add debug

sinamajidian · sinamajidian · commit 4ea1139fda80 · 2025-09-22T14:23:18.000-04:00
diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
@@ -58,7 +58,7 @@ jobs:
       -
         name: Test
         run: |
-          docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run ${{ env.TEST_TAG }} --tree --standalone_path /input/marker_genes --dna_reference /input/dna_ref.fa --reads /reads/sample_1.fastq --output_path /out/output
+          docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run ${{ env.TEST_TAG }} --tree --standalone_path /input/marker_genes --dna_reference /input/dna_ref.fa --reads /reads/sample_1.fastq --output_path /out/output --debug --threads 1
           if [ ! -f output/tree_sample_1.nwk ] ; then exit 1; fi
       -
         name: Login to DockerHub

Original file line number	Diff line number	Diff line change
`@@ -58,7 +58,7 @@ jobs:`
`58`	`58`	`-`
`59`	`59`	`name: Test`
`60`	`60`	`run: \|`
`61`		`- docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run ${{ env.TEST_TAG }} --tree --standalone_path /input/marker_genes --dna_reference /input/dna_ref.fa --reads /reads/sample_1.fastq --output_path /out/output`
	`61`	`+ docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run ${{ env.TEST_TAG }} --tree --standalone_path /input/marker_genes --dna_reference /input/dna_ref.fa --reads /reads/sample_1.fastq --output_path /out/output --debug --threads 1`
`62`	`62`	`if [ ! -f output/tree_sample_1.nwk ] ; then exit 1; fi`
`63`	`63`	`-`
`64`	`64`	`name: Login to DockerHub`