Remove lima report from MultiQC output

environment-pipeline.yml

@@ -18,4 +18,4 @@ dependencies:
   - conda-forge::r-tidyr=1.3.1
 
   - pip:
-    - git+https://github.com/seqwell/longplexpy@0.2.1
+    - git+https://github.com/seqwell/longplexpy@0.2.2

main.nf

@@ -65,16 +65,14 @@ workflow {
         .map { _meta, stats -> stats }
         .collect()
 
-    // temp remove lima from the multiqc
-    // MULTIQC(
-    //    FASTQC.out.archive.collect().ifEmpty([]),
-    //    both_end_stats,
-    //    either_end_stats
-    // )
-
-      MULTIQC(
-        FASTQC.out.archive.collect().ifEmpty([])
-      )
+
+     MULTIQC(
+        FASTQC.out.archive.collect().ifEmpty([]),
+        both_end_stats,
+        either_end_stats
+     )
+
+
 
     // Pipeline Cleanup ////////////////////////////////////////////////////////////////////////////
 

modules/multiqc.nf

@@ -2,8 +2,8 @@ process MULTIQC {
 
     input:
     path('fastqc/*')
-    //path('demux_i7_i5/*')
-    //path('demux_either_i7_i5/*')
+    path('demux_i7_i5/*')
+    path('demux_either_i7_i5/*')
 
     output:
     path('*multiqc_report.html')
@@ -17,6 +17,9 @@ process MULTIQC {
         --force \\
         --interactive \\
         --no-data-dir \\
-        --verbose
+        --verbose \\
+        --ignore demux_i7_i5/ \\
+        --ignore demux_either_i7_i5
+
     """
 }

nextflow.config

@@ -108,7 +108,7 @@ process {
     withName: MULTIQC {
         memory = '8.0G'
         cpus = 4
-        container = 'seqwell/longplexpy:0.2.1'
+        container = 'seqwell/longplexpy:0.2.2-2-gd350815'
         publishDir = [
             path: "${params.output}/multiqc",
             pattern: '*.html',