Publish SR output in {meta.id}/spaceranger/outs

Publish Space Ranger count output in `{meta.id}/spaceranger/outs`
instead of just `{meta.id}/outs`, which adheres better to the
"results/{software}" strategy for other modules.

This was hard-coded in the Space Ranger module as `{meta.id}/outs`. This
commit achieves the change by modifying the module code to instead be
just `outs`, so that the exact publishDir may be specified in
`modules.config` as `${params.outdir}/{meta.id}/spaceranger` instead.
This did not work before, as modifying `modules.config` could just add
paths on top of the already hard-coded `${params.outdir}/{meta.id}/outs`
module publishDir.

A PR with these changes will be submitted to the modules repo.

conf/modules.config

@@ -62,9 +62,7 @@ process {
 
     withName: SPACERANGER_COUNT {
         publishDir = [
-            // NOTE: the sample name is already included in the path that's getting published.
-            // This publishDir directive puts spaceranger outputs in results/${meta.id}/outs
-            path: { "${params.outdir}" },
+            path: { "${params.outdir}/${meta.id}/spaceranger" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

modules.json

@@ -23,7 +23,8 @@
                     "spaceranger/count": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/spaceranger/count/spaceranger-count.diff"
                     },
                     "untar": {
                         "branch": "master",