small reformat exercises

Author: kobelavaerts

docs/nextflow/first_pipeline.md

@@ -218,7 +218,11 @@ include { multiqc } from "${projectDir}/../../modules/multiqc"
 
 workflow {
   ...
-  multiqc((fastqc_raw.out.fastqc_out).mix(fastqc_trim.out.fastqc_out).collect())
+  multiqc_input = fastqc_raw.out.fastqc_out
+    .mix(fastqc_trim.out.fastqc_out)
+    .collect()
+
+  multiqc(multiqc_input)
 } 
 ```
 ```` 

exercises/03_first_pipeline/solutions/2.7_RNAseq.nf

@@ -71,5 +71,9 @@ workflow {
   star_alignment(trimmomatic.out.trim_fq, star_idx.out.index, gtf)
 
   // Multi QC on all results
-  multiqc((fastqc_raw.out.fastqc_out).mix(fastqc_trim.out.fastqc_out).collect())
+  multiqc_input = fastqc_raw.out.fastqc_out
+    .mix(fastqc_trim.out.fastqc_out)
+    .collect()
+
+  multiqc(multiqc_input)
 }

exercises/03_first_pipeline/solutions/ex.1_RNAseq.nf

@@ -71,7 +71,11 @@ workflow {
   star_alignment(trimmomatic.out.trim_fq, star_idx.out.index, gtf)
 
   // Multi QC on all results
-  multiqc((fastqc_raw.out.fastqc_out).mix(fastqc_trim.out.fastqc_out).collect())
+  multiqc_input = fastqc_raw.out.fastqc_out
+    .mix(fastqc_trim.out.fastqc_out)
+    .collect()
+
+  multiqc(multiqc_input)
 }
 
 workflow.onComplete {

exercises/03_first_pipeline/solutions/ex.2_RNAseq.nf

@@ -64,7 +64,11 @@ workflow {
   salmon_quant(salmon_idx.out, read_pairs_ch)
 
   // Multi QC on all results
-  multiqc((fastqc_raw.out.fastqc_out).mix(fastqc_trim.out.fastqc_out).collect())
+  multiqc_input = fastqc_raw.out.fastqc_out
+    .mix(fastqc_trim.out.fastqc_out)
+    .collect()
+
+  multiqc(multiqc_input)
 }
 
 workflow.onComplete {