Merge pull request #3 from tylergross97/seqera-ai/20260220-180341-fix-test-samplesheet-urls

tylergross97 · web-flow · commit 3621b5abc30f · 2026-02-20T13:06:53.000-05:00
Fix test profile to use GitHub URLs for test data
diff --git a/nextflow.config b/nextflow.config
@@ -49,9 +49,9 @@ profiles {
             }
         }
         params {
-            input = "${projectDir}/tests/data/xengsort/samplesheet.csv"
-            hg38_fasta = "${projectDir}/tests/data/xengsort/human.fa"
-            nsg_fasta = "${projectDir}/tests/data/xengsort/mouse.fa"
+            input = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/samplesheet.csv"
+            hg38_fasta = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/human.fa"
+            nsg_fasta = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/mouse.fa"
             outdir_base = 'results_test'
             outdir_references = "results_test/references"
             outdir_fastp = "results_test/fastp"
diff --git a/tests/data/xengsort/samplesheet.csv b/tests/data/xengsort/samplesheet.csv
@@ -1,4 +1,4 @@
 sample,fastq1,fastq2
-human,tests/data/xengsort/human_R1.fastq.gz,tests/data/xengsort/human_R2.fastq.gz
-mouse,tests/data/xengsort/mouse_R1.fastq.gz,tests/data/xengsort/mouse_R2.fastq.gz
-mixed,tests/data/xengsort/mixed_R1.fastq.gz,tests/data/xengsort/mixed_R2.fastq.gz
+human,https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/human_R1.fastq.gz,https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/human_R2.fastq.gz
+mouse,https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/mouse_R1.fastq.gz,https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/mouse_R2.fastq.gz
+mixed,https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/mixed_R1.fastq.gz,https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/mixed_R2.fastq.gz

Original file line number	Diff line number	Diff line change
`@@ -49,9 +49,9 @@ profiles {`
`49`	`49`	`}`
`50`	`50`	`}`
`51`	`51`	`params {`
`52`		`- input = "${projectDir}/tests/data/xengsort/samplesheet.csv"`
`53`		`- hg38_fasta = "${projectDir}/tests/data/xengsort/human.fa"`
`54`		`- nsg_fasta = "${projectDir}/tests/data/xengsort/mouse.fa"`
	`52`	`+ input = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/samplesheet.csv"`
	`53`	`+ hg38_fasta = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/human.fa"`
	`54`	`+ nsg_fasta = "https://raw.githubusercontent.com/tylergross97/nextflow_xengsort/main/tests/data/xengsort/mouse.fa"`
`55`	`55`	`outdir_base = 'results_test'`
`56`	`56`	`outdir_references = "results_test/references"`
`57`	`57`	`outdir_fastp = "results_test/fastp"`