test: Add --outdir

tests/test_default.yml

@@ -1,6 +1,6 @@
 # NOTE For now these tests don't support any containers beside docker
 - name: Run default pipeline with test data
-  command: nextflow run main.nf -profile test,docker
+  command: nextflow run main.nf -profile test,docker --outdir results
   tags:
     - default
   files:

tests/test_hisat2.yml

@@ -1,12 +1,12 @@
 # NOTE For now these tests don't support any containers beside docker
 - name: Test HISAT2 with skip_qc workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner hisat2 --skip_qc
+  command: nextflow run main.nf -profile test,docker --aligner hisat2 --skip_qc --outdir results
   tags:
     - hisat2
     - skip_qc
 
 - name: Test HISAT2 with hisat2_index false workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner hisat2 --hisat2_index false
+  command: nextflow run main.nf -profile test,docker --aligner hisat2 --hisat2_index false --outdir results
   tags:
     - hisat2
-    - "hisat2_index false"
+    - 'hisat2_index false'

tests/test_salmon.yml

@@ -1,14 +1,14 @@
 # NOTE For now these tests don't support any containers beside docker
 - name: Test Salmon with skip_qc skip_alignment workflow parameters
-  command: nextflow run main.nf -profile test,docker --pseudo_aligner salmon --skip_qc --skip_alignment
+  command: nextflow run main.nf -profile test,docker --pseudo_aligner salmon --skip_qc --skip_alignment --outdir results
   tags:
     - salmon
     - skip_qc
     - skip_alignment
     - "skip_qc skip_alignment"
 
 - name: Test Salmon with salmon_index false transcript_fasta false workflow parameters
-  command: nextflow run main.nf -profile test,docker --salmon_index false --transcript_fasta false
+  command: nextflow run main.nf -profile test,docker --salmon_index false --transcript_fasta false --outdir results
   tags:
     - salmon
     - salmon_index

tests/test_sra_download.yml

@@ -1,5 +1,5 @@
 # NOTE For now these tests don't support any containers beside docker
 - name: Run pipeline to download public data
-  command: nextflow run main.nf -profile test_sra,docker
+  command: nextflow run main.nf -profile test_sra,docker --outdir results
   tags:
     - sra_download

tests/test_star_rsem.yml

@@ -1,13 +1,13 @@
 # NOTE For now these tests don't support any containers beside docker
 - name: Test STAR RSEM with skip_qc workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_rsem --skip_qc
+  command: nextflow run main.nf -profile test,docker --aligner star_rsem --skip_qc --outdir results
   tags:
     - star
     - rsem
     - skip_qc
 
 - name: Test STAR RSEM with rsem_index false workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_rsem --rsem_index false
+  command: nextflow run main.nf -profile test,docker --aligner star_rsem --rsem_index false --outdir results
   tags:
     - star
     - rsem

tests/test_star_salmon.yml

@@ -1,13 +1,13 @@
 # NOTE For now these tests don't support any containers beside docker
 - name: Test STAR Salmon with skip_qc workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --skip_qc
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --skip_qc --outdir results
   tags:
     - star
     - salmon
     - skip_qc
 
 - name: Test STAR Salmon with remove_ribo_rna workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --remove_ribo_rna
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --remove_ribo_rna --outdir results
   tags:
     - star
     - salmon
@@ -16,71 +16,71 @@
   exit_code: 1
 
 - name: Test STAR Salmon with skim_trimming workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --skim_trimming
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --skim_trimming --outdir results
   tags:
     - star
     - salmon
     - skim_trimming
 
 - name: Test STAR Salmon with gtf false workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --gtf false
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --gtf false --outdir results
   tags:
     - star
     - salmon
     - "gtf false"
 
 - name: Test STAR Salmon with star_index false workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --star_index false
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --star_index false --outdir results
   tags:
     - star
     - salmon
     - "star_index false"
 
 - name: Test STAR Salmon with transcript_fasta false workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --transcript_fasta false
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --transcript_fasta false --outdir results
   tags:
     - star
     - salmon
     - "transcript_fasta"
 
 - name: Test STAR Salmon with min_mapped_reads 90 workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --min_mapped_reads 90
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --min_mapped_reads 90 --outdir results
   tags:
     - star
     - salmon
     - "min_mapped_reads 90"
 
 - name: Test STAR Salmon with with_umi workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --with_umi
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --with_umi --outdir results
   tags:
     - star
     - salmon
     - with_umi
 
 - name: Test STAR Salmon with with_umi skip_trimming workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --with_umi --skip_trimming
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --with_umi --skip_trimming --outdir results
   tags:
     - star
     - salmon
     - with_umi
     - skip_trimming
 
 - name: Test STAR Salmon with bam_csi_index workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --bam_csi_index
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --bam_csi_index --outdir results
   tags:
     - star
     - salmon
     - "bam_csi_index"
 
 - name: Test STAR Salmon with save_align_intermeds save_reference workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --save_align_intermeds --save_reference
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --save_align_intermeds --save_reference --outdir results
   tags:
     - star
     - salmon
     - "save_reference"
 
 - name: Test STAR Salmon with featurecounts_group_type false workflow parameters
-  command: nextflow run main.nf -profile test,docker --aligner star_salmon --featurecounts_group_type false
+  command: nextflow run main.nf -profile test,docker --aligner star_salmon --featurecounts_group_type false --outdir results
   tags:
     - star
     - salmon