Add archr qc filtering method and entry point

vib-singlecell-nf · Dec 11, 2020 · 7606659 · 7606659
1 parent f9d54ba
commit 7606659
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Showing 2 changed files with 18 additions and 13 deletions.
diff --git a/main_atac.nf b/main_atac.nf
@@ -69,6 +69,16 @@ workflow atac_qc_filtering {
 
 }
 
+workflow atac_qc_filtering_archr {
+
+    include {
+        ATAC_QC_FILTERING;
+    } from './workflows/atac/qc_filtering.nf' params(params)
+
+    getDataChannel | ATAC_QC_FILTERING
+
+}
+
 workflow atac_preprocess_freemuxlet {
 
     // generic ATAC-seq preprocessing pipeline: adapter trimming, mapping, fragments file generation

diff --git a/workflows/atac/qc_filtering.nf b/workflows/atac/qc_filtering.nf
@@ -2,12 +2,10 @@ nextflow.preview.dsl=2
 
 //////////////////////////////////////////////////////
 // process imports:
-/*
 include { SC__ARCHR__CREATE_ARROW_UNFILTERED; } from './../../src/archr/processes/createArrow_unfiltered.nf' params(params)
 include { SC__ARCHR__CELL_CALLING; } from './../../src/archr/processes/cell_calling.nf' params(params)
 
 include { SC__PYCISTOPIC__MACS2_CALL_PEAKS; } from './../../src/pycistopic/processes/macs2_call_peaks.nf' params(params)
-*/
 
 //////////////////////////////////////////////////////
 //  Define the workflow 
@@ -27,29 +25,26 @@ workflow ATAC_QC_PREFILTER {
 }
 
 
-/*
 workflow ATAC_QC_FILTERING {
 
     take:
         data
 
     main:
 
-        data.view()
-        //data.branch {
-        //    fragments: it[3] == 'fragments'
-        //    bam: it[3] == 'bam'
-        //}
-        //.set{ data_split }
-        //data_split.fragments.view()
-
-        SC__ARCHR__CREATE_ARROW_UNFILTERED(data) |
+        data.branch {
+            fragments: it[3] == 'fragments'
+            bam: it[3] == 'bam'
+        }
+        .set{ data_split }
+
+        SC__ARCHR__CREATE_ARROW_UNFILTERED(data_split.fragments) |
             SC__ARCHR__CELL_CALLING
 
     /*
         cell_calling
         doublet_freemuxlet
         bap_multiplets
     */
-//}
+}