diff --git a/conf/output_directories.config b/conf/output_directories.config
new file mode 100644
index 0000000..57d2270
--- /dev/null
+++ b/conf/output_directories.config
@@ -0,0 +1,23 @@
+
+params {
+    output_directories = [
+        panorama:         "${params.result_dir}/panorama",
+        aws:              "${params.result_dir}/aws",
+        msconvert:        "${params.result_dir}/msconvert",
+        diann:            "${params.result_dir}/diann",
+        qc_report:        "${params.result_dir}/qc_report",
+        qc_report_tables: "${params.result_dir}/qc_report/tables",
+        gene_reports:     "${params.result_dir}/gene_reports",
+        encyclopedia: [
+            convert_blib: "${params.result_dir}/encyclopedia/convert-blib",
+            search_file:  "${params.result_dir}/encyclopedia/search-file",
+            create_elib:  "${params.result_dir}/encyclopedia/create-elib"
+        ],
+        skyline: [
+            add_lib:        "${params.result_dir}/skyline/add-lib",
+            import_spectra: "${params.result_dir}/skyline/import-spectra",
+            minimize:       "${params.result_dir}/skyline/minimize",
+            reports:        "${params.result_dir}/skyline/reports"
+        ]
+    ]
+}
diff --git a/main.nf b/main.nf
index db0064d..ed641cf 100644
--- a/main.nf
+++ b/main.nf
@@ -16,6 +16,7 @@ include { panorama_upload_results } from "./workflows/panorama_upload"
 include { panorama_upload_mzmls } from "./workflows/panorama_upload"
 include { save_run_details } from "./workflows/save_run_details"
 include { get_pdc_files } from "./workflows/get_pdc_files"
+include { combine_file_hashes } from "./workflows/combine_file_hashes"
 
 // modules
 include { ENCYCLOPEDIA_BLIB_TO_DLIB } from "./modules/encyclopedia"
@@ -197,12 +198,14 @@ workflow {
             )
 
             quant_library = encyclopeda_export_elib.out.elib
+            spec_lib_hashes = encyclopeda_export_elib.out.output_file_stats
 
             all_elib_ch = encyclopeda_export_elib.out.elib.concat(
                 encyclopeda_export_elib.out.individual_elibs
             )
         } else {
             quant_library = spectral_library_to_use
+            spec_lib_hashes = Channel.empty()
             all_mzml_ch = wide_mzml_ch
             all_elib_ch = Channel.empty()
         }
@@ -219,6 +222,7 @@ workflow {
         )
 
         encyclopedia_version = encyclopedia_quant.out.encyclopedia_version
+        search_file_stats = encyclopedia_quant.out.output_file_stats.concat(spec_lib_hashes)
 
         final_elib = encyclopedia_quant.out.elib
         all_elib_ch = all_elib_ch.concat(
@@ -284,6 +288,7 @@ workflow {
         )
 
         diann_version = diann_search.out.diann_version
+        search_file_stats = diann_search.out.output_file_stats
 
         // create compatible spectral library for Skyline, if needed
         if(!params.skyline.skip) {
@@ -329,11 +334,17 @@ workflow {
         }
 
         final_skyline_file = skyline_import.out.skyline_results
+        final_skyline_hash = skyline_import.out.skyline_results_hash
 
         // generate QC report
         if(!params.qc_report.skip) {
             generate_dia_qc_report(final_skyline_file, replicate_metadata)
             dia_qc_version = generate_dia_qc_report.out.dia_qc_version
+            qc_report_files = generate_dia_qc_report.out.qc_reports.concat(
+                generate_dia_qc_report.out.qc_report_qmd,
+                generate_dia_qc_report.out.qc_report_db,
+                generate_dia_qc_report.out.qc_tables
+            )
 
             // Export PDC gene tables
             if(params.pdc.gene_level_data != null) {
@@ -346,6 +357,8 @@ workflow {
             }
         } else {
             dia_qc_version = Channel.empty()
+            qc_report_files = Channel.empty()
+            gene_reports = Channel.empty()
         }
 
         // run reports if requested
@@ -367,6 +380,7 @@ workflow {
         final_skyline_file = Channel.empty()
         qc_report_files = Channel.empty()
         proteowizard_version = Channel.empty()
+        final_skyline_hash = Channel.empty()
         dia_qc_version = Channel.empty()
         gene_reports = Channel.empty()
     }
@@ -382,6 +396,15 @@ workflow {
     save_run_details(input_files.collect(), version_files.collect())
     run_details_file = save_run_details.out.run_details
 
+    combine_file_hashes(fasta, spectral_library,
+                        search_file_stats,
+                        final_skyline_file,
+                        final_skyline_hash,
+                        skyline_reports_ch,
+                        qc_report_files,
+                        gene_reports,
+                        run_details_file)
+
     // upload results to Panorama
     if(params.panorama.upload) {
 
diff --git a/modules/aws.nf b/modules/aws.nf
index 53509fe..0928586 100644
--- a/modules/aws.nf
+++ b/modules/aws.nf
@@ -36,7 +36,7 @@ process BUILD_AWS_SECRETS {
     label 'process_low_constant'
     secret 'PANORAMA_API_KEY'
     executor 'local'    // always run this locally
-    publishDir "${params.result_dir}/aws", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.aws, failOnError: true, mode: 'copy'
     cache false         // never cache 
 
     input:
@@ -123,4 +123,4 @@ process BUILD_AWS_SECRETS {
 //         touch aws-destroy-secrets.stderr
 //         touch aws-destroy-secrets.stdout
 //         """
-// }
\ No newline at end of file
+// }
diff --git a/modules/diann.nf b/modules/diann.nf
index 95a7e44..a7c8cfe 100644
--- a/modules/diann.nf
+++ b/modules/diann.nf
@@ -1,5 +1,5 @@
 process DIANN_SEARCH {
-    publishDir "${params.result_dir}/diann", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.diann, failOnError: true, mode: 'copy'
     label 'process_high_constant'
     container params.images.diann
     
@@ -16,6 +16,7 @@ process DIANN_SEARCH {
         path("report.tsv"), emit: precursor_tsv
         path("*.quant"), emit: quant_files
         path("diann_version.txt"), emit: version
+        path("output_file_stats.txt"), emit: output_file_stats
 
     script:
 
@@ -37,6 +38,10 @@ process DIANN_SEARCH {
         mv -v lib.tsv.speclib report.tsv.speclib
 
         head -n 1 diann.stdout | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "diann_version=%s\\n" > diann_version.txt
+
+        md5sum '${ms_files.join('\' \'')}' report.tsv.speclib report.tsv *.quant | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt
+        stat -L --printf='%n\t%s\n' '${ms_files.join('\' \'')}' report.tsv.speclib report.tsv *.quant | sort > sizes.txt
+        join -t'\t' hashes.txt sizes.txt > output_file_stats.txt
         """
 
     stub:
@@ -44,11 +49,15 @@ process DIANN_SEARCH {
         touch report.tsv.speclib report.tsv stub.quant
         touch stub.stderr stub.stdout
         diann | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "diann_version=%s\\n" > diann_version.txt
+
+        md5sum '${ms_files.join('\' \'')}' report.tsv.speclib report.tsv *.quant | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt
+        stat -L --printf='%n\t%s\n' '${ms_files.join('\' \'')}' report.tsv.speclib report.tsv *.quant | sort > sizes.txt
+        join -t'\t' hashes.txt sizes.txt > output_file_stats.txt
         """
 }
 
 process DIANN_SEARCH_LIB_FREE {
-    publishDir "${params.result_dir}/diann", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.diann, failOnError: true, mode: 'copy'
     label 'process_high_constant'
     container params.images.diann
     
@@ -65,6 +74,7 @@ process DIANN_SEARCH_LIB_FREE {
         path("*.quant"), emit: quant_files
         path("lib.predicted.speclib"), emit: predicted_speclib
         path("diann_version.txt"), emit: version
+        path("output_file_stats.txt"), emit: output_file_stats
 
     script:
 
@@ -87,6 +97,10 @@ process DIANN_SEARCH_LIB_FREE {
         mv -v lib.tsv.speclib report.tsv.speclib
 
         head -n 1 diann.stdout | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "diann_version=%s\\n" > diann_version.txt
+
+        md5sum '${ms_files.join('\' \'')}' report.tsv.speclib report.tsv *.quant | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt
+        stat -L --printf='%n\t%s\n' '${ms_files.join('\' \'')}' report.tsv.speclib report.tsv *.quant | sort > sizes.txt
+        join -t'\t' hashes.txt sizes.txt > output_file_stats.txt
         """
 
     stub:
@@ -94,12 +108,16 @@ process DIANN_SEARCH_LIB_FREE {
         touch lib.predicted.speclib report.tsv.speclib report.tsv stub.quant
         touch stub.stderr stub.stdout
         diann | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "diann_version=%s\\n" > diann_version.txt
+
+        md5sum '${ms_files.join('\' \'')}' report.tsv.speclib report.tsv *.quant | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt
+        stat -L --printf='%n\t%s\n' '${ms_files.join('\' \'')}' report.tsv.speclib report.tsv *.quant | sort > sizes.txt
+        join -t'\t' hashes.txt sizes.txt > output_file_stats.txt
         """
 }
 
 
 process BLIB_BUILD_LIBRARY {
-    publishDir "${params.result_dir}/diann", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.diann, failOnError: true, mode: 'copy'
     label 'process_medium'
     container params.images.bibliospec
 
diff --git a/modules/encyclopedia.nf b/modules/encyclopedia.nf
index b9edaaa..07f9048 100644
--- a/modules/encyclopedia.nf
+++ b/modules/encyclopedia.nf
@@ -4,13 +4,12 @@ def exec_java_command(mem) {
 }
 
 process ENCYCLOPEDIA_SEARCH_FILE {
-    publishDir "${params.result_dir}/encyclopedia/search-file", pattern: "*.stderr", failOnError: true, mode: 'copy'
-    publishDir "${params.result_dir}/encyclopedia/search-file", pattern: "*.stdout", failOnError: true, mode: 'copy'
-    publishDir "${params.result_dir}/encyclopedia/search-file", pattern: "*.elib", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
-    publishDir "${params.result_dir}/encyclopedia/search-file", pattern: "*.dia", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
-    publishDir "${params.result_dir}/encyclopedia/search-file", pattern: "*.features.txt", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
-    publishDir "${params.result_dir}/encyclopedia/search-file", pattern: "*.encyclopedia.txt", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
-    publishDir "${params.result_dir}/encyclopedia/search-file", pattern: "*.encyclopedia.decoy.txt", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
+    publishDir params.output_directories.encyclopedia.search_file, pattern: "*.stderr", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.encyclopedia.search_file, pattern: "*.stdout", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.encyclopedia.search_file, pattern: "*.elib", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
+    publishDir params.output_directories.encyclopedia.search_file, pattern: "*.features.txt", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
+    publishDir params.output_directories.encyclopedia.search_file, pattern: "*.encyclopedia.txt", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
+    publishDir params.output_directories.encyclopedia.search_file, pattern: "*.encyclopedia.decoy.txt", failOnError: true, mode: 'copy', enabled: params.encyclopedia.save_output
     label 'process_high_constant'
     container params.images.encyclopedia
 
@@ -28,6 +27,7 @@ process ENCYCLOPEDIA_SEARCH_FILE {
         path("${mzml_file}.features.txt"), emit: features
         path("${mzml_file}.encyclopedia.txt"), emit: results_targets
         path("${mzml_file}.encyclopedia.decoy.txt"), emit: results_decoys
+        path("output_file_stats.txt"), emit: output_file_stats
 
 
     script:
@@ -40,6 +40,10 @@ process ENCYCLOPEDIA_SEARCH_FILE {
         -percolatorVersion /usr/local/bin/percolator \\
         ${encyclopedia_params} \\
         > >(tee "encyclopedia-${mzml_file.baseName}.stdout") 2> >(tee "encyclopedia-${mzml_file.baseName}.stderr" >&2)
+
+    md5sum *.elib *.features.txt *.encyclopedia.txt *.encyclopedia.decoy.txt *.mzML | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt
+    stat -L --printf='%n\t%s\n' *.elib *.features.txt *.encyclopedia.txt *.encyclopedia.decoy.txt *.mzML | sort > sizes.txt
+    join -t'\t' hashes.txt sizes.txt > output_file_stats.txt
     """
 
     stub:
@@ -50,11 +54,15 @@ process ENCYCLOPEDIA_SEARCH_FILE {
     touch "${mzml_file}.features.txt"
     touch "${mzml_file}.encyclopedia.txt"
     touch "${mzml_file}.encyclopedia.decoy.txt"
+
+    md5sum *.elib *.features.txt *.encyclopedia.txt *.encyclopedia.decoy.txt *.mzML | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt
+    stat -L --printf='%n\t%s\n' *.elib *.features.txt *.encyclopedia.txt *.encyclopedia.decoy.txt *.mzML | sort > sizes.txt
+    join -t'\t' hashes.txt sizes.txt > output_file_stats.txt
     """
 }
 
 process ENCYCLOPEDIA_CREATE_ELIB {
-    publishDir "${params.result_dir}/encyclopedia/create-elib", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.encyclopedia.create_elib, failOnError: true, mode: 'copy'
     label 'process_memory_high_constant'
     container params.images.encyclopedia
 
@@ -113,7 +121,7 @@ process ENCYCLOPEDIA_CREATE_ELIB {
 }
 
 process ENCYCLOPEDIA_BLIB_TO_DLIB {
-    publishDir "${params.result_dir}/encyclopedia/convert-blib", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.encyclopedia.convert_blib, failOnError: true, mode: 'copy'
     label 'process_medium'
     label 'process_high_memory'
     container params.images.encyclopedia
@@ -147,7 +155,7 @@ process ENCYCLOPEDIA_BLIB_TO_DLIB {
 }
 
 process ENCYCLOPEDIA_DLIB_TO_TSV {
-    publishDir "${params.result_dir}/encyclopedia/convert-blib", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.encyclopedia.convert_blib, failOnError: true, mode: 'copy'
     label 'process_medium'
     label 'process_high_memory'
     container params.images.encyclopedia3_mriffle
diff --git a/modules/file_stats.nf b/modules/file_stats.nf
new file mode 100644
index 0000000..196b2e2
--- /dev/null
+++ b/modules/file_stats.nf
@@ -0,0 +1,37 @@
+
+process CALCULATE_MD5 {
+    label 'process_low'
+    container params.images.ubuntu
+
+    input:
+        path(file_to_check)
+
+    output:
+        tuple val("${file_to_check.name}"), env(md5_sum)
+
+    shell:
+        '''
+        md5_sum=$( md5sum !{file_to_check} |awk '{print $1}' )
+        '''
+}
+
+process WRITE_FILE_STATS {
+    label 'process_low'
+    container params.images.ubuntu
+    publishDir "${params.result_dir}", failOnError: true, mode: 'copy'
+
+    input:
+        val file_stats
+
+    output:
+        path("file_checksums.tsv")
+
+    script:
+    data = file_stats.join('\\n')
+    """
+    text="${data}"
+
+    echo -e 'file\\tpath\\tmd5_hash\\tsize' > file_checksums.tsv
+    echo -e \$text >> file_checksums.tsv
+    """
+}
diff --git a/modules/msconvert.nf b/modules/msconvert.nf
index 1861e77..5f2dd27 100644
--- a/modules/msconvert.nf
+++ b/modules/msconvert.nf
@@ -1,6 +1,6 @@
 process MSCONVERT {
     storeDir "${params.mzml_cache_directory}/${workflow.commitId}/${params.msconvert.do_demultiplex}/${params.msconvert.do_simasspectra}"
-    publishDir "${params.result_dir}/msconvert", pattern: "*.mzML", failOnError: true, mode: 'copy', enabled: params.msconvert_only && !params.panorama.upload
+    publishDir params.output_directories.msconvert, pattern: "*.mzML", failOnError: true, mode: 'copy', enabled: params.msconvert_only && !params.panorama.upload
     label 'process_medium'
     label 'process_high_memory'
     label 'error_retry'
diff --git a/modules/panorama.nf b/modules/panorama.nf
index e5a90e3..07b86e5 100644
--- a/modules/panorama.nf
+++ b/modules/panorama.nf
@@ -55,7 +55,7 @@ process PANORAMA_GET_RAW_FILE_LIST {
     label 'process_low_constant'
     label 'error_retry'
     container params.images.panorama_client
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy'
     secret 'PANORAMA_API_KEY'
 
     input:
@@ -93,8 +93,8 @@ process PANORAMA_GET_FILE {
     label 'process_low_constant'
     label 'error_retry'
     container params.images.panorama_client
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy', pattern: "*.stdout"
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy', pattern: "*.stderr"
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy', pattern: "*.stdout"
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy', pattern: "*.stderr"
     secret 'PANORAMA_API_KEY'
 
     input:
@@ -169,8 +169,8 @@ process PANORAMA_GET_SKYR_FILE {
     label 'process_low_constant'
     label 'error_retry'
     container params.images.panorama_client
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy', pattern: "*.stdout"
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy', pattern: "*.stderr"
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy', pattern: "*.stdout"
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy', pattern: "*.stderr"
     secret 'PANORAMA_API_KEY'
 
     input:
@@ -202,8 +202,8 @@ process UPLOAD_FILE {
     label 'error_retry'
     maxForks 2
     container params.images.panorama_client
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy', pattern: "*.stdout"
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy', pattern: "*.stderr"
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy', pattern: "*.stdout"
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy', pattern: "*.stderr"
     secret 'PANORAMA_API_KEY'
 
     input:
@@ -239,8 +239,8 @@ process UPLOAD_FILE {
 process IMPORT_SKYLINE {
     label 'process_low_constant'
     container params.images.panorama_client
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy', pattern: "*.stdout"
-    publishDir "${params.result_dir}/panorama", failOnError: true, mode: 'copy', pattern: "*.stderr"
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy', pattern: "*.stdout"
+    publishDir params.output_directories.panorama, failOnError: true, mode: 'copy', pattern: "*.stderr"
     secret 'PANORAMA_API_KEY'
 
     input:
diff --git a/modules/qc_report.nf b/modules/qc_report.nf
index f93c9d8..427aaf4 100644
--- a/modules/qc_report.nf
+++ b/modules/qc_report.nf
@@ -28,7 +28,7 @@ process MAKE_EMPTY_FILE {
 }
 
 process PARSE_REPORTS {
-    publishDir "${params.result_dir}/qc_report", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.qc_report, failOnError: true, mode: 'copy'
     label 'process_high_memory'
     container params.images.qc_pipeline
 
@@ -79,9 +79,9 @@ process PARSE_REPORTS {
 }
 
 process EXPORT_TABLES {
-    publishDir "${params.result_dir}/qc_report/tables", pattern: '*.tsv', failOnError: true, mode: 'copy'
-    publishDir "${params.result_dir}/qc_report", pattern: '*.stdout', failOnError: true, mode: 'copy'
-    publishDir "${params.result_dir}/qc_report", pattern: '*.stderr', failOnError: true, mode: 'copy'
+    publishDir params.output_directories.qc_report_tables, pattern: '*.tsv', failOnError: true, mode: 'copy'
+    publishDir params.output_directories.qc_report, pattern: '*.stdout', failOnError: true, mode: 'copy'
+    publishDir params.output_directories.qc_report, pattern: '*.stderr', failOnError: true, mode: 'copy'
     label 'process_high_memory'
     container params.images.qc_pipeline
 
@@ -106,9 +106,9 @@ process EXPORT_TABLES {
 }
 
 process RENDER_QC_REPORT {
-    publishDir "${params.result_dir}/qc_report", pattern: 'qc_report.*', failOnError: true, mode: 'copy'
-    publishDir "${params.result_dir}/qc_report", pattern: '*.stdout', failOnError: true, mode: 'copy'
-    publishDir "${params.result_dir}/qc_report", pattern: '*.stderr', failOnError: true, mode: 'copy'
+    publishDir params.output_directories.qc_report, pattern: 'qc_report.*', failOnError: true, mode: 'copy'
+    publishDir params.output_directories.qc_report, pattern: '*.stdout', failOnError: true, mode: 'copy'
+    publishDir params.output_directories.qc_report, pattern: '*.stderr', failOnError: true, mode: 'copy'
     label 'process_high_memory'
     container params.images.qc_pipeline
 
@@ -136,7 +136,7 @@ process RENDER_QC_REPORT {
 }
 
 process EXPORT_GENE_REPORTS {
-    publishDir "${params.result_dir}/gene_reports", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.gene_reports, failOnError: true, mode: 'copy'
     label 'process_high_memory'
     container params.images.qc_pipeline
 
diff --git a/modules/skyline.nf b/modules/skyline.nf
index 780b60b..467c50f 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -4,7 +4,7 @@ def sky_basename(path) {
 }
 
 process SKYLINE_ADD_LIB {
-    publishDir "${params.result_dir}/skyline/add-lib", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.skyline.add_lib, failOnError: true, mode: 'copy'
     label 'process_medium'
     label 'process_short'
     label 'error_retry'
@@ -86,7 +86,7 @@ process SKYLINE_ADD_LIB {
 }
 
 process SKYLINE_IMPORT_MZML {
-    publishDir "${params.result_dir}/skyline/import-spectra", pattern: '*.std[oe][ur][tr]', failOnError: true, mode: 'copy'
+    publishDir params.output_directories.skyline.import_spectra, pattern: '*.std[oe][ur][tr]', failOnError: true, mode: 'copy'
     label 'process_medium'
     label 'process_high_memory'
     label 'process_short'
@@ -123,7 +123,7 @@ process SKYLINE_IMPORT_MZML {
 }
 
 process SKYLINE_MERGE_RESULTS {
-    publishDir "${params.result_dir}/skyline/import-spectra", enabled: params.replicate_metadata == null && params.pdc.study_id == null, failOnError: true, mode: 'copy'
+    publishDir params.output_directories.skyline.import_spectra, enabled: params.replicate_metadata == null && params.pdc.study_id == null, failOnError: true, mode: 'copy'
     label 'process_high'
     label 'error_retry'
     container params.images.proteowizard
@@ -139,7 +139,7 @@ process SKYLINE_MERGE_RESULTS {
         path("${params.skyline.document_name}.sky.zip"), emit: final_skyline_zipfile
         path("skyline-merge.stdout"), emit: stdout
         path("skyline-merge.stderr"), emit: stderr
-        env(sky_zip_hash), emit: file_hash
+        path('output_file_hashes.txt'), emit: output_file_hashes
 
     script:
     import_files_params = "--import-file=${(mzml_files as List).collect{ "/tmp/" + file(it).name }.join(' --import-file=')}"
@@ -163,19 +163,19 @@ process SKYLINE_MERGE_RESULTS {
         --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}' )
+    md5sum ${params.skyline.document_name}.sky.zip | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\1\\t\\2/' > output_file_hashes.txt
     """
 
     stub:
     """
     touch "${params.skyline.document_name}.sky.zip"
     touch "skyline-merge.stderr" "skyline-merge.stdout"
-    sky_zip_hash=\$( md5sum ${params.skyline.document_name}.sky.zip |awk '{print \$1}' )
+    md5sum ${params.skyline.document_name}.sky.zip | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\1\\t\\2/' > output_file_hashes.txt
     """
 }
 
 process ANNOTATION_TSV_TO_CSV {
-    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.skyline.import_spectra, failOnError: true, mode: 'copy'
     label 'process_low'
     label 'error_retry'
     container params.images.qc_pipeline
@@ -199,7 +199,7 @@ process ANNOTATION_TSV_TO_CSV {
 }
 
 process SKYLINE_MINIMIZE_DOCUMENT {
-    publishDir "${params.result_dir}/skyline/minimize", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.skyline.minimize, failOnError: true, mode: 'copy'
     label 'error_retry'
     label 'process_high'
     container params.images.proteowizard
@@ -211,7 +211,7 @@ process SKYLINE_MINIMIZE_DOCUMENT {
         path("${sky_basename(skyline_zipfile)}_minimized.sky.zip"), emit: final_skyline_zipfile
         path("*.stdout"), emit: stdout
         path("*.stderr"), emit: stderr
-        env(sky_zip_hash), emit: file_hash
+        path('output_file_hashes.txt'), emit: output_file_hashes
 
     script:
         """
@@ -227,19 +227,19 @@ process SKYLINE_MINIMIZE_DOCUMENT {
             --share-type="minimal" \
         > >(tee 'minimize_skyline.stdout') 2> >(tee 'minimize_skyline.stderr' >&2)
 
-        sky_zip_hash=\$( md5sum ${sky_basename(skyline_zipfile)}_minimized.sky.zip |awk '{print \$1}' )
+        md5sum ${sky_basename(skyline_zipfile)}_minimized.sky.zip | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\1\\t\\2/' > output_file_hashes.txt
         """
 
     stub:
     """
     touch ${sky_basename(skyline_zipfile)}_minimized.sky.zip
     touch stub.stdout stub.stderr
-    sky_zip_hash=\$( md5sum ${sky_basename(skyline_zipfile)}_minimized.sky.zip |awk '{print \$1}' )
+    md5sum ${sky_basename(skyline_zipfile)}_minimized.sky.zip | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\1\\t\\2/' > output_file_hashes.txt
     """
 }
 
 process SKYLINE_ANNOTATE_DOCUMENT {
-    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.skyline.import_spectra, failOnError: true, mode: 'copy'
     label 'process_memory_high_constant'
     container params.images.proteowizard
 
@@ -252,7 +252,7 @@ process SKYLINE_ANNOTATE_DOCUMENT {
         path("${sky_basename(skyline_zipfile)}_annotated.sky.zip"), emit: final_skyline_zipfile
         path("*.stdout"), emit: stdout
         path("*.stderr"), emit: stderr
-        env(sky_zip_hash), emit: file_hash
+        path('output_file_hashes.txt'), emit: output_file_hashes
 
     shell:
     """
@@ -268,19 +268,19 @@ process SKYLINE_ANNOTATE_DOCUMENT {
     wine SkylineCmd --batch-commands=add_annotations.bat \
         > >(tee 'annotate_doc.stdout') 2> >(tee 'annotate_doc.stderr' >&2)
 
-    sky_zip_hash=\$( md5sum ${sky_basename(skyline_zipfile)}_annotated.sky.zip |awk '{print \$1}' )
+    md5sum ${sky_basename(skyline_zipfile)}_annotated.sky.zip | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\1\\t\\2/' > output_file_hashes.txt
     """
 
     stub:
     """
     touch "${sky_basename(skyline_zipfile)}_annotated.sky.zip"
     touch stub.stdout stub.stderr
-    sky_zip_hash=\$( md5sum ${sky_basename(skyline_zipfile)}_annotated.sky.zip |awk '{print \$1}' )
+    md5sum ${sky_basename(skyline_zipfile)}_annotated.sky.zip | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\1\\t\\2/' > output_file_hashes.txt
     """
 }
 
 process SKYLINE_RUN_REPORTS {
-    publishDir "${params.result_dir}/skyline/reports", failOnError: true, mode: 'copy'
+    publishDir params.output_directories.skyline.reports, failOnError: true, mode: 'copy'
     label 'process_high'
     label 'error_retry'
     container params.images.proteowizard
diff --git a/nextflow.config b/nextflow.config
index 2f80c0d..82abcec 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -237,6 +237,9 @@ includeConfig 'conf/base.config'
 // Load the images to use for all processes
 includeConfig 'container_images.config'
 
+// Load the output file directories
+includeConfig 'conf/output_directories.config'
+
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit. Copied from the nf-core template.
 def check_max(obj, type) {
diff --git a/workflows/combine_file_hashes.nf b/workflows/combine_file_hashes.nf
new file mode 100644
index 0000000..df1d6d3
--- /dev/null
+++ b/workflows/combine_file_hashes.nf
@@ -0,0 +1,83 @@
+
+include { CALCULATE_MD5 } from "../modules/file_stats"
+include { WRITE_FILE_STATS } from "../modules/file_stats"
+
+def get_search_file_dir() {
+    if(params.search_engine.toLowerCase() == 'encyclopedia') {
+        return params.output_directories.encyclopedia.search_file
+    }
+    if(params.search_engine.toLowerCase() == 'diann') {
+        return params.output_directories.diann
+    }
+    return 'UNKNOWN_SEARCH_ENGINE'
+}
+
+
+workflow combine_file_hashes {
+    take:
+        fasta
+        spectral_library
+
+        search_file_stats
+
+        final_skyline_file
+        final_skyline_hash
+        skyline_reports
+
+        qc_report_files
+        gene_reports
+
+        workflow_versions
+
+    emit:
+        output_file_hashes
+
+    main:
+
+        // process hash text files produced by search
+        search_file_data = search_file_stats.splitText().map{
+            it -> tuple(it.split('\\t'))
+        }.branch{
+            mzml_files: it[0].endsWith("mzML")
+                tuple(it[0], "${params.mzml_cache_directory}", it[1], it[2])
+            search_files: true
+                tuple(it[0], get_search_file_dir(), it[1], it[2])
+        }
+
+        // process skyline hash text files
+        skyline_doc_data = final_skyline_file.map{
+            it -> tuple(it.name, params.output_directories.skyline.import_spectra, it.size())
+        }.join(
+            final_skyline_hash.splitText().map{ it ->
+                elems = it.split('\t')
+                tuple(elems[1], elems[0])
+            }
+        ).map{ it -> tuple(it[0], it[1], it[3], it[2])}
+
+        // Combine files we need to calculate the hash of into a single channel
+        file_stat_files = fasta.concat(spectral_library).map{
+            it -> tuple(it.name, it, params.result_dir, it.size())
+        }.concat(
+            skyline_reports.map{ tuple(it.name, it, params.output_directories.skyline.reports, it.size()) },
+            qc_report_files.map{ tuple(it.name, it, params.output_directories.qc_report, it.size()) },
+            gene_reports.map{ tuple(it.name, it, params.output_directories.gene_reports, it.size()) },
+            workflow_versions.map{ tuple(it.name, it, params.result_dir, it.size()) }
+        )
+
+        md5_input = file_stat_files.map{ it -> it[1] }
+        CALCULATE_MD5(md5_input)
+
+        // Combine all file hashes into a single channel
+        output_file_hashes = search_file_data.mzml_files.concat(
+            file_stat_files.join(CALCULATE_MD5.out).map{
+                it -> tuple(it[0], it[2], it[4], it[3])
+            }
+        ).concat(search_file_data.search_files, skyline_doc_data).map{
+            it -> it.join('\\t')
+        }
+
+        // output_file_hashes.view()
+
+        WRITE_FILE_STATS(output_file_hashes.collect())
+}
+
diff --git a/workflows/diann_search.nf b/workflows/diann_search.nf
index 2af93ae..64c954c 100644
--- a/workflows/diann_search.nf
+++ b/workflows/diann_search.nf
@@ -4,7 +4,7 @@ include { DIANN_SEARCH } from "../modules/diann"
 include { DIANN_SEARCH_LIB_FREE } from "../modules/diann"
 
 workflow diann_search {
-    
+
     take:
         ms_file_ch
         fasta
@@ -18,6 +18,7 @@ workflow diann_search {
         stderr
         predicted_speclib
         diann_version
+        output_file_stats
 
     main:
 
@@ -30,6 +31,7 @@ workflow diann_search {
                 params.diann.params
             )
             diann_version = DIANN_SEARCH.out.version
+            output_file_stats = DIANN_SEARCH.out.output_file_stats
 
             predicted_speclib = Channel.empty()
         } else {
@@ -41,6 +43,7 @@ workflow diann_search {
 
             diann_version = DIANN_SEARCH_LIB_FREE.out.version
             predicted_speclib = diann_results.predicted_speclib
+            output_file_stats = DIANN_SEARCH_LIB_FREE.out.output_file_stats
         }
 
         quant_files       = diann_results.quant_files
diff --git a/workflows/encyclopedia_search.nf b/workflows/encyclopedia_search.nf
index f62cdd2..4c0271a 100644
--- a/workflows/encyclopedia_search.nf
+++ b/workflows/encyclopedia_search.nf
@@ -18,6 +18,7 @@ workflow encyclopedia_search {
         peptide_quant
         protein_quant
         encyclopedia_version
+        output_file_stats
 
     main:
 
@@ -49,4 +50,5 @@ workflow encyclopedia_search {
         peptide_quant = ENCYCLOPEDIA_CREATE_ELIB.out.peptide_quant
         protein_quant = ENCYCLOPEDIA_CREATE_ELIB.out.protein_quant
         encyclopedia_version = ENCYCLOPEDIA_CREATE_ELIB.out.version
+        output_file_stats = ENCYCLOPEDIA_SEARCH_FILE.out.output_file_stats
 }
diff --git a/workflows/get_input_files.nf b/workflows/get_input_files.nf
index 22b500a..f938ec5 100644
--- a/workflows/get_input_files.nf
+++ b/workflows/get_input_files.nf
@@ -46,7 +46,7 @@ workflow get_input_files {
             PANORAMA_GET_FASTA(params.fasta, aws_secret_id)
             fasta = PANORAMA_GET_FASTA.out.panorama_file
         } else {
-            fasta = file(params.fasta, checkIfExists: true)
+            fasta = Channel.value(file(params.fasta, checkIfExists: true))
         }
 
         if(params.spectral_library) {
@@ -54,7 +54,7 @@ workflow get_input_files {
                 PANORAMA_GET_SPECTRAL_LIBRARY(params.spectral_library, aws_secret_id)
                 spectral_library = PANORAMA_GET_SPECTRAL_LIBRARY.out.panorama_file
             } else {
-                spectral_library = file(params.spectral_library, checkIfExists: true)
+                spectral_library = Channel.value(file(params.spectral_library, checkIfExists: true))
             }
         } else {
             spectral_library = null
diff --git a/workflows/skyline_import.nf b/workflows/skyline_import.nf
index ec15da7..d999ff3 100644
--- a/workflows/skyline_import.nf
+++ b/workflows/skyline_import.nf
@@ -47,16 +47,16 @@ workflow skyline_import {
                                       ANNOTATION_TSV_TO_CSV.out.annotation_definitions)
 
             skyline_results = SKYLINE_ANNOTATE_DOCUMENT.out.final_skyline_zipfile
-            skyline_results_hash = SKYLINE_ANNOTATE_DOCUMENT.out.file_hash
+            skyline_results_hash = SKYLINE_ANNOTATE_DOCUMENT.out.output_file_hashes
         } else {
             skyline_results = SKYLINE_MERGE_RESULTS.out.final_skyline_zipfile
-            skyline_results_hash = SKYLINE_MERGE_RESULTS.out.file_hash
+            skyline_results_hash = SKYLINE_MERGE_RESULTS.out.output_file_hashes
         }
 
         if(params.skyline.minimize) {
             SKYLINE_MINIMIZE_DOCUMENT(skyline_results)
             skyline_minimized_results = SKYLINE_MINIMIZE_DOCUMENT.out.final_skyline_zipfile
-            skyline_minimized_results_hash = SKYLINE_MINIMIZE_DOCUMENT.out.file_hash
+            skyline_minimized_results_hash = SKYLINE_MINIMIZE_DOCUMENT.out.output_file_hashes
         } else {
             skyline_minimized_results = Channel.empty()
             skyline_minimized_results_hash = Channel.empty()