Don't let QC_FILTER handle any pre-filter or annotation of the data. …

…Let this be handled by the parent workflows. This option is better especially when when don't what to perform the basic filtering but want to annotate the data.
vib-singlecell-nf · Oct 29, 2020 · a463b8a · a463b8a
1 parent 4915786
commit a463b8a
Show file tree

Hide file tree

Showing 6 changed files with 38 additions and 12 deletions.
diff --git a/docs/development.rst b/docs/development.rst
@@ -482,9 +482,10 @@ Steps:
                 data
 
             main:
-                // run the pipeline
-                out = data
-                out = SC__FILE_CONVERTER( data )
+                out = data | \
+                    SC__FILE_CONVERTER | \
+                    FILTER_AND_ANNOTATE_AND_CLEAN
+
                 if(params.sc.scanpy.containsKey("filter")) {
                     out = QC_FILTER( out ).filtered // Remove concat
                 }

diff --git a/workflows/bbknn.nf b/workflows/bbknn.nf
@@ -16,6 +16,9 @@ include {
 include {
     FINALIZE;
 } from '../src/utils/workflows/finalize.nf' params(params)
+include {
+    FILTER_AND_ANNOTATE_AND_CLEAN;
+} from '../src/utils/workflows/filterAnnotateClean.nf' params(params)
 include {
     UTILS__GENERATE_WORKFLOW_CONFIG_REPORT;
 } from '../src/utils/processes/reports.nf' params(params)
@@ -69,8 +72,10 @@ workflow bbknn {
         /*******************************************
         * Data processing
         */
-        out = data
-        out = SC__FILE_CONVERTER( data )
+        out = data | \
+            SC__FILE_CONVERTER | \
+            FILTER_AND_ANNOTATE_AND_CLEAN
+
         if(params.sc.scanpy.containsKey("filter")) {
             out = QC_FILTER( out ).filtered // Remove concat
         }

diff --git a/workflows/harmony.nf b/workflows/harmony.nf
@@ -16,6 +16,9 @@ include {
 include {
     FINALIZE;
 } from '../src/utils/workflows/finalize.nf' params(params)
+include {
+    FILTER_AND_ANNOTATE_AND_CLEAN;
+} from '../src/utils/workflows/filterAnnotateClean.nf' params(params)
 include {
     UTILS__GENERATE_WORKFLOW_CONFIG_REPORT;
 } from '../src/utils/processes/reports.nf' params(params)
@@ -71,8 +74,10 @@ workflow harmony {
         /*******************************************
         * Data processing
         */
-        out = data
-        out = SC__FILE_CONVERTER( data )
+        out = data | \
+            SC__FILE_CONVERTER | \
+            FILTER_AND_ANNOTATE_AND_CLEAN
+
         if(params.sc.scanpy.containsKey("filter")) {
             out = QC_FILTER( out ).filtered // Remove concat
         }

diff --git a/workflows/mnncorrect.nf b/workflows/mnncorrect.nf
@@ -22,6 +22,9 @@ include {
 include {
     FILE_CONVERTER;
 } from '../src/utils/workflows/fileConverter.nf' params(params)
+include {
+    FILTER_AND_ANNOTATE_AND_CLEAN;
+} from '../src/utils/workflows/filterAnnotateClean.nf' params(params)
 include {
     UTILS__GENERATE_WORKFLOW_CONFIG_REPORT;
 } from '../src/utils/processes/reports.nf' params(params)
@@ -80,8 +83,10 @@ workflow mnncorrect {
         /*******************************************
         * Data processing
         */
-        out = data
-        out = SC__FILE_CONVERTER( data )
+        out = data | \
+            SC__FILE_CONVERTER | \
+            FILTER_AND_ANNOTATE_AND_CLEAN
+
         if(params.sc.scanpy.containsKey("filter")) {
             out = QC_FILTER( out ).filtered // Remove concat
         }

diff --git a/workflows/multi_sample.nf b/workflows/multi_sample.nf
@@ -23,6 +23,9 @@ include {
 include {
     FILE_CONVERTER;
 } from '../src/utils/workflows/fileConverter.nf' params(params)
+include {
+    FILTER_AND_ANNOTATE_AND_CLEAN;
+} from '../src/utils/workflows/filterAnnotateClean.nf' params(params)
 include {
     UTILS__GENERATE_WORKFLOW_CONFIG_REPORT;
 } from '../src/utils/processes/reports.nf' params(params)
@@ -77,7 +80,10 @@ workflow multi_sample {
         /*******************************************
         * Data processing
         */
-        out = SC__FILE_CONVERTER( data )
+        out = data | \
+            SC__FILE_CONVERTER | \
+            FILTER_AND_ANNOTATE_AND_CLEAN
+
         if(params.sc.scanpy.containsKey("filter")) {
             out = QC_FILTER( out ).filtered // Remove concat
         }

diff --git a/workflows/single_sample_star.nf b/workflows/single_sample_star.nf
@@ -74,8 +74,12 @@ workflow single_sample_star {
     UTILS__GENERATE_WORKFLOW_CONFIG_REPORT(
         file(workflow.projectDir + params.utils.workflow_configuration.report_ipynb)
     )
-    QC_FILTER( data )
-    NORMALIZE_TRANSFORM( QC_FILTER.out.filtered )
+    out = FILTER_AND_ANNOTATE_AND_CLEAN( data )
+
+    if(params.sc.scanpy.containsKey("filter")) {
+        out = QC_FILTER( out ).filtered // Remove concat
+    }    
+    NORMALIZE_TRANSFORM( out )
     HVG_SELECTION( NORMALIZE_TRANSFORM.out )
     if(params.sc.scanpy.containsKey("regress_out")) {
         preprocessed_data = SC__SCANPY__REGRESS_OUT( HVG_SELECTION.out.scaled )