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test v0.1.3
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@andyjslee
andyjslee committed Aug 7, 2024
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356 changes: 356 additions & 0 deletions nextflow/nexus_v0.1.3_nextflow_slurm.config
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process {
standard {
process.executor = 'slurm'
process.queue = 'allnodes'
executor.queueSize = '95'
executor.submitRateLimit = '10s'
singularity.enabled = true
singularity.cacheDir = "$PWD"
nodes = 1
}
}

process {
withLabel: 'abra2' {
container = 'ajslee/abra2:2.23'
cpus = 48
memory = '192.GB'
time = '7days'
java_max_mem = 192.GB
}
withLabel: 'arcashla' {
container = 'ajslee/arcashla:0.6.0'
cpus = 48
memory = '192.GB'
time = '3days'
}
withLabel: 'arriba' {
container = 'ajslee/arriba:2.4.0'
cpus = 8
memory = '192.GB'
time = '3days'
}
withLabel: 'bwamem2' {
container = 'ajslee/bwamem2:2.2.1'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'clairs' {
container = 'hkubal/clairs:v0.3.0'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'copy_bam_file' {
cpus = 2
memory = '16.GB'
time = '1day'
}
withLabel: 'copy_vcf_file' {
cpus = 2
memory = '16.GB'
time = '1day'
}
withLabel: 'cutesv' {
container = 'ajslee/cutesv:2.1.1'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'deepvariant' {
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'delly2' {
container = 'ajslee/delly2:1.2.6'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'fastqc' {
container = 'ajslee/fastqc:0.12.1'
cpus = 2
memory = '16.GB'
fastqc_memory = 16.GB
time = '1days'
}
withLabel: 'flair' {
container = 'ajslee/flair:2.0.0'
cpus = 48
memory = '192.GB'
time = '3days'
}
withLabel: 'gatk4_applybqsr' {
container = 'ajslee/gatk4:4.4.0.0'
cpus = 4
memory = '128.GB'
time = '7days'
java_max_mem = 128.GB
}
withLabel: 'gatk4_baserecalibrator' {
container = 'ajslee/gatk4:4.4.0.0'
cpus = 4
memory = '32.GB'
time = '7days'
java_max_mem = 32.GB
}
withLabel: 'gatk4_calculatecontamination' {
container = 'ajslee/gatk4:4.4.0.0'
cpus = 4
memory = '128.GB'
time = '3days'
java_max_mem = 128.GB
}
withLabel: 'gatk4_filtermutectcalls' {
container = 'ajslee/gatk4:4.4.0.0'
cpus = 4
memory = '32.GB'
time = '3days'
java_max_mem = 32.GB
}
withLabel: 'gatk4_gatherbqsrreports' {
container = 'ajslee/gatk4:4.4.0.0'
cpus = 4
memory = '128.GB'
time = '7days'
java_max_mem = 128.GB
}
withLabel: 'gatk4_getpileupsummaries' {
container = 'ajslee/gatk4:4.4.0.0'
cpus = 4
memory = '128.GB'
time = '7days'
java_max_mem = 128.GB
}
withLabel: 'gatk4_learnreadorientationmodel' {
container = 'ajslee/gatk4:4.4.0.0'
cpus = 4
memory = '32.GB'
time = '3days'
java_max_mem = 32.GB
}
withLabel: 'gatk4_mutect2' {
container = 'ajslee/gatk4:4.4.0.0'
cpus = 6
memory = '24.GB'
time = '7days'
java_max_mem = 24.GB
hmm_threads = 4
}
withLabel: 'gridss' {
container = 'ajslee/gridss:2.13.2'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'hiphase' {
container = 'ajslee/hiphase:1.4.0'
cpus = 48
memory = '192.GB'
time = '3days'
}
withLabel: 'hlaprofiler' {
container = 'ajslee/hlaprofiler:1.0.5'
cpus = 48
memory = '192.GB'
time = '3days'
}
withLabel: 'isoquant' {
container = 'ajslee/isoquant:3.3.1'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'isoseq_cluster' {
container = 'ajslee/isoseq:4.0.0'
cpus = 32
memory = '128.GB'
time = '3days'
}
withLabel: 'lumpy' {
container = 'ajslee/lumpy:0.3.1'
cpus = 48
memory = '192.GB'
time = '7days'
samtools_cpus = 48
samtools_memory = 1.GB
}
withLabel: 'minimap2' {
container = 'ajslee/minimap2:2.22'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'pbsv' {
container = 'ajslee/pbsv:2.9.0'
cpus = 48
memory = '192.GB'
time = '3days'
}
withLabel: 'picard_fastqtosam' {
container = 'ajslee/picard:3.1.1'
cpus = 4
memory = '64.GB'
time = '3days'
java_max_mem = 64.GB
}
withLabel: 'picard_mergevcfs' {
container = 'ajslee/picard:3.1.1'
cpus = 4
memory = '128.GB'
time = '3days'
java_max_mem = 128.GB
}
withLabel: 'manta' {
container = 'ajslee/manta:1.6.0'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'ratatosk' {
container = 'ajslee/ratatosk:0.9.0'
cpus = 48
memory = '192.GB'
time = '21days'
}
withLabel: 'rnabloom2' {
container = 'ajslee/rnabloom2:2.0.1'
cpus = 48
memory = '192.GB'
time = '7days'
java_max_mem = 192.GB
}
withLabel: 'salmon' {
container = 'ajslee/salmon:1.10.3'
cpus = 48
memory = '192.GB'
time = '3days'
}
withLabel: 'samtools_calmd' {
container = 'ajslee/samtools:1.18'
cpus = 48
memory = '192.GB'
time = '3days'
}
withLabel: 'samtools_coverage' {
container = 'ajslee/samtools:1.18'
cpus = 4
memory = '32.GB'
time = '3days'
}
withLabel: 'samtools_fixmate' {
container = 'ajslee/samtools:1.18'
cpus = 48
memory = '64.GB'
time = '7days'
samtools_memory = 1.GB
}
withLabel: 'samtools_index' {
container = 'ajslee/samtools:1.18'
cpus = 4
memory = '64.GB'
time = '3days'
}
withLabel: 'samtools_markdup' {
container = 'ajslee/samtools:1.18'
cpus = 32
memory = '64.GB'
time = '7days'
samtools_memory = 1.GB
}
withLabel: 'samtools_samtobam' {
container = 'ajslee/samtools:1.18'
cpus = 32
memory = '64.GB'
time = '3days'
samtools_memory = 1.GB
}
withLabel: 'samtools_sort' {
container = 'ajslee/samtools:1.18'
cpus = 32
memory = '64.GB'
time = '3days'
samtools_memory = 1.GB
}
withLabel: 'savana' {
container = 'ajslee/savana:1.0.5'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'seq2hla' {
container = 'ajslee/seq2hla:2.3'
cpus = 48
memory = '192.GB'
time = '3days'
}
withLabel: 'sequenza' {
container = 'ajslee/sequenza:3.0.0'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'severus' {
container = 'ajslee/severus:1.1'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'sniffles2' {
container = 'ajslee/sniffles2:2.3.3'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'star' {
container = 'ajslee/star:2.7.11b'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'strelka2' {
container = 'ajslee/strelka2:2.9.10'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'stringtie2' {
container = 'ajslee/stringtie2:2.2.2'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'svaba' {
container = 'ajslee/svaba:1.2.0'
cpus = 48
memory = '192.GB'
time = '14days'
}
withLabel: 'svim' {
container = 'ajslee/svim:2.0.0'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'svisionpro' {
container = 'ajslee/svisionpro:1.8'
cpus = 48
memory = '192.GB'
time = '7days'
}
withLabel: 'ultra' {
container = 'ajslee/ultra:0.1'
cpus = 48
memory = '192.GB'
samtools_memory = 1.GB
time = '7days'
}
withLabel: 'whatshap' {
container = 'ajslee/whatshap:2.3.0'
cpus = 48
memory = '192.GB'
time = '7days'
}
}
2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -5,7 +5,7 @@ requires = [

[project]
name = "nexus"
version = "0.1.2"
version = "0.1.3"
description = "NEXflow's Ultimate Streamliner"
requires-python = ">=3.10"
readme = "README.md"
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4 changes: 2 additions & 2 deletions ...xuslib/pipelines/variant_calling/long_read_dna_variant_calling_clairs/README.md
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Expand Up @@ -23,7 +23,7 @@ nexus run --nf-workflow long_read_dna_variant_calling_clairs.nf \
--output_dir OUTPUT_DIR \
--reference_genome_fasta_file REFERENCE_GENOME_FASTA_FILE \
--reference_genome_fasta_fai_file REFERENCE_GENOME_FASTA_FAI_FILE \
--params_clairs '"--platform hifi_revio"'
--params_clairs '"--platform hifi_revio --enable_indel_calling"'
```

### Usage
Expand All @@ -43,7 +43,7 @@ required arguments:
optional arguments:
--reference_genome_fasta_file : Reference genome FASTA file (default: /datastore/lbcfs/collaborations/pirl/seqdata/references/hg38.fa).
--reference_genome_fasta_fai_file : Reference genome FASTA file (default: /datastore/lbcfs/collaborations/pirl/seqdata/references/hg38.fa.fai).
--params_clairs : ClairS parameters (default: '"--platform hifi_revio"').
--params_clairs : ClairS parameters (default: '"--platform hifi_revio --enable_indel_calling"').
Note that the parameters need to be wrapped in quotes.
--delete_work_dir : Delete work directory (default: false).
```
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