update subworkflows

Euro-BioImaging · Feb 19, 2024 · 3fcce94 · 3fcce94
1 parent 183f9dc
commit 3fcce94
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/modules/subworkflows_ometiff.nf b/modules/subworkflows_ometiff.nf
@@ -209,7 +209,8 @@ workflow Convert2OMETIFF_FromS3_CSV { // s3 &! merged && CSV
         ch1f = ch1.flatMap { file(it).Name }
         ch = Transfer_S3Storage2Local(ch1, ch1f)
         output = Convert_EachFile2SeparateOMETIFF(ch)
-        UpdateCsv(parsedCsv, "RootOriginal", "ImageNameOriginal", "ometiff")
+        mock = output.collect().flatten().first()
+        UpdateCsv(parsedCsv, "RootOriginal", "ImageNameOriginal", "ometiff", mock)
         if (params.dest_type == "s3") {
             Transfer_Local2S3Storage(output)
             Transfer_CSV2S3Storage(UpdateCsv.out)

diff --git a/modules/subworkflows_omezarr.nf b/modules/subworkflows_omezarr.nf
@@ -209,7 +209,8 @@ workflow Convert2OMEZARR_FromS3_CSV { // s3 &! merged && CSV
         ch1f = ch1.flatMap { file(it).Name }
         ch = Transfer_S3Storage2Local(ch1, ch1f)
         output = Convert_EachFile2SeparateOMEZARR(ch)
-        UpdateCsv(parsedCsv, "RootOriginal", "ImageNameOriginal", "ometiff")
+        mock = output.collect().flatten().first()
+        UpdateCsv(parsedCsv, "RootOriginal", "ImageNameOriginal", "ometiff", mock)
         if (params.dest_type == "s3") {
             Transfer_Local2S3Storage(output)
             Transfer_CSV2S3Storage(UpdateCsv.out)