Merge branch 'example-cmd-again' into 'dev'

example cmd update

See merge request epi2melabs/workflows/wf-transcriptomes!145

Author: sarahjeeeze

nextflow.config

@@ -92,13 +92,16 @@ params {
 
     wf {
       example_cmd = [
-        "--condition_sheet 'wf-transcriptomes-demo/condition_sheet.tsv'",
+        "--de_analysis",
         "--direct_rna",
         "--fastq 'wf-transcriptomes-demo/differential_expression_fastq'",
+        "--jaffal_annotation 'genCode22'",
+        "--jaffal_genome 'hg38_chr20'",
+        "--jaffal_refBase 'wf-transcriptomes-demo/chr20'",
         "--minimap2_index_opts '-k15'",
         "--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
         "--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
-        "--de_analysis",
+        "--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'",
       ]
     agent = null
     container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867"