Develop fix nextflow metrics

envs/env.yml

@@ -49,6 +49,8 @@ dependencies:
   - openssl=3.0.5=h166bdaf_2
   - pip=22.3=pyhd8ed1ab_0
   - python=3.9.13=h2660328_0_cpython
+  - pandas=2.1.1=py39hddac248_1
+  - biopython=1.81=py39h72bdee0_0
   - readline=8.1.2=h0f457ee_0
   - setuptools=65.5.0=pyhd8ed1ab_0
   - singularity=3.8.7=h8e8409e_0

vfnext/configs/containers.config

@@ -50,9 +50,6 @@ process {
     withName:fixWGS {
         container = "$projectDir/containers/singularity_pythonScripts.sif"
     }
-    withName:compileOutputs {
-        container = "$projectDir/containers/singularity_pythonScripts.sif"
-    }
     withName:runSnpEff{
         container = "$projectDir/containers/singularity_snpeff.sif"
     }

vfnext/containers/Singularity_bwa_v0717

@@ -46,7 +46,7 @@ Usage:
     apt update
     #for security fixe:
     #apt upgrade -y
-    apt install -y wget bzip2
+    apt install -y wget bzip2 procps
 
     #install conda
     cd /opt

vfnext/containers/Singularity_fastp_v0201

@@ -46,7 +46,7 @@ Usage:
     apt update
     #for security fixe:
     #apt upgrade -y
-    apt install -y wget bzip2
+    apt install -y wget bzip2 procps
 
     #install conda
     cd /opt

vfnext/containers/Singularity_nextclade

@@ -2,6 +2,7 @@ Bootstrap: docker
 From: continuumio/miniconda3:4.7.12
 
 %post
+conda install -c conda-forge procps-ng
 wget https://github.com/nextstrain/nextclade/releases/download/2.4.0/nextclade-x86_64-unknown-linux-gnu
 chmod 755 nextclade-x86_64-unknown-linux-gnu
 mv nextclade-x86_64-unknown-linux-gnu /usr/bin/nextclade
@@ -11,4 +12,3 @@ exec nextclade "$@"
 
 %startscript
 exec nextclade "$@"
-

vfnext/containers/Singularity_pythonScripts

@@ -10,12 +10,15 @@ Stage: spython-base
 DEBIAN_FRONTEND=noninteractive
 
 # Install OS dependencies
-apt-get update -qq -y && \
+apt-get update -qq -y && apt install -y procps &&\
 
 # Install Python dependencies
 pip install --upgrade pip
 pip install -r requirements.txt
 
+# Explicitly add /bin to the PATH
+echo 'export PATH=$PATH:/bin' >> /root/.bashrc
+
 %runscript
 cd /
 exec /bin/bash "$@"

vfnext/containers/Singularity_snpEff

@@ -6,6 +6,7 @@ conda install -c bioconda samtools=1.9 --force-reinstall
 conda install -c bioconda freebayes
 conda install -c bioconda snpeff=5.0
 conda install -c bioconda entrez-direct
+conda install -c conda-forge procps-ng
 
 %runscript
 cd /

vfnext/containers/Singularity_vfreport

@@ -8,7 +8,7 @@ DEBIAN_FRONTEND=noninteractive
 
 # Install OS dependencies
 apt-get update -qq -y && \
-apt install git -y 
+apt install git -y procps
 
 # Install Python dependencies
 pip install --upgrade pip

vfnext/modules/compileOutput.nf

@@ -10,7 +10,7 @@ process compileOutputs{
     path("*")
   script:
     """
-    compileOutput.py -dD ${params.outDir} \
+    python $projectDir/bin/compileOutput.py -dD ${params.outDir} \
                             -oD ./ \
                             --depth ${params.depth} \
                             -virus_tag ${virus_tag}

vfnext/modules/runSnpEff.nf

@@ -28,7 +28,6 @@ process runSnpEff{
     """
     freebayes -p 1 --reference-quality ${params.mapping_quality},${params.base_quality} \
             -f ${ref_fa} ${sorted_bam} > ${sample_id}.vcf
-    snpEff download -v ${genome_code}
     snpEff ann -Xmx4g \
             ${genome_code} ${sample_id}.vcf > ${sample_id}.ann.vcf
     # add sample id to htmls