Merge branch 'master' of git.unl.edu:aknecht2/chipathlon into 3-method-auto-doc

chipathlon/jobs/modules/align.yaml

@@ -43,7 +43,7 @@ align:
             outputs:
               - align.sam:
                   type: file
-      paired[read_end]:
+    - paired[read_end]:
         - bwa_align_paired:
             inputs:
               - ref_genome:
@@ -94,7 +94,7 @@ align:
                   type: file
               - align.quality:
                   type: stderr
-      paired[read_end]:
+    - paired[read_end]:
         - bowtie2_align_paired:
             inputs:
               - ref_genome_prefix: