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BCCDC-PHL · May 31, 2024 · 34bde5a · 34bde5a
1 parent 5c4004e
commit 34bde5a
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Showing 4 changed files with 8 additions and 7 deletions.
diff --git a/.github/data/reads_to_simulate.csv b/.github/data/reads_to_simulate.csv
@@ -1 +1 @@
-NC002973.6,.github/data/assemblies/NC_002973.6.fa
+NC_000962.3,.github/data/refs/NC_000962.3.fa
diff --git a/.github/scripts/download_assemblies.sh b/.github/scripts/download_assemblies.sh
diff --git a/.github/scripts/download_refs.sh b/.github/scripts/download_refs.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+mkdir -p .github/data/refs
+
+curl -o .github/data/refs/NC_000962.3.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_000962.3&db=nucleotide&rettype=fasta"
+curl -o .github/data/refs/NC_002973.6.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_002973.6&db=nucleotide&rettype=fasta"
diff --git a/.github/scripts/run_pipeline.sh b/.github/scripts/run_pipeline.sh
@@ -15,6 +15,6 @@ nextflow run main.nf \
 	 --fastq_input .github/data/fastq \
 	 --outdir .github/data/test_output \
 	 --min_depth 5 \
-	 --ref .github/data/refs/NC_045512.2.fasta \
+	 --ref .github/data/refs/NC_000962.3.fa \
 	 -with-report .github/data/test_output/nextflow_report.html \
  	 -with-trace .github/data/test_output/nextflow_trace.tsv
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		NC002973.6,.github/data/assemblies/NC_002973.6.fa
		NC_000962.3,.github/data/refs/NC_000962.3.fa