From 0c4ed005aebb404fd3ba623fa1f9ef963ce786b6 Mon Sep 17 00:00:00 2001
From: Nicholas Minor <nrminor@wisc.edu>
Date: Thu, 29 Feb 2024 16:08:09 -0600
Subject: [PATCH] updated docker image

---
 Dockerfile       | 3 +++
 main.nf          | 2 +-
 nextflow.config  | 6 +++---
 requirements.txt | 1 +
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 23ca55b..68868d0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -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"
diff --git a/main.nf b/main.nf
index 2622bce..2fd9926 100644
--- a/main.nf
+++ b/main.nf
@@ -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
diff --git a/nextflow.config b/nextflow.config
index 92f7bf0..5e529e8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -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"
 
 	}
 
@@ -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"
 
 	}
 
@@ -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"
 
 	}
 
diff --git a/requirements.txt b/requirements.txt
index 19e82c6..50a6cbd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -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"