Olamide Isreal
9ffba5cb2c
- Disable MSA to reduce GPU memory for large complexes - Default to 1 diffusion sample to fit within GPU VRAM - Add errorStrategy 'ignore' so pipeline completes even if individual tasks fail (standard bioinformatics pattern) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
47 lines
1.1 KiB
Plaintext
Executable File
47 lines
1.1 KiB
Plaintext
Executable File
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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params.input_dir = 's3://omic/eureka/chai1/input'
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params.outdir = 's3://omic/eureka/chai1/output'
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params.use_msa = false
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params.msa_server = 'https://api.colabfold.com'
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params.num_samples = 1
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process CHAI1 {
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container 'harbor.cluster.omic.ai/omic/chai1:v3'
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publishDir params.outdir, mode: 'copy'
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stageInMode 'copy'
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maxForks 1
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errorStrategy 'ignore'
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input:
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path fasta
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output:
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path "${fasta.simpleName.replace('.fasta', '')}", emit: output_dir
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script:
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"""
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OUTPUT_DIR=\$(basename ${fasta} .fasta)
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mkdir -p \$OUTPUT_DIR
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# Construct MSA parameters
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MSA_OPTIONS=""
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if ${params.use_msa}; then
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MSA_OPTIONS="--use-msa-server --msa-server-url ${params.msa_server}"
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fi
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# Run CHAI1
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chai fold \\
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\$MSA_OPTIONS \\
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--num-diffn-samples ${params.num_samples} \\
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${fasta} \\
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\$OUTPUT_DIR
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"""
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}
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workflow {
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fasta_ch = Channel.fromPath(params.input_dir + '/*.fasta')
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CHAI1(fasta_ch)
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}
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