chore: add --verbose flag to tests

Author: adthrasher

tests/tools/test_arriba.yaml

@@ -3,7 +3,7 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba -i tests/tools/input_json/arriba.json tools/arriba.wdl
+    miniwdl run --verbose -d test-output/. --task arriba -i tests/tools/input_json/arriba.json tools/arriba.wdl
   files:
     - path: test-output/out/fusions/fusions.tsv
     - path: test-output/out/discarded_fusions/fusions.discarded.tsv
@@ -13,7 +13,7 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba_tsv_to_vcf tools/arriba.wdl fusions="tests/input/fusions.tsv" reference_fasta="tests/input/GRCh38.chr9_chr22.fa.gz"
+    miniwdl run --verbose -d test-output/. --task arriba_tsv_to_vcf tools/arriba.wdl fusions="tests/input/fusions.tsv" reference_fasta="tests/input/GRCh38.chr9_chr22.fa.gz"
   files:
     - path: test-output/out/fusions_vcf/fusions.vcf
 
@@ -22,7 +22,7 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba_extract_fusion_supporting_alignments tools/arriba.wdl fusions="tests/input/fusions.tsv" bam="tests/input/Aligned.sortedByCoord.chr9_chr22.bam" bam_index="tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai"
+    miniwdl run --verbose -d test-output/. --task arriba_extract_fusion_supporting_alignments tools/arriba.wdl fusions="tests/input/fusions.tsv" bam="tests/input/Aligned.sortedByCoord.chr9_chr22.bam" bam_index="tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai"
   files:
     - path: test-output/out/fusion_bams/0/fusions_1.bam
 
@@ -31,6 +31,6 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba_annotate_exon_numbers tools/arriba.wdl fusions="tests/input/fusions.tsv" gtf="tests/input/gencode.v31.chr9_chr22.gtf.gz"
+    miniwdl run --verbose -d test-output/. --task arriba_annotate_exon_numbers tools/arriba.wdl fusions="tests/input/fusions.tsv" gtf="tests/input/gencode.v31.chr9_chr22.gtf.gz"
   files:
     - path: test-output/out/fusion_tsv/fusions.annotated.tsv

tests/tools/test_picard.yaml

@@ -121,7 +121,7 @@
     - miniwdl
     - picard
   command: >-
-    miniwdl run -d test-output/. --task merge_vcfs -i tests/tools/input_json/picard_merge_vcfs.json tools/picard.wdl
+    miniwdl run --verbose -d test-output/. --task merge_vcfs -i tests/tools/input_json/picard_merge_vcfs.json tools/picard.wdl
   files:
     - path: test-output/out/merged_vcf/test.vcf.gz
 
@@ -130,7 +130,7 @@
     - miniwdl
     - picard
   command: >-
-    miniwdl run -d test-output/. --task scatter_interval_list tools/picard.wdl interval_list="tests/input/wgs_calling_regions.hg38.interval_list" scatter_count=3
+    miniwdl run --verbose -d test-output/. --task scatter_interval_list tools/picard.wdl interval_list="tests/input/wgs_calling_regions.hg38.interval_list" scatter_count=3
   files:
     - path: test-output/out/interval_lists_scatter/0/1scattered.interval_list
     - path: test-output/out/interval_lists_scatter/1/2scattered.interval_list
@@ -141,6 +141,6 @@
     - miniwdl
     - picard
   command: >-
-    miniwdl run -d test-output/. --task create_sequence_dictionary tools/picard.wdl fasta="tests/input/GRCh38.chrY_chrM.fa" outfile_name="GRCh38.chrY_chrM.dict"
+    miniwdl run --verbose -d test-output/. --task create_sequence_dictionary tools/picard.wdl fasta="tests/input/GRCh38.chrY_chrM.fa" outfile_name="GRCh38.chrY_chrM.dict"
   files:
     - path: test-output/out/dictionary/GRCh38.chrY_chrM.dict

tests/tools/test_sambamba.yaml

@@ -3,7 +3,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task index tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
+    miniwdl run --verbose -d test-output/. --task index tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
     - path: test-output/out/bam_index/test.bwa_aln_pe.chrY_chrM.bam.bai
 
@@ -12,7 +12,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task merge -i tests/tools/input_json/sambamba_merge.json tools/sambamba.wdl
+    miniwdl run --verbose -d test-output/. --task merge -i tests/tools/input_json/sambamba_merge.json tools/sambamba.wdl
   files:
     - path: test-output/out/merged_bam/test.bam
 
@@ -21,7 +21,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task sort tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
+    miniwdl run --verbose -d test-output/. --task sort tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
     - path: test-output/out/sorted_bam/test.bwa_aln_pe.chrY_chrM.sorted.bam
 
@@ -30,7 +30,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task flagstat tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
+    miniwdl run --verbose -d test-output/. --task flagstat tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
     - path: test-output/out/flagstat_report/test.bwa_aln_pe.chrY_chrM.flagstat.txt
 
@@ -39,7 +39,7 @@
     - miniwdl
     - sambamba
   command: >-
-    miniwdl run -d test-output/. --task markdup tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
+    miniwdl run --verbose -d test-output/. --task markdup tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
     - path: test-output/out/duplicate_marked_bam/test.bwa_aln_pe.chrY_chrM.markdup.bam
     - path: test-output/out/duplicate_marked_bam_index/test.bwa_aln_pe.chrY_chrM.markdup.bam.bai

tests/tools/test_samtools.yaml

@@ -110,6 +110,6 @@
     - miniwdl
     - samtools
   command: >-
-    miniwdl run -d test-output/. --task faidx tools/samtools.wdl fasta="tests/input/test.fa"
+    miniwdl run --verbose -d test-output/. --task faidx tools/samtools.wdl fasta="tests/input/test.fa"
   files:
     - path: test-output/out/fasta_index/test.fa.fai

tests/tools/test_util.yaml

@@ -128,6 +128,6 @@
     - miniwdl
     - util
   command: >-
-    miniwdl run -d test-output/. --task split_fastq tools/util.wdl fastq="tests/input/test_R1.fq.gz" prefix="test.R1."
+    miniwdl run --verbose -d test-output/. --task split_fastq tools/util.wdl fastq="tests/input/test_R1.fq.gz" prefix="test.R1."
   files:
     - path: "test-output/out/fastqs/0/test.R1.000000.fastq.gz"

tests/workflows/test-methylation-cohort.yaml

@@ -3,7 +3,7 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task combine_data -i tests/workflows/input_json/combine_data.json workflows/methylation/methylation-cohort.wdl
+    miniwdl run --verbose -d test-output/. --task combine_data -i tests/workflows/input_json/combine_data.json workflows/methylation/methylation-cohort.wdl
   files:
     - path: test-output/out/combined_beta/combined_beta.csv
 
@@ -12,7 +12,7 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task filter_probes -i tests/workflows/input_json/filter_probes.json workflows/methylation/methylation-cohort.wdl
+    miniwdl run --verbose -d test-output/. --task filter_probes -i tests/workflows/input_json/filter_probes.json workflows/methylation/methylation-cohort.wdl
   files:
     - path: test-output/out/filtered_beta_values/filtered.beta.csv
     - path: test-output/out/filtered_probes/filtered.probes.csv
@@ -22,7 +22,7 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task generate_umap -i tests/workflows/input_json/generate_umap.json workflows/methylation/methylation-cohort.wdl
+    miniwdl run --verbose -d test-output/. --task generate_umap -i tests/workflows/input_json/generate_umap.json workflows/methylation/methylation-cohort.wdl
   files:
     - path: test-output/out/umap/umap.csv
 
@@ -31,6 +31,6 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task plot_umap -i tests/workflows/input_json/plot_umap.json workflows/methylation/methylation-cohort.wdl
+    miniwdl run --verbose -d test-output/. --task plot_umap -i tests/workflows/input_json/plot_umap.json workflows/methylation/methylation-cohort.wdl
   files:
     - path: test-output/out/umap_plot/umap.png

tests/workflows/test-methylation-preprocess.yaml

@@ -3,7 +3,7 @@
     - miniwdl
     - methylation
   command: >-
-    miniwdl run -d test-output/. --task process_raw_idats -i tests/workflows/input_json/process_raw_idats.json workflows/methylation/methylation-preprocess.wdl
+    miniwdl run --verbose -d test-output/. --task process_raw_idats -i tests/workflows/input_json/process_raw_idats.json workflows/methylation/methylation-preprocess.wdl
   files:
     - path: test-output/out/beta_swan_norm_unfiltered/201533520001_R03C01.beta_swan_norm_unfiltered.csv
     - path: test-output/out/beta_swan_norm_unfiltered_genomic/201533520001_R03C01.beta_swan_norm_unfiltered.genomic.csv