Aarch64 support #134
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Aarch64 support #134
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@brainstorm can you please take a look at adding ARM64 support for ESVEE 1.0? See here for logs of Wave build failure |
scwatts
reviewed
Feb 25, 2025
| @@ -2,6 +2,7 @@ process STAR_ALIGN { | |||
| tag "${meta.id}" | |||
| label 'process_high' | |||
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| conda "${moduleDir}/environment.yml" | |||
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This change is pending elsewhere :) Could you please not include this in the final PR?
… recent sambamba version. We'll have to make a second pass when singularity/biocontainers get the new release for hmftools-esvee from bioconda, later on
…hmftools codebase for esvee, still present in the esvee/README.md though
-known_hotspot_file: type(PATH) desc(Known fusion hotspot BED file) Command error: 06:51:31.804 [ERROR] unregistered config item: -known_fusion_file 06:51:31.806 [INFO ] registered config items: 06:51:31.806 [INFO ] -bam_file: type(PATHS) desc(BAM file paths separated by ',') 06:51:31.806 [INFO ] -bam_validation: default(LENIENT) desc(BAM validation: STRICT (default), LENIENT or SILENT) 06:51:31.806 [INFO ] -bamtool: type(PATH) desc(Path to sambamba or samtools for sort/merge) 06:51:31.806 [INFO ] -blacklist_bed: type(PATH) desc(Blacklist regions BED file) 06:51:31.806 [INFO ] -known_hotspot_file: type(PATH) desc(Known fusion hotspot BED file) 06:51:31.806 [INFO ] -log_debug: type(FLAG) desc(Log at DEBUG level) 06:51:31.806 [INFO ] -log_level: desc(Specify log level: ERROR, WARN, INFO, DEBUG or TRACE) 06:51:31.806 [INFO ] -log_read_ids: desc(Log specific read IDs, separated by ';') 06:51:31.806 [INFO ] -low_base_qual: type(INTEGER) default(26) desc(Level below which a base is consider low-quality) 06:51:31.806 [INFO ] -max_frag_length_override: type(INTEGER) default(-1) desc(Set max fragment length instead of calculating) 06:51:31.806 [INFO ] -min_align_bases: type(INTEGER) default(50) desc(Junction fragment min aligned bases) 06:51:31.806 [INFO ] -min_junction_frags: type(INTEGER) default(2) desc(Required fragments to keep a junction) 06:51:31.806 [INFO ] -no_cache_bam: type(FLAG) desc(Write a BAM to cache candidate reads) 06:51:31.806 [INFO ] -no_clean_up: type(FLAG) desc(Keep candidate cache BAM files) 06:51:31.806 [INFO ] -no_trim_read_id: type(FLAG) desc(Disable use of a shortened readId internally) 06:51:31.806 [INFO ] -output_dir: desc(Output directory) 06:51:31.806 [INFO ] -output_id: desc(Output file suffix) 06:51:31.806 [INFO ] -partition_size: type(INTEGER) default(1000000) desc(Partition size) 06:51:31.806 [INFO ] -perf_debug: type(FLAG) desc(Detailed performance tracking and logging) 06:51:31.807 [INFO ] -read_length: type(INTEGER) default(151) desc(Read length) 06:51:31.807 [INFO ] -ref_genome: type(PATH) REQUIRED desc(Path to reference genome fasta files) 06:51:31.807 [INFO ] -ref_genome_version: REQUIRED desc(Ref genome version, 37 or 38) 06:51:31.807 [INFO ] -sample: desc(List of samples separated by ',') 06:51:31.807 [INFO ] -sequencing_type: default(ILLUMINA) desc(Sequencing types: ILLUMINA, ULTIMA, SBX, BIOMODAL) 06:51:31.807 [INFO ] -specific_chr: desc(Restrict to chromosome(s) separated by ';') 06:51:31.807 [INFO ] -specific_regions: desc(Restrict to regions(s) separated by ';' in format Chr:PosStart:PosEnd or Chr:PosStart-PosEnd) 06:51:31.807 [INFO ] -threads: type(INTEGER) default(1) desc(Number of threads, 0 or 1 not multi-threaded) 06:51:31.807 [INFO ] -track_remotes: type(FLAG) desc(Track support for remote junctions) 06:51:31.807 [INFO ] -write_types: desc(Write types: PREP_JUNCTION;PREP_READ;PREP_BAM;UNSORTED_BAM;CACHE_BAM;FRAGMENT_LENGTH_DIST;DISCORDANT_STATS separated by ';')
… long-running bwa index processes during test runs
…, up memory for test to 100GB too (minimum 72GB for STAR)
…it back to default and re-running...
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Work left to do for final merge/inclusion:
/cc @ohofmann |
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Running tests for newly published aarch64 packages for Oncoanalyser:
bioconda/bioconda-recipes#47228
bioconda/bioconda-recipes#53769
bioconda/bioconda-recipes#54125
bioconda/bioconda-recipes#54134
bioconda/bioconda-recipes#54172
bioconda/bioconda-recipes#54169
broadinstitute/gatk-bwamem-jni#23
Fixes #139