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Triage arm deps
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‎conf/arm.config‎

Lines changed: 121 additions & 108 deletions
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process {
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//
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// Apply software overrides for ARM compatibility
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withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
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conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
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//conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
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}
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withName: 'STAR_GENOMEGENERATE_IGENOMES' {
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conda = 'bioconda::star bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
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//conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
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}
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withName: 'BBSPLIT' {
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conda = 'bioconda::bbmap'
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// conda = 'bioconda::bbmap=39.01'
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}
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withName: 'CAT_FASTQ' {
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conda = 'conda-forge::coreutils'
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//conda = 'conda-forge::coreutils=8.30'
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}
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withName: 'CAT_ADDITIONAL_FASTA' {
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conda = 'conda-forge::python'
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//conda = 'conda-forge::coreutils=3.9.5'
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}
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//
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//// Tested, working, module updates in progress on main dev branch
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withName: 'CUSTOM_GETCHROMSIZES' {
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conda = 'bioconda::samtools=1.21'
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//conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20'
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}
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withName: 'CUSTOM_TX2GENE' {
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conda = 'python=3.13.0'
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//conda = 'python=3.9.5'
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}
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withName: 'FASTP' {
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conda = 'bioconda::fastp'
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//conda = 'bioconda::fastp=0.23.4'
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}
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withName: 'FQ_SUBSAMPLE' {
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conda = 'bioconda::fq'
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//conda = 'bioconda::fq=0.9.1'
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}
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withName: 'GFFREAD' {
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conda = 'bioconda::gffread'
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//conda = 'bioconda::gffread=0.12.7'
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}
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withName: 'GUNZIP' {
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conda = 'conda-forge::sed'
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//conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34'
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}
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withName: 'HISAT2_ALIGN' {
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conda = 'bioconda::hisat2 bioconda::samtools'
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//conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1'
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}
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withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' {
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conda = 'bioconda::hisat2'
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//conda = 'bioconda::hisat2=2.2.1'
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}
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withName: 'KALLISTO_INDEX|KALLISTO_QUANT' {
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conda = 'bioconda::kallisto'
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//conda = 'bioconda::kallisto=0.48.0'
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}
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withName: 'PICARD_MARKDUPLICATES' {
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conda = 'bioconda::picard=3.3.0'
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//conda = 'bioconda::picard=3.1.1'
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}
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withName: 'PRESEQ_LCEXTRAP' {
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conda = 'bioconda::preseq'
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//conda = 'bioconda::preseq=3.1.2'
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}
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withName: 'RSEM_CALCULATEEXPRESSION' {
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conda = 'bioconda::rsem bioconda::star'
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//conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
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}
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withName: 'RSEM_PREPAREREFERENCE' {
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conda = 'seqera::rsem seqera::star=2.6.1d'
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//conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
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}
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withName: 'SALMON_INDEX|SALMON_QUANT' {
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conda = 'bioconda::salmon=1.10.3'
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//conda = 'bioconda::salmon=1.10.1'
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}
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withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' {
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conda = 'bioconda::samtools=1.21 bioconda::htslib'
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//conda = 'bioconda::samtools=1.20 bioconda::htslib'
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}
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withName: 'SORTMERNA' {
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conda = 'bioconda::sortmerna'
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//conda = 'bioconda::sortmerna=4.3.6'
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}
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withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' {
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conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk'
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//conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0'
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withName: 'TRIMGALORE' {
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conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9'
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//conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4'
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}
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withName: 'STRINGTIE_STRINGTIE' {
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conda = 'bioconda::stringtie=2.2.3'
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//conda = 'bioconda::stringtie=2.2.1'
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}
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withName: 'SUBREAD_FEATURECOUNTS' {
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conda = 'bioconda::subread=2.0.6'
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//conda = 'bioconda::subread=2.0.1'
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}
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withName: 'TRIMGALORE' {
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conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9'
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//conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4'
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}
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withName: 'UCSC_BEDGRAPHTOBIGWIG' {
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conda = 'bioconda::ucsc-bedgraphtobigwig=469'
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//conda = 'bioconda::ucsc-bedgraphtobigwig=445'
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}
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withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' {
136-
conda = 'bioconda::umi_tools'
137-
//conda = 'bioconda::umi_tools=1.1.5'
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//// Untested, but have aarch conda builds in bioconda/ conda-forge channels.
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//// Should update the nf-core modules
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withName: 'BBSPLIT' {
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conda = 'bioconda::bbmap=39.10'
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// conda = 'bioconda::bbmap=39.01'
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}
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withName: 'CAT_FASTQ' {
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conda = 'conda-forge::coreutils=9.5'
59+
//conda = 'conda-forge::coreutils=8.30'
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}
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62+
withName: 'CAT_ADDITIONAL_FASTA' {
63+
conda = 'python=3.13.0'
64+
//conda = 'conda-forge::coreutils=3.9.5'
65+
}
66+
67+
withName: 'FQ_SUBSAMPLE' {
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conda = 'bioconda::fq=0.12.0'
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//conda = 'bioconda::fq=0.9.1'
13870
}
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withName: 'KALLISTO_INDEX|KALLISTO_QUANT' {
73+
conda = 'bioconda::kallisto=0.51.1'
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//conda = 'bioconda::kallisto=0.48.0'
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}
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withName: 'PRESEQ_LCEXTRAP' {
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conda = 'bioconda::preseq=3.2.0'
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//conda = 'bioconda::preseq=3.1.2'
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}
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withName: 'SORTMERNA' {
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conda = 'bioconda::sortmerna=4.3.7'
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//conda = 'bioconda::sortmerna=4.3.6'
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}
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//// No longer necessary- dev branch version has an aarch 64 build (s)
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//withName: 'GUNZIP' {
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// conda = 'conda-forge::sed'
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// //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34'
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//}
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//withName: 'UNTAR' {
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// conda = 'conda-forge::grep conda-forge::sed conda-forge::tar'
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// //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34'
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//}
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//withName: 'FASTP' {
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// conda = 'bioconda::fastp'
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// //conda = 'bioconda::fastp=0.23.4'
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//}
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//withName: 'GFFREAD' {
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// conda = 'bioconda::gffread'
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// //conda = 'bioconda::gffread=0.12.7'
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//}
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//withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' {
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// conda = 'bioconda::umi_tools'
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// //conda = 'bioconda::umi_tools=1.1.5'
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//}
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//// No aarch64 builds in bioconda / conda-forge channels
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//// a) have seqera aarch64 conda builds
139117

140-
withName: 'UNTAR' {
141-
conda = 'conda-forge::grep conda-forge::sed conda-forge::tar'
142-
//conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34'
118+
withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
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conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
120+
//conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
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}
122+
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withName: 'STAR_GENOMEGENERATE_IGENOMES' {
124+
conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
125+
//conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
143126
}
144-
}
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128+
withName: 'RSEM_PREPAREREFERENCE' {
129+
conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d'
130+
//conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
131+
}
132+
133+
withName: 'RSEM_CALCULATEEXPRESSION' {
134+
conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d'
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//conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
136+
}
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// NOTE THE OLDER STAR VERSION HERE!
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withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' {
141+
conda = 'seqera::star2.6.1d bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0'
142+
//conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0'
143+
}
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//// b) need aarch64 conda builds
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//withName: 'HISAT2_ALIGN' {
148+
// conda = 'bioconda::hisat2 bioconda::samtools'
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// //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1'
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//}
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//withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' {
153+
// conda = 'bioconda::hisat2'
154+
// //conda = 'bioconda::hisat2=2.2.1'
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//}
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}

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