add another sample to simulate, this one directly from FluViewer db

BCCDC-PHL · Jun 5, 2024 · 11ed458 · 11ed458
1 parent ecb4da1
commit 11ed458
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diff --git a/.github/data/reads_to_simulate.csv b/.github/data/reads_to_simulate.csv
@@ -1,2 +1,3 @@
+HQ011408.1,.github/data/assemblies/HQ011408.1.fa
 NC026423.1,.github/data/assemblies/NC_026423.1.fa
 NC026431.1,.github/data/assemblies/NC_026431.1.fa
diff --git a/.github/scripts/download_assemblies.sh b/.github/scripts/download_assemblies.sh
@@ -2,5 +2,6 @@
 
 mkdir -p .github/data/assemblies
 
+curl -o .github/data/assemblies/HQ011408.1.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=HQ011408.1&db=nucleotide&rettype=fasta"
 curl -o .github/data/assemblies/NC_026423.1.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_026423.1&db=nucleotide&rettype=fasta"
 curl -o .github/data/assemblies/NC_026431.1.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_026431.1&db=nucleotide&rettype=fasta"
diff --git a/.github/scripts/run_pipeline.sh b/.github/scripts/run_pipeline.sh
@@ -6,6 +6,8 @@ source ${HOME}/.bashrc
 
 eval "$(conda shell.bash hook)"
 
+conda activate base
+
 sed -i 's/cpus = 8/cpus = 4/g' nextflow.config
 sed -i "s/memory = '32 GB'/memory = '2 GB'/g" nextflow.config