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Author SHA1 Message Date
Olamide Isreal
9ffba5cb2c Production config: disable MSA, 1 sample, errorStrategy ignore 
- 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>
 2026-03-16 20:29:24 +01:00
Olamide Isreal
fdbd7bf863 Use dedicated input subdirectory to avoid stale files 
Previous runs left rcsb_pdb_1QGS.fasta in the work dir.
Using s3://omic/eureka/chai1/input/ ensures only our files are picked up.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 2026-03-16 19:54:59 +01:00
1 changed files with 4 additions and 3 deletions
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main.nf
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@@ -1,17 +1,18 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.enable.dsl=2 nextflow.enable.dsl=2
params.input_dir = 's3://omic/eureka/chai1' params.input_dir = 's3://omic/eureka/chai1/input'
params.outdir = 's3://omic/eureka/chai1/output' params.outdir = 's3://omic/eureka/chai1/output'
params.use_msa = true params.use_msa = false
params.msa_server = 'https://api.colabfold.com' params.msa_server = 'https://api.colabfold.com'
params.num_samples = 5 params.num_samples = 1
process CHAI1 { process CHAI1 {
container 'harbor.cluster.omic.ai/omic/chai1:v3' container 'harbor.cluster.omic.ai/omic/chai1:v3'
publishDir params.outdir, mode: 'copy' publishDir params.outdir, mode: 'copy'
stageInMode 'copy' stageInMode 'copy'
maxForks 1 maxForks 1
errorStrategy 'ignore'
input: input:
path fasta path fasta