zipfile}

wine SkylineCmd \
--in="!{skyline_template_zipfile.baseName}" \
--log-file=skyline_add_library.log \
--in="!{skyline_template_zipfile.baseName}" --memstamp \
--import-fasta="!{fasta}" \
--add-library-path="!{elib}" \
--out="results.sky" \
--save \
--share-zip="results.sky.zip" \
--share-type="complete"
--share-type="complete" \
> >(tee 'skyline_add_library.stdout') 2> >(tee 'skyline_add_library.stderr' >&2)

# parse Skyline version info
wine SkylineCmd --version > version.txt
Expand All @@ -59,7 +60,7 @@ process SKYLINE_ADD_LIB {
stub:
'''
touch "results.sky.zip"
touch "skyline_add_library.log"
touch "skyline_add_library.stderr" "skyline_add_library.stdout"

# parse Skyline version info
wine SkylineCmd --version > version.txt
Expand Down Expand Up @@ -99,7 +100,8 @@ process SKYLINE_IMPORT_MZML {

output:
path("*.skyd"), emit: skyd_file
path("${mzml_file.baseName}.log"), emit: log_file
path("${mzml_file.baseName}.stdout"), emit: stdout
path("${mzml_file.baseName}.stderr"), emit: stderr

script:
"""
Expand All @@ -108,15 +110,15 @@ process SKYLINE_IMPORT_MZML {
cp ${mzml_file} /tmp/${mzml_file}

wine SkylineCmd \
--in="${skyline_zipfile.baseName}" \
--in="${skyline_zipfile.baseName}" --memstamp \
--import-no-join \
--log-file="${mzml_file.baseName}.log" \
--import-file="/tmp/${mzml_file}" \
> >(tee '${mzml_file.baseName}.stdout') 2> >(tee '${mzml_file.baseName}.stderr' >&2)
"""

stub:
"""
touch "${mzml_file.baseName}.log" "${mzml_file.baseName}.skyd"
touch "${mzml_file.baseName}.stdout" "${mzml_file.baseName}.stderr" "${mzml_file.baseName}.skyd"
"""
}

Expand All @@ -135,14 +137,15 @@ process SKYLINE_MERGE_RESULTS {

output:
path("${params.skyline.document_name}.sky.zip"), emit: final_skyline_zipfile
path("skyline-merge.log"), emit: log
path("skyline-merge.stdout"), emit: stdout
path("skyline-merge.stderr"), emit: stderr
env(sky_zip_hash), emit: file_hash

script:
import_files_params = "--import-file=${(mzml_files as List).collect{ "/tmp/" + file(it).name }.join(' --import-file=')}"
protein_parsimony_args = "--import-fasta=${fasta} --associate-proteins-shared-peptides=DuplicatedBetweenProteins --associate-proteins-min-peptides=1 --associate-proteins-remove-subsets --associate-proteins-minimal-protein-list"
if(params.skyline.group_by_gene) {
protein_parsimony_args += ' --associate-proteins-gene-level-parsimony'
protein_parsimony_args += ' --associate-proteins-gene-level-parsimony'
}

"""
Expand All @@ -151,22 +154,22 @@ process SKYLINE_MERGE_RESULTS {
cp -v ${skyd_files} /tmp/

wine SkylineCmd \
--in="${skyline_zipfile.baseName}" \
--log-file="skyline-merge.log" \
--in="${skyline_zipfile.baseName}" --memstamp \
${import_files_params} \
${params.skyline.protein_parsimony ? protein_parsimony_args : ''} \
--out="${params.skyline.document_name}.sky" \
--save \
--share-zip="${params.skyline.document_name}.sky.zip" \
--share-type="complete"
--share-type="complete" \
> >(tee 'skyline-merge.stdout') 2> >(tee 'skyline-merge.stderr' >&2)

sky_zip_hash=\$( md5sum ${params.skyline.document_name}.sky.zip |awk '{print \$1}' )
"""

stub:
"""
touch "${params.skyline.document_name}.sky.zip"
touch "skyline-merge.log"
touch "skyline-merge.stderr" "skyline-merge.stdout"
sky_zip_hash=\$( md5sum ${params.skyline.document_name}.sky.zip |awk '{print \$1}' )
"""
}
Expand Down Expand Up @@ -214,7 +217,7 @@ process SKYLINE_MINIMIZE_DOCUMENT {
unzip ${skyline_zipfile}

wine SkylineCmd \
--in="${skyline_zipfile.baseName}" \
--in="${skyline_zipfile.baseName}" --memstamp \
--chromatograms-discard-unused \
--chromatograms-limit-noise=1 \
--out="${sky_basename(skyline_zipfile)}_minimized.sky" \
Expand Down Expand Up @@ -255,7 +258,7 @@ process SKYLINE_ANNOTATE_DOCUMENT {
unzip ${skyline_zipfile}

# Create Skyline batch file with annotation definitions
echo '--in="${skyline_zipfile.baseName}"' > add_annotations.bat
echo '--in="${skyline_zipfile.baseName}" --memstamp' > add_annotations.bat
cat ${annotation_definitions} >> add_annotations.bat
echo '--import-annotations="${annotation_csv}"' >> add_annotations.bat
echo '--save --out="${sky_basename(skyline_zipfile)}_annotated.sky"' >> add_annotations.bat
Expand Down Expand Up @@ -295,7 +298,7 @@ process SKYLINE_RUN_REPORTS {
unzip !{skyline_zipfile}

# generate skyline batch file to export reports
echo "--in=\\"!{skyline_zipfile.baseName}\\"" > export_reports.bat
echo "--in=\\"!{skyline_zipfile.baseName}\\" --memstamp" > export_reports.bat

for skyrfile in ./*.skyr; do
# Add report to document
Expand Down
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