update arm conf

Author: pinin4fjords

conf/arm.config

@@ -45,25 +45,12 @@ process {
         conda = 'bioconda::ucsc-bedgraphtobigwig=469'
         //conda = 'bioconda::ucsc-bedgraphtobigwig=445'
     }
-
-    //// Untested, but have aarch conda builds in bioconda/ conda-forge channels.
-    //// Should update the nf-core modules
-
+    
     withName: 'BBSPLIT' {
         conda = 'bioconda::bbmap=39.10'
         // conda = 'bioconda::bbmap=39.01'
     }
 
-    withName: 'CAT_FASTQ' {
-        conda = 'conda-forge::coreutils=9.5'
-        //conda = 'conda-forge::coreutils=8.30'
-    }
-
-    withName: 'CAT_ADDITIONAL_FASTA' {
-        conda = 'python=3.13.0'
-        //conda = 'conda-forge::coreutils=3.9.5'
-    }
-
     withName: 'FQ_SUBSAMPLE' {
         conda = 'bioconda::fq=0.12.0'
         //conda = 'bioconda::fq=0.9.1'
@@ -73,48 +60,32 @@ process {
         conda = 'bioconda::kallisto=0.51.1'
         //conda = 'bioconda::kallisto=0.48.0'
     }
-
+    
     withName: 'PRESEQ_LCEXTRAP' {
         conda = 'bioconda::preseq=3.2.0'
         //conda = 'bioconda::preseq=3.1.2'
     }
-
-    withName: 'SORTMERNA' {
-        conda = 'bioconda::sortmerna=4.3.7'
-        //conda = 'bioconda::sortmerna=4.3.6'
-    }
 
-    withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' {
-        conda = 'seqera::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0'
-        //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0'
+    withName: 'CAT_ADDITIONAL_FASTA' {
+        conda = 'python=3.13.0'
+        //conda = 'conda-forge::coreutils=3.9.5'
     }
 
-    //// No longer necessary- dev branch version has an aarch 64 build (s)
-
-    //withName: 'GUNZIP' {
-    //    conda = 'conda-forge::sed'
-    //    //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34'
-    //}
-
-    //withName: 'UNTAR' {
-    //    conda = 'conda-forge::grep conda-forge::sed conda-forge::tar'
-    //    //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34'
-    //}
-
-    //withName: 'FASTP' {
-    //    conda = 'bioconda::fastp'
-    //    //conda = 'bioconda::fastp=0.23.4'
-    //}
+    //// Proposed to nf-core with Seqera container
+    
+    // Seqera container, since coreutils in existing image (ubuntu) wouldn't
+    // match update
+    withName: 'CAT_FASTQ' {
+        conda = 'conda-forge::coreutils=9.5'
+        //conda = 'conda-forge::coreutils=8.30'
+    }
 
-    //withName: 'GFFREAD' {
-    //    conda = 'bioconda::gffread'
-    //    //conda = 'bioconda::gffread=0.12.7'
-    //}
+    // Seqera container to avoid updating a mulled container
 
-    //withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' {
-    //    conda = 'bioconda::umi_tools'
-    //    //conda = 'bioconda::umi_tools=1.1.5'
-    //}
+    withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' {
+        conda = 'bioconda::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0'
+        //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0'
+    }
 
     //// No aarch64 builds in bioconda / conda-forge channels
 
@@ -152,4 +123,12 @@ process {
     //    //conda = 'bioconda::hisat2=2.2.1'
     //}
 
+    //// c) have aarch64 builds in bioconda, but with problems
+    // sortmerna gives 'illegal instruction' errors at 5.3.7 with either
+    // Biocontainers or Seqera Containers
+    withName: 'SORTMERNA' {
+        conda = 'bioconda::sortmerna=4.3.7'
+        //conda = 'bioconda::sortmerna=4.3.6'
+    }
+
 }