From 94600114cc8cfdb60f6d9063f1f1b1ea8634f869 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Thu, 7 Mar 2024 10:14:59 +0100
Subject: [PATCH] Enable workflow

---
 main.nf               | 40 +++++++++++++++++++---------------------
 workflows/scrnaseq.nf |  3 +--
 2 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/main.nf b/main.nf
index 4f96908f..3471e5b0 100644
--- a/main.nf
+++ b/main.nf
@@ -82,27 +82,25 @@ workflow {
         params.input
     )
 
-    PIPELINE_INITIALISATION.out.samplesheet.view()
-
-    // //
-    // // WORKFLOW: Run main workflow
-    // //
-    // NFCORE_SCRNASEQ (
-    //     PIPELINE_INITIALISATION.out.samplesheet.view()
-    // )
-
-    // //
-    // // SUBWORKFLOW: Run completion tasks
-    // //
-    // PIPELINE_COMPLETION (
-    //     params.email,
-    //     params.email_on_fail,
-    //     params.plaintext_email,
-    //     params.outdir,
-    //     params.monochrome_logs,
-    //     params.hook_url,
-    //     NFCORE_SCRNASEQ.out.multiqc_report
-    // )
+    //
+    // WORKFLOW: Run main workflow
+    //
+    NFCORE_SCRNASEQ (
+        PIPELINE_INITIALISATION.out.samplesheet
+    )
+
+    //
+    // SUBWORKFLOW: Run completion tasks
+    //
+    PIPELINE_COMPLETION (
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url,
+        NFCORE_SCRNASEQ.out.multiqc_report
+    )
 }
 
 /*
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
index 916533c2..ab1fa3a1 100644
--- a/workflows/scrnaseq.nf
+++ b/workflows/scrnaseq.nf
@@ -18,10 +18,9 @@ include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
 workflow SCRNASEQ {
 
     take:
-    ch_input // channel: samplesheet read in from --input
+    ch_fastq
 
     main:
-    ch_fastq = Channel.empty()
 
     protocol_config = WorkflowScrnaseq.getProtocol(workflow, log, params.aligner, params.protocol)
     if (protocol_config['protocol'] == 'auto' && params.aligner != "cellranger") {