basic testing for runReadsToContig

LANL-Bioinformatics · Dec 17, 2024 · 46f4aa2 · 46f4aa2
1 parent 76c285d
commit 46f4aa2
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Showing 5 changed files with 11 additions and 7 deletions.
diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -1,6 +1,6 @@
 name: CI Tests
 
-on: [push, pull_request]
+on: [push]
 
 jobs:
   test:

diff --git a/main.nf b/main.nf
@@ -44,11 +44,10 @@ workflow {
     }
 
     if(params.modules.runAssembly && !params.r2c.useAssembledContigs) {
-       ASSEMBLY(params.assembly.plus(params.shared), paired, unpaired, avgLen)
-       contigs = ASSEMBLY.out.outContigs
+        ASSEMBLY(params.assembly.plus(params.shared), paired, unpaired, avgLen)
+        contigs = ASSEMBLY.out.outContigs
+        READSTOCONTIGS(params.r2c.plus(params.shared), paired, unpaired, contigs)
     }
 
-    READSTOCONTIGS(params.r2c.plus(params.shared), paired, unpaired, contigs)
-
 
 }
diff --git a/modules/runReadsToContig/Dockerfile b/modules/runReadsToContig/Dockerfile
@@ -1,5 +1,5 @@
 # syntax=docker/dockerfile:1
-FROM continuumio/miniconda3:23.5.2-0 AS build
+FROM continuumio/miniconda3:main AS build
 
 ENV container=docker
 
@@ -14,6 +14,7 @@ RUN conda init bash \
 
 RUN conda install -n readsToContig -c conda-forge r-base
 RUN conda install -n readsToContig -c conda-forge python=3.11
+RUN conda install -n readsToContig -c bioconda minimap2=2.24
 RUN conda install -n readsToContig -c bioconda perl-json
 RUN conda install -n readsToContig -c bioconda samclip=0.4.0
 RUN conda install -n readsToContig -c bioconda bwa
@@ -39,6 +40,7 @@ FROM debian:buster AS runtime
 #RUN apk add --no-cache bash
 
 COPY --from=build /venv /venv
+RUN apt-get update && apt-get install procps -y && apt-get clean
 ENV PERL5LIB=/venv/lib/perl5/core_perl
 ENV PATH=/venv/bin:$PATH
 

diff --git a/nextflow.config b/nextflow.config
@@ -141,7 +141,7 @@ process {
         container = 'apwat/run_assembly:1.5'
     }
     withLabel: 'r2c' {
-        container = 'apwat/run_r2c:1.3'
+        container = 'apwat/run_r2c:1.6'
     }
 }
 

diff --git a/tests/modules/runAssembly/runAssembly.nf.test b/tests/modules/runAssembly/runAssembly.nf.test
@@ -79,6 +79,9 @@ nextflow_workflow {
                 }
                 assembly{
                     assembler = "lrasm"
+                    lrasm {
+                        ec = true
+                    }
                 }
             }
             workflow {