Remove sortmerna patch again, retain workaround for aarch64

Author: pinin4fjords

conf/arm.config

@@ -132,10 +132,6 @@ process {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f89ab1fef6e38e572ad1844d06f6d3d334d2b19a70c9e5d87bfc862b88728c23/data' : 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' }
     }
 
-    withName: 'SORTMERNA' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' }
-    }
-
     withName: 'PRESEQ_LCEXTRAP' {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5ab535d5b4c88dc4837cab00919d4d5ea66dd4d6dc837d841886bef72145f435/data' : 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' }
     }
@@ -252,6 +248,14 @@ process {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/648fd6bc2805481aa60db7ee9e37d41d7643eaaabd92f21bf1019f8b3f0879a6/data' : 'community.wave.seqera.io/library/bracken:3.1--0b6ab6dde7667f60' }
     }
 
+    // SortMeRNA does not yet have aarch64 builds conda forge. Working on it, using builds from Seqera channel for now
+    // See https://github.com/conda-forge/conda-forge-pinning-feedstock/pull/7454
+
+    withName: 'SORTMERNA' {
+        conda = 'seqera::sortmerna=4.3.7'
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' }
+    }
+
     //
     // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in 'seqera' Conda channel.
     //

modules.json

@@ -220,9 +220,8 @@
                     },
                     "sortmerna": {
                         "branch": "master",
-                        "git_sha": "8c44d9ce28f5f8abdbe08c21f08bd8c329fcb235",
-                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"],
-                        "patch": "modules/nf-core/sortmerna/sortmerna.diff"
+                        "git_sha": "d4a425ce59fc803a11e520f16680ede9af09761f",
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
                     "star/align": {
                         "branch": "master",