From 11ed458293aa2730828220cbb59c8b095717f660 Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Wed, 5 Jun 2024 12:31:24 -0700 Subject: [PATCH] add another sample to simulate, this one directly from FluViewer db --- .github/data/reads_to_simulate.csv | 1 + .github/scripts/download_assemblies.sh | 1 + .github/scripts/run_pipeline.sh | 2 ++ 3 files changed, 4 insertions(+) diff --git a/.github/data/reads_to_simulate.csv b/.github/data/reads_to_simulate.csv index 283cbd2..75255d7 100644 --- 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 index b9b618a..8db2f56 100755 --- 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 index 76d0abe..0bd5c23 100755 --- 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