Move SKYLINE_ANNOTATE_DOCUMENT to skyline_import sub-workflow.

mriffle · Sep 13, 2024 · 1e40958 · 1e40958
1 parent 67c107a
commit 1e40958
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Showing 4 changed files with 31 additions and 45 deletions.
diff --git a/main.nf b/main.nf
@@ -10,7 +10,6 @@ include { diann_search } from "./workflows/diann_search"
 include { get_mzmls as get_narrow_mzmls } from "./workflows/get_mzmls"
 include { get_mzmls as get_wide_mzmls } from "./workflows/get_mzmls"
 include { skyline_import } from "./workflows/skyline_import"
-include { skyline_annotate_doc } from "./workflows/skyline_annotate_document"
 include { skyline_reports } from "./workflows/skyline_run_reports"
 include { generate_dia_qc_report } from "./workflows/generate_qc_report"
 include { panorama_upload_results } from "./workflows/panorama_upload"
@@ -88,7 +87,6 @@ workflow {
         }
     }
 
-
     // if accessing panoramaweb and running on aws, set up an aws secret
     if(workflow.profile == 'aws' && is_panorama_used) {
         GET_AWS_USER_ID()
@@ -324,19 +322,13 @@ workflow {
                 skyline_template_zipfile,
                 fasta,
                 final_elib,
-                wide_mzml_ch
+                wide_mzml_ch,
+                replicate_metadata
             )
             proteowizard_version = skyline_import.out.proteowizard_version
         }
 
-        // annotate skyline document if replicate_metadata was specified
-        if(params.replicate_metadata != null || params.pdc.study_id != null) {
-            skyline_annotate_doc(skyline_import.out.skyline_results,
-                                 replicate_metadata)
-            final_skyline_file = skyline_annotate_doc.out.skyline_results
-        } else {
-            final_skyline_file = skyline_import.out.skyline_results
-        }
+        final_skyline_file = skyline_import.out.skyline_results
 
         // generate QC report
         if(!params.qc_report.skip) {

diff --git a/modules/skyline.nf b/modules/skyline.nf
@@ -86,7 +86,7 @@ process SKYLINE_ADD_LIB {
 }
 
 process SKYLINE_IMPORT_MZML {
-    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
+    publishDir "${params.result_dir}/skyline/import-spectra", pattern: '*.log', 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 "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
+    publishDir "${params.result_dir}/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
@@ -175,7 +175,7 @@ process SKYLINE_MERGE_RESULTS {
 }
 
 process ANNOTATION_TSV_TO_CSV {
-    publishDir "${params.result_dir}/skyline/annotate", failOnError: true, mode: 'copy'
+    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
     label 'process_low'
     label 'error_retry'
     container params.images.qc_pipeline
@@ -199,6 +199,7 @@ process ANNOTATION_TSV_TO_CSV {
 }
 
 process SKYLINE_MINIMIZE_DOCUMENT {
+    publishDir "${params.result_dir}/skyline/minimize", failOnError: true, mode: 'copy'
     label 'error_retry'
     label 'process_high'
     container params.images.proteowizard
@@ -238,7 +239,7 @@ process SKYLINE_MINIMIZE_DOCUMENT {
 }
 
 process SKYLINE_ANNOTATE_DOCUMENT {
-    publishDir "${params.result_dir}/skyline/annotate", failOnError: true, mode: 'copy'
+    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
     label 'process_memory_high_constant'
     container params.images.proteowizard
 

diff --git a/workflows/skyline_annotate_document.nf b/workflows/skyline_annotate_document.nf
diff --git a/workflows/skyline_import.nf b/workflows/skyline_import.nf
@@ -2,6 +2,9 @@
 include { SKYLINE_ADD_LIB } from "../modules/skyline"
 include { SKYLINE_IMPORT_MZML } from "../modules/skyline"
 include { SKYLINE_MERGE_RESULTS } from "../modules/skyline"
+include { ANNOTATION_TSV_TO_CSV } from "../modules/skyline"
+include { SKYLINE_MINIMIZE_DOCUMENT } from "../modules/skyline"
+include { SKYLINE_ANNOTATE_DOCUMENT } from "../modules/skyline"
 
 workflow skyline_import {
 
@@ -10,6 +13,7 @@ workflow skyline_import {
         fasta
         elib
         wide_mzml_file_ch
+        replicate_metadata
 
     emit:
         skyline_results
@@ -32,6 +36,24 @@ workflow skyline_import {
             fasta
         )
 
-        skyline_results = SKYLINE_MERGE_RESULTS.out.final_skyline_zipfile
+        if(params.replicate_metadata != null || params.pdc.study_id != null) {
+            ANNOTATION_TSV_TO_CSV(replicate_metadata)
+
+            SKYLINE_ANNOTATE_DOCUMENT(SKYLINE_MERGE_RESULTS.out.final_skyline_zipfile,
+                                      ANNOTATION_TSV_TO_CSV.out.annotation_csv,
+                                      ANNOTATION_TSV_TO_CSV.out.annotation_definitions)
+
+            sky_minimize_input = SKYLINE_ANNOTATE_DOCUMENT.out.final_skyline_zipfile
+        } else {
+            sky_minimize_input = SKYLINE_MERGE_RESULTS.out.final_skyline_zipfile
+        }
+
+        if(params.skyline.minimize) {
+            SKYLINE_MINIMIZE_DOCUMENT(sky_minimize_input)
+            skyline_results = SKYLINE_MINIMIZE_DOCUMENT.out.final_skyline_zipfile
+        } else {
+            skyline_results = sky_minimize_input
+        }
+
         proteowizard_version = SKYLINE_ADD_LIB.out.version
 }