Merge pull request #16 from ajmaurais/skyline_logging

Skyline logging
mriffle · Sep 11, 2024 · 9faf68b · 9faf68b
2 parents 29f4f53 + 28174b9
commit 9faf68b
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Showing 2 changed files with 27 additions and 25 deletions.
diff --git a/main.nf b/main.nf
@@ -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) {
 
@@ -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
     }
 

diff --git a/modules/skyline.nf b/modules/skyline.nf
@@ -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
@@ -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
@@ -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:
     """
@@ -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"
     """
 }
 
@@ -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'
     }
 
     """
@@ -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}' )
     """
 }
@@ -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" \
@@ -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
@@ -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