Cut out module redundant software overrides

Author: pinin4fjords

conf/arm.config

@@ -1,92 +1,5 @@
 process {
 
-    //
-    // Apply software overrides for ARM compatibility
-    //
-
-    //// Tested, working, module updates in progress on main dev branch
-
-    withName: 'CUSTOM_GETCHROMSIZES' {
-        conda = 'bioconda::samtools=1.21'
-        //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20'
-    }
-
-    withName: 'CUSTOM_TX2GENE' {
-        conda = 'python=3.13.0'
-        //conda = 'python=3.9.5'
-    }
-
-    withName: 'SALMON_INDEX|SALMON_QUANT' {
-        conda = 'bioconda::salmon=1.10.3'
-        //conda = 'bioconda::salmon=1.10.1'
-    }
-
-    withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' {
-        conda = 'bioconda::samtools=1.21 bioconda::htslib'
-        //conda = 'bioconda::samtools=1.20 bioconda::htslib'
-    }
-
-    withName: 'TRIMGALORE' {
-        conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9'
-        //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4'
-    }
-
-    withName: 'STRINGTIE_STRINGTIE' {
-        conda = 'bioconda::stringtie=2.2.3'
-        //conda = 'bioconda::stringtie=2.2.1'
-    }
-
-    withName: 'SUBREAD_FEATURECOUNTS' {
-        conda = 'bioconda::subread=2.0.6'
-        //conda = 'bioconda::subread=2.0.1'
-    }
-
-    withName: 'UCSC_BEDGRAPHTOBIGWIG' {
-        conda = 'bioconda::ucsc-bedgraphtobigwig=469'
-        //conda = 'bioconda::ucsc-bedgraphtobigwig=445'
-    }
-    
-    withName: 'BBSPLIT' {
-        conda = 'bioconda::bbmap=39.10'
-        // conda = 'bioconda::bbmap=39.01'
-    }
-
-    withName: 'FQ_SUBSAMPLE' {
-        conda = 'bioconda::fq=0.12.0'
-        //conda = 'bioconda::fq=0.9.1'
-    }
- 
-    withName: 'KALLISTO_INDEX|KALLISTO_QUANT' {
-        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: 'CAT_ADDITIONAL_FASTA' {
-        conda = 'python=3.13.0'
-        //conda = 'conda-forge::coreutils=3.9.5'
-    }
-
-    //// 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'
-    }
-
-    // Seqera container to avoid updating a mulled container
-
-    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
 
     //// a) have seqera aarch64 conda builds
@@ -123,12 +36,4 @@ 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'
-    }
-
 }