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Co-authored-by: Harshil Patel <[email protected]>
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conf/arm.config

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process {
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//// Frozen ARM buids from Wave
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//
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// Tools that have native Conda builds for AMD and ARM
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//
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withName: GTF_FILTER {
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container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' }
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}
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//// No aarch64 builds in bioconda / conda-forge channels
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//
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// Tools that do not have native Conda builds for AMD and ARM. Required custom builds in seqera Conda channel.
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//
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//// a) have seqera aarch64 conda builds
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withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
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//conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
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conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
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container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' }
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}
@@ -247,7 +248,9 @@ process {
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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' }
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}
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//// b) need aarch64 conda builds
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//
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// Tools currently unsupported for ARM
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//
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//withName: 'HISAT2_ALIGN' {
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// conda = 'bioconda::hisat2 bioconda::samtools'

modules/nf-core/trimgalore/main.nf

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subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test

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