Merge pull request #903 from claire-prince/Fix-SAMTOOLS_INDEX-output

Fix SAMTOOLS_INDEX output

Author: drpatelh

conf/modules.config

@@ -321,7 +321,7 @@ if (!params.skip_alignment) {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
                 mode: params.publish_dir_mode,
-                pattern: "*.{bam,csi}",
+                pattern: "*.{bai,csi}",
                 enabled: ( ['star_salmon','hisat2'].contains(params.aligner) &&
                     ( params.save_align_intermeds ||
                         ( !params.with_umi && params.skip_markduplicates )