Merge pull request #1414 from pabloaledo/dev

Backport support for Graviton 4 to version 3.16.1

Author: pinin4fjords

conf/arm.config

@@ -0,0 +1,39 @@
+process {
+
+    //// No aarch64 builds in bioconda / conda-forge channels
+
+    //// a) have seqera aarch64 conda builds
+    
+    withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
+        conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
+        //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
+    }
+
+    withName: 'STAR_GENOMEGENERATE_IGENOMES' {
+        conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
+        //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
+    }
+
+    withName: 'RSEM_PREPAREREFERENCE' {
+        conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d'
+        //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
+    }
+
+    withName: 'RSEM_CALCULATEEXPRESSION' {
+        conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d'
+        //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
+    }
+
+    //// b) need aarch64 conda builds
+
+    //withName: 'HISAT2_ALIGN' {
+    //    conda = 'bioconda::hisat2 bioconda::samtools'
+    //    //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1'
+    //}
+
+    //withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' {
+    //    conda = 'bioconda::hisat2'
+    //    //conda = 'bioconda::hisat2=2.2.1'
+    //}
+
+}

modules/nf-core/samtools/sort/main.nf

@@ -186,6 +186,7 @@ profiles {
     }
     arm {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        includeConfig 'conf/arm.config'
     }
     singularity {
         singularity.enabled     = true