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Merge pull request #19 from nrminor/wf_wrapper
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Updating docker image to contain nextflow
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nrminor authored Feb 29, 2024
2 parents 95abf28 + 49d6fd7 commit b2d6c52
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Showing 4 changed files with 8 additions and 4 deletions.
3 changes: 3 additions & 0 deletions Dockerfile
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Expand Up @@ -63,6 +63,9 @@ RUN llm sentence-transformers register all-mpnet-base-v2
RUN llm sentence-transformers register all-MiniLM-L12-v2
RUN llm sentence-transformers register multi-qa-mpnet-base-dot-v1

# install nextflow
RUN python3 -m pip install nextflow

# set cache and config directories for llm
ENV LLM_USER_PATH "/scratch/.llm/.config"
ENV HF_HOME "/scratch/.llm"
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -140,7 +140,7 @@ process CLUSTER_WITH_LLM {
process FIND_QUALIFYING_RECORDS {

tag "${gene}"
publishDir params.remapped, mode: 'copy', overwrite: true
publishDir params.remapped, mode: 'copy', pattern: "*qualifying*" overwrite: true

errorStrategy { task.attempt < 3 ? 'retry' : params.errorMode }
maxRetries 2
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6 changes: 3 additions & 3 deletions nextflow.config
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Expand Up @@ -59,7 +59,7 @@ profiles {
apptainer.enabled = false
conda.enabled = false

process.container = "nrminor/ncbi-ml-ai:v0.0.1"
process.container = "nrminor/ncbi-ml-ai:v0.0.2"

}

Expand All @@ -69,7 +69,7 @@ profiles {
apptainer.enabled = false
conda.enabled = false

process.container = "nrminor/ncbi-ml-ai:v0.0.1"
process.container = "nrminor/ncbi-ml-ai:v0.0.2"

}

Expand All @@ -79,7 +79,7 @@ profiles {
docker.enabled = false
conda.enabled = false

process.container = "nrminor/ncbi-ml-ai:v0.0.1"
process.container = "nrminor/ncbi-ml-ai:v0.0.2"

}

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1 change: 1 addition & 0 deletions requirements.txt
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Expand Up @@ -76,6 +76,7 @@ msal-extensions==1.1.0 ; python_version >= "3.10" and python_version < "3.13"
msal==1.27.0 ; python_version >= "3.10" and python_version < "3.13"
multidict==6.0.5 ; python_version >= "3.10" and python_version < "3.13"
mypy-extensions==1.0.0 ; python_version >= "3.10" and python_version < "3.13"
nextflow==23.10.1 ; python_version >= "3.10" and python_version < "3.13"
numpy==1.26.4 ; python_version >= "3.10" and python_version < "3.13"
oauthlib==3.2.2 ; python_version >= "3.10" and python_version < "3.13"
openai==1.13.3 ; python_version >= "3.10" and python_version < "3.13"
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