Temporary Trimgalore override, singularity fixes for rsem processes

Author: pinin4fjords

conf/arm.config

@@ -210,6 +210,18 @@ process {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' }
     }
 
+    //// Remove this once we've got a new Biocontainer for trimgalore with the
+    //// newer cutadapt, and we've update the nf-core module
+    //// https://github.com/bioconda/bioconda-recipes/pull/51563
+
+    withName: TRIMGALORE {
+        //conda = 'bioconda::cutadapt=4.2 trim-galore=0.6.10'
+
+        conda = 'bioconda::cutadapt=4.9 trim-galore=0.6.10'
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0d/0dda1e09d10d1e2994ea85843b1e3d62212598ca5047e0ab419d5d87db637057/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:1cd58fa242e634da' }
+
+    }
+
     //// No aarch64 builds in bioconda / conda-forge channels
 
     //// a) have seqera aarch64 conda builds
@@ -232,14 +244,14 @@ process {
         //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
 
         conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a'
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' }
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' }
     }
 
     withName: 'RSEM_CALCULATEEXPRESSION' {
         //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
 
         conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d'
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' }
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' }
     }
 
     //// b) need aarch64 conda builds