Add docker image tags to version file.

mriffle · Aug 26, 2024 · ed1b5e2 · ed1b5e2
1 parent 737528f
commit ed1b5e2
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Showing 2 changed files with 14 additions and 8 deletions.
diff --git a/main.nf b/main.nf
@@ -192,7 +192,6 @@ workflow {
                 'narrow',
                 params.encyclopedia.chromatogram.params
             )
-            encyclopedia_version = encyclopeda_export_elib.out.encyclopedia_version
 
             quant_library = encyclopeda_export_elib.out.elib
 
@@ -216,8 +215,9 @@ workflow {
 
         )
 
-        final_elib = encyclopedia_quant.out.elib
+        encyclopedia_version = encyclopedia_quant.out.encyclopedia_version
 
+        final_elib = encyclopedia_quant.out.elib
         all_elib_ch = all_elib_ch.concat(
             encyclopedia_quant.out.individual_elibs,
             encyclopedia_quant.out.elib,
@@ -412,7 +412,7 @@ def is_panorama_used() {
            (params.quant_spectra_dir && any_entry_is_panorama(params.quant_spectra_dir)) ||
            (params.chromatogram_library_spectra_dir && any_entry_is_panorama(params.chromatogram_library_spectra_dir)) ||
            (params.skyline_skyr_file && any_entry_is_panorama(params.skyline_skyr_file))
-           
+
 }
 
 //

diff --git a/workflows/save_run_details.nf b/workflows/save_run_details.nf
@@ -38,15 +38,17 @@ workflow save_run_details {
 
     main:
 
-        // split program version variable names and value
+        // Read version txt files and create a channel of variable name, value pairs
         version_vars = version_files.map{
             program -> program.collect{ it ->
-                elems = it.split('=') 
-                [elems[0].strip(), elems[1].strip()]
+                elems = it.split('=').collect{ str ->
+                    str.strip().replaceAll(/^['"]|['"]$/, '')
+                }
+                [elems[0], elems[1]]
             }
         }
 
-
+        // Create channel of workflow run metadata
         workflow_vars = Channel.fromList([["Nextflow run at", workflow.start],
                                           ["Nextflow version", nextflow.version],
                                           ["Workflow git address", "${workflow.repository}"],
@@ -55,9 +57,13 @@ workflow save_run_details {
                                           ["Run session ID", workflow.sessionId],
                                           ["Command line", workflow.commandLine]])
 
+        // Create channel of docker image names and paths
+        docker_images = Channel.fromList(params.images.collect{k, v -> ["${k} docker image", v]})
+
         all_vars = workflow_vars.concat(
             input_files.flatten().collate(2),
-            version_vars.flatten().collate(2)
+            version_vars.flatten().collate(2),
+            docker_images
         )
 
         var_names = all_vars.map{ it -> it[0] }