fixed docker output folder

sinamajidian · sinamajidian · commit 533b34a9d637 · 2025-09-22T15:29:53.000-04:00
diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
@@ -60,8 +60,11 @@ jobs:
       -
         name: Test
         run: |
+          echo "docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/outside_docker_out:/inside_docker_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 /inside_docker_out/output --debug --threads 1"; 
           docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/outside_docker_out:/inside_docker_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 /inside_docker_out/output --debug --threads 1
+          echo "ls -l $PWD/outside_docker_out"
           ls -l $PWD/outside_docker_out
+          echo "ls -l $PWD/outside_docker_out/output"
           ls -l $PWD/outside_docker_out/output
           if [ ! -f $PWD/outside_docker_out/output/tree_sample_1.nwk ] ; then exit 1; fi
       -

Original file line number	Diff line number	Diff line change
`@@ -60,8 +60,11 @@ jobs:`
`60`	`60`	`-`
`61`	`61`	`name: Test`
`62`	`62`	`run: \|`
	`63`	`+ echo "docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/outside_docker_out:/inside_docker_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 /inside_docker_out/output --debug --threads 1";`
`63`	`64`	`docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/outside_docker_out:/inside_docker_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 /inside_docker_out/output --debug --threads 1`
	`65`	`+ echo "ls -l $PWD/outside_docker_out"`
`64`	`66`	`ls -l $PWD/outside_docker_out`
	`67`	`+ echo "ls -l $PWD/outside_docker_out/output"`
`65`	`68`	`ls -l $PWD/outside_docker_out/output`
`66`	`69`	`if [ ! -f $PWD/outside_docker_out/output/tree_sample_1.nwk ] ; then exit 1; fi`
`67`	`70`	`-`