chore: move tests/tools/input to tests/input

stjudecloud · Nov 25, 2024 · f75b2b9 · f75b2b9
1 parent 48cea9c
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Showing 86 changed files with 114 additions and 144 deletions.
diff --git a/tests/tools/input/1scattered.interval_list → tests/input/1scattered.interval_list b/tests/tools/input/1scattered.interval_list → tests/input/1scattered.interval_list
diff --git a/...s/input/Aligned.sortedByCoord.out.bam.bai → ...s/input/Aligned.sortedByCoord.out.bam.bai b/...s/input/Aligned.sortedByCoord.out.bam.bai → ...s/input/Aligned.sortedByCoord.out.bam.bai
diff --git a/tests/tools/input/GRCh38.chr1_chr19.dict → tests/input/GRCh38.chr1_chr19.dict b/tests/tools/input/GRCh38.chr1_chr19.dict → tests/input/GRCh38.chr1_chr19.dict
diff --git a/tests/tools/input/GRCh38.chr1_chr19.fa.fai → tests/input/GRCh38.chr1_chr19.fa.fai b/tests/tools/input/GRCh38.chr1_chr19.fa.fai → tests/input/GRCh38.chr1_chr19.fa.fai
diff --git a/tests/tools/input/GRCh38.chr9_chr22.fa.gz → tests/input/GRCh38.chr9_chr22.fa.gz b/tests/tools/input/GRCh38.chr9_chr22.fa.gz → tests/input/GRCh38.chr9_chr22.fa.gz
diff --git a/tests/tools/input/GRCh38.chrY_chrM.fa.gz → tests/input/GRCh38.chrY_chrM.fa.gz b/tests/tools/input/GRCh38.chrY_chrM.fa.gz → tests/input/GRCh38.chrY_chrM.fa.gz
diff --git a/tests/tools/input/GRCh38.tar.gz → tests/input/GRCh38.tar.gz b/tests/tools/input/GRCh38.tar.gz → tests/input/GRCh38.tar.gz
diff --git a/...o_sapiens_assembly38.dbsnp138.top5000.vcf → ...o_sapiens_assembly38.dbsnp138.top5000.vcf b/...o_sapiens_assembly38.dbsnp138.top5000.vcf → ...o_sapiens_assembly38.dbsnp138.top5000.vcf
diff --git a/...piens_assembly38.dbsnp138.top5000.vcf.idx → ...piens_assembly38.dbsnp138.top5000.vcf.idx b/...piens_assembly38.dbsnp138.top5000.vcf.idx → ...piens_assembly38.dbsnp138.top5000.vcf.idx
diff --git a/...nd_1000G_gold_standard.indels.hg38.vcf.gz → ...nd_1000G_gold_standard.indels.hg38.vcf.gz b/...nd_1000G_gold_standard.indels.hg38.vcf.gz → ...nd_1000G_gold_standard.indels.hg38.vcf.gz
diff --git a/...000G_gold_standard.indels.hg38.vcf.gz.tbi → ...000G_gold_standard.indels.hg38.vcf.gz.tbi b/...000G_gold_standard.indels.hg38.vcf.gz.tbi → ...000G_gold_standard.indels.hg38.vcf.gz.tbi
diff --git a/.../input/SJBT031344_D1.Exome.multiqc.tar.gz → .../input/SJBT031344_D1.Exome.multiqc.tar.gz b/.../input/SJBT031344_D1.Exome.multiqc.tar.gz → .../input/SJBT031344_D1.Exome.multiqc.tar.gz
diff --git a/tests/tools/input/bwa_db.tar.gz → tests/input/bwa_db.tar.gz b/tests/tools/input/bwa_db.tar.gz → tests/input/bwa_db.tar.gz
diff --git a/tests/tools/input/chr1.interval_list → tests/input/chr1.interval_list b/tests/tools/input/chr1.interval_list → tests/input/chr1.interval_list
diff --git a/tests/tools/input/fusions.tsv → tests/input/fusions.tsv b/tests/tools/input/fusions.tsv → tests/input/fusions.tsv
diff --git a/...tools/input/gencode.v31.chr9_chr22.gtf.gz → tests/input/gencode.v31.chr9_chr22.gtf.gz b/...tools/input/gencode.v31.chr9_chr22.gtf.gz → tests/input/gencode.v31.chr9_chr22.gtf.gz
diff --git a/tests/tools/input/genes.genelengths.txt → tests/input/genes.genelengths.txt b/tests/tools/input/genes.genelengths.txt → tests/input/genes.genelengths.txt
diff --git a/tests/tools/input/genes.gtf.gz → tests/input/genes.gtf.gz b/tests/tools/input/genes.gtf.gz → tests/input/genes.gtf.gz
diff --git a/...tools/input/kraken2_custom_library.tar.gz → tests/input/kraken2_custom_library.tar.gz b/...tools/input/kraken2_custom_library.tar.gz → tests/input/kraken2_custom_library.tar.gz
diff --git a/tests/tools/input/kraken2_db.tar.gz → tests/input/kraken2_db.tar.gz b/tests/tools/input/kraken2_db.tar.gz → tests/input/kraken2_db.tar.gz
diff --git a/tests/tools/input/kraken2_taxonomy.tar.gz → tests/input/kraken2_taxonomy.tar.gz b/tests/tools/input/kraken2_taxonomy.tar.gz → tests/input/kraken2_taxonomy.tar.gz
diff --git a/tests/tools/input/pbmc_1k_v3.tar.gz → tests/input/pbmc_1k_v3.tar.gz b/tests/tools/input/pbmc_1k_v3.tar.gz → tests/input/pbmc_1k_v3.tar.gz
diff --git a/tests/tools/input/star_db.tar.gz → tests/input/star_db.tar.gz b/tests/tools/input/star_db.tar.gz → tests/input/star_db.tar.gz
diff --git a/tests/tools/input/test.bam.bai → tests/input/test.bam.bai b/tests/tools/input/test.bam.bai → tests/input/test.bam.bai
diff --git a/tests/tools/input/test.bwa_aln_pe.TPM.txt → tests/input/test.bwa_aln_pe.TPM.txt b/tests/tools/input/test.bwa_aln_pe.TPM.txt → tests/input/test.bwa_aln_pe.TPM.txt
diff --git a/tests/tools/input/test.bwa_aln_pe.bam.bai → tests/input/test.bwa_aln_pe.bam.bai b/tests/tools/input/test.bwa_aln_pe.bam.bai → tests/input/test.bwa_aln_pe.bam.bai
diff --git a/.../input/test.bwa_aln_pe.feature-counts.txt → .../input/test.bwa_aln_pe.feature-counts.txt b/.../input/test.bwa_aln_pe.feature-counts.txt → .../input/test.bwa_aln_pe.feature-counts.txt
diff --git a/...ools/input/test.bwa_aln_pe.readlength.txt → tests/input/test.bwa_aln_pe.readlength.txt b/...ools/input/test.bwa_aln_pe.readlength.txt → tests/input/test.bwa_aln_pe.readlength.txt
diff --git a/tests/tools/input/test.tar.gz → tests/input/test.tar.gz b/tests/tools/input/test.tar.gz → tests/input/test.tar.gz
diff --git a/tests/tools/input/test1.vcf.gz → tests/input/test1.vcf.gz b/tests/tools/input/test1.vcf.gz → tests/input/test1.vcf.gz
diff --git a/tests/tools/input/test1.vcf.gz.tbi → tests/input/test1.vcf.gz.tbi b/tests/tools/input/test1.vcf.gz.tbi → tests/input/test1.vcf.gz.tbi
diff --git a/tests/tools/input/test2.vcf.gz → tests/input/test2.vcf.gz b/tests/tools/input/test2.vcf.gz → tests/input/test2.vcf.gz
diff --git a/tests/tools/input/test2.vcf.gz.tbi → tests/input/test2.vcf.gz.tbi b/tests/tools/input/test2.vcf.gz.tbi → tests/input/test2.vcf.gz.tbi
diff --git a/tests/tools/input/test_R1.fq.gz → tests/input/test_R1.fq.gz b/tests/tools/input/test_R1.fq.gz → tests/input/test_R1.fq.gz
diff --git a/tests/tools/input/test_R2.fq.gz → tests/input/test_R2.fq.gz b/tests/tools/input/test_R2.fq.gz → tests/input/test_R2.fq.gz
diff --git a/...s/tools/input/test_rnaseq_variant.bam.bai → tests/input/test_rnaseq_variant.bam.bai b/...s/tools/input/test_rnaseq_variant.bam.bai → tests/input/test_rnaseq_variant.bam.bai
diff --git a/...tools/input/test_rnaseq_variant.recal.txt → tests/input/test_rnaseq_variant.recal.txt b/...tools/input/test_rnaseq_variant.recal.txt → tests/input/test_rnaseq_variant.recal.txt
diff --git a/...ut/wgs_calling_regions.hg38.interval_list → ...ut/wgs_calling_regions.hg38.interval_list b/...ut/wgs_calling_regions.hg38.interval_list → ...ut/wgs_calling_regions.hg38.interval_list
diff --git a/tests/tools/input/Aligned.sortedByCoord.out.bam b/tests/tools/input/Aligned.sortedByCoord.out.bam
diff --git a/tests/tools/input/GRCh38.chr1_chr19.fa b/tests/tools/input/GRCh38.chr1_chr19.fa
diff --git a/tests/tools/input/possorted_genome_bam.bam b/tests/tools/input/possorted_genome_bam.bam
diff --git a/tests/tools/input/test.bam b/tests/tools/input/test.bam
diff --git a/tests/tools/input/test.bwa_aln_pe.bam b/tests/tools/input/test.bwa_aln_pe.bam
diff --git a/tests/tools/input/test.extra_RG.bam b/tests/tools/input/test.extra_RG.bam
diff --git a/tests/tools/input/test.fa b/tests/tools/input/test.fa
diff --git a/tests/tools/input/test.unaccounted_read.bam b/tests/tools/input/test.unaccounted_read.bam
diff --git a/tests/tools/input/test2.bam b/tests/tools/input/test2.bam
diff --git a/tests/tools/input/test_rnaseq_variant.bam b/tests/tools/input/test_rnaseq_variant.bam
diff --git a/tests/tools/input_json/arriba.json b/tests/tools/input_json/arriba.json
@@ -1,7 +1,7 @@
 {
-    "bam": "tests/tools/input/Aligned.sortedByCoord.out.bam",
-    "gtf": "tests/tools/input/gencode.v31.chr9_chr22.gtf.gz",
-    "reference_fasta_gz": "tests/tools/input/GRCh38.chr9_chr22.fa.gz",
+    "bam": "tests/input/Aligned.sortedByCoord.out.bam",
+    "gtf": "tests/input/gencode.v31.chr9_chr22.gtf.gz",
+    "reference_fasta_gz": "tests/input/GRCh38.chr9_chr22.fa.gz",
     "disable_filters": ["blacklist"],
     "prefix": "fusions"
 }
diff --git a/tests/tools/input_json/bwa_aln.json b/tests/tools/input_json/bwa_aln.json
@@ -1,5 +1,5 @@
 {
-    "fastq": "tests/tools/input/test_R1.fq.gz",
+    "fastq": "tests/input/test_R1.fq.gz",
     "read_group": "@RG\\tID:test\\tSM:test",
-    "bwa_db_tar_gz": "tests/tools/input/bwa_db.tar.gz"
+    "bwa_db_tar_gz": "tests/input/bwa_db.tar.gz"
 }
diff --git a/tests/tools/input_json/bwa_aln_pe.json b/tests/tools/input_json/bwa_aln_pe.json
@@ -1,6 +1,6 @@
 {
-    "read_one_fastq_gz": "tests/tools/input/test_R1.fq.gz",
-    "read_two_fastq_gz": "tests/tools/input/test_R2.fq.gz",
+    "read_one_fastq_gz": "tests/input/test_R1.fq.gz",
+    "read_two_fastq_gz": "tests/input/test_R2.fq.gz",
     "read_group": "@RG\\tID:test\\tSM:test",
-    "bwa_db_tar_gz": "tests/tools/input/bwa_db.tar.gz"
+    "bwa_db_tar_gz": "tests/input/bwa_db.tar.gz"
 }
diff --git a/tests/tools/input_json/bwa_mem.json b/tests/tools/input_json/bwa_mem.json
@@ -1,5 +1,5 @@
 {
-    "read_one_fastq_gz": "tests/tools/input/test_R1.fq.gz",
+    "read_one_fastq_gz": "tests/input/test_R1.fq.gz",
     "read_group": "@RG\\tID:test\\tSM:test",
-    "bwa_db_tar_gz": "tests/tools/input/bwa_db.tar.gz"
+    "bwa_db_tar_gz": "tests/input/bwa_db.tar.gz"
 }
diff --git a/tests/tools/input_json/cellranger_count.json b/tests/tools/input_json/cellranger_count.json
@@ -1,5 +1,5 @@
 {
-    "fastqs_tar_gz": "tests/tools/input/pbmc_1k_v3.tar.gz",
-    "transcriptome_tar_gz": "tests/tools/input/GRCh38.tar.gz",
+    "fastqs_tar_gz": "tests/input/pbmc_1k_v3.tar.gz",
+    "transcriptome_tar_gz": "tests/input/GRCh38.tar.gz",
     "id": "pbmc_1k_v3"
 }
diff --git a/tests/tools/input_json/gatk4_apply_bqsr.json b/tests/tools/input_json/gatk4_apply_bqsr.json
@@ -1,5 +1,5 @@
 {
-    "bam": "tests/tools/input/test_rnaseq_variant.bam",
-    "bam_index": "tests/tools/input/test_rnaseq_variant.bam.bai",
-    "recalibration_report": "tests/tools/input/test_rnaseq_variant.recal.txt"
+    "bam": "tests/input/test_rnaseq_variant.bam",
+    "bam_index": "tests/input/test_rnaseq_variant.bam.bai",
+    "recalibration_report": "tests/input/test_rnaseq_variant.recal.txt"
 }
diff --git a/tests/tools/input_json/gatk4_base_recalibrator.json b/tests/tools/input_json/gatk4_base_recalibrator.json
@@ -1,11 +1,11 @@
 {
-    "bam": "tests/tools/input/test_rnaseq_variant.bam",
-    "bam_index": "tests/tools/input/test_rnaseq_variant.bam.bai",
-    "fasta": "tests/tools/input/GRCh38.chr1_chr19.fa",
-    "fasta_index": "tests/tools/input/GRCh38.chr1_chr19.fa.fai",
-    "dict": "tests/tools/input/GRCh38.chr1_chr19.dict",
-    "dbSNP_vcf":"tests/tools/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf",
-    "dbSNP_vcf_index": "tests/tools/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx",
-    "known_indels_sites_vcfs": ["tests/tools/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"],
-    "known_indels_sites_indices": ["tests/tools/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi"]
+    "bam": "tests/input/test_rnaseq_variant.bam",
+    "bam_index": "tests/input/test_rnaseq_variant.bam.bai",
+    "fasta": "tests/input/GRCh38.chr1_chr19.fa",
+    "fasta_index": "tests/input/GRCh38.chr1_chr19.fa.fai",
+    "dict": "tests/input/GRCh38.chr1_chr19.dict",
+    "dbSNP_vcf":"tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf",
+    "dbSNP_vcf_index": "tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx",
+    "known_indels_sites_vcfs": ["tests/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"],
+    "known_indels_sites_indices": ["tests/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi"]
 }
diff --git a/tests/tools/input_json/gatk4_haplotype_caller.json b/tests/tools/input_json/gatk4_haplotype_caller.json
@@ -1,10 +1,10 @@
 {
-    "bam": "tests/tools/input/test_rnaseq_variant.bam",
-    "bam_index": "tests/tools/input/test_rnaseq_variant.bam.bai",
-    "fasta": "tests/tools/input/GRCh38.chr1_chr19.fa", 
-    "fasta_index": "tests/tools/input/GRCh38.chr1_chr19.fa.fai",
-    "dict": "tests/tools/input/GRCh38.chr1_chr19.dict",
-    "dbSNP_vcf": "tests/tools/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf",
-    "dbSNP_vcf_index": "tests/tools/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx",
-    "interval_list": "tests/tools/input/chr1.interval_list"
+    "bam": "tests/input/test_rnaseq_variant.bam",
+    "bam_index": "tests/input/test_rnaseq_variant.bam.bai",
+    "fasta": "tests/input/GRCh38.chr1_chr19.fa", 
+    "fasta_index": "tests/input/GRCh38.chr1_chr19.fa.fai",
+    "dict": "tests/input/GRCh38.chr1_chr19.dict",
+    "dbSNP_vcf": "tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf",
+    "dbSNP_vcf_index": "tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx",
+    "interval_list": "tests/input/chr1.interval_list"
 }
diff --git a/tests/tools/input_json/gatk4_split_n_cigar_reads.json b/tests/tools/input_json/gatk4_split_n_cigar_reads.json
@@ -1,8 +1,8 @@
 {
-    "bam": "tests/tools/input/test.bam",
-    "bam_index": "tests/tools/input/test.bam.bai",
-    "fasta": "tests/tools/input/GRCh38.chr1_chr19.fa",
-    "fasta_index": "tests/tools/input/GRCh38.chr1_chr19.fa.fai",
-    "dict": "tests/tools/input/GRCh38.chr1_chr19.dict",
+    "bam": "tests/input/test.bam",
+    "bam_index": "tests/input/test.bam.bai",
+    "fasta": "tests/input/GRCh38.chr1_chr19.fa",
+    "fasta_index": "tests/input/GRCh38.chr1_chr19.fa.fai",
+    "dict": "tests/input/GRCh38.chr1_chr19.dict",
     "prefix": "split"
 }
diff --git a/tests/tools/input_json/gatk4_variant_filtration.json b/tests/tools/input_json/gatk4_variant_filtration.json
@@ -1,7 +1,7 @@
 {
-    "vcf": "tests/tools/input/test1.vcf.gz",
-    "vcf_index": "tests/tools/input/test1.vcf.gz.tbi",
-    "fasta": "tests/tools/input/GRCh38.chr1_chr19.fa",
-    "fasta_index": "tests/tools/input/GRCh38.chr1_chr19.fa.fai",
-    "dict": "tests/tools/input/GRCh38.chr1_chr19.dict"
+    "vcf": "tests/input/test1.vcf.gz",
+    "vcf_index": "tests/input/test1.vcf.gz.tbi",
+    "fasta": "tests/input/GRCh38.chr1_chr19.fa",
+    "fasta_index": "tests/input/GRCh38.chr1_chr19.fa.fai",
+    "dict": "tests/input/GRCh38.chr1_chr19.dict"
 }
diff --git a/tests/tools/input_json/kraken_build_db.json b/tests/tools/input_json/kraken_build_db.json
@@ -1,3 +1,3 @@
 {
-    "tarballs": ["tests/tools/input/kraken2_taxonomy.tar.gz", "tests/tools/input/kraken2_custom_library.tar.gz"]
+    "tarballs": ["tests/input/kraken2_taxonomy.tar.gz", "tests/input/kraken2_custom_library.tar.gz"]
 }
diff --git a/tests/tools/input_json/multiqc.json b/tests/tools/input_json/multiqc.json
@@ -1,4 +1,4 @@
 {
-    "files": ["tests/tools/input/test.bwa_aln_pe.readlength.txt"],
+    "files": ["tests/input/test.bwa_aln_pe.readlength.txt"],
     "prefix": "test.bwa_aln_pe"
 }
diff --git a/tests/tools/input_json/ngsderive_encoding.json b/tests/tools/input_json/ngsderive_encoding.json
@@ -1,4 +1,4 @@
 {
-    "ngs_files": ["tests/tools/input/test.bwa_aln_pe.bam"],
+    "ngs_files": ["tests/input/test.bwa_aln_pe.bam"],
     "outfile_name": "test.bwa_aln_pe.encoding.tsv"
 }
diff --git a/tests/tools/input_json/picard_merge_sam_files.json b/tests/tools/input_json/picard_merge_sam_files.json
@@ -1,4 +1,4 @@
 {
-    "bams": ["tests/tools/input/possorted_genome_bam.bam", "tests/tools/input/test.bwa_aln_pe.bam"],
+    "bams": ["tests/input/possorted_genome_bam.bam", "tests/input/test.bwa_aln_pe.bam"],
     "prefix": "test"
 }
diff --git a/tests/tools/input_json/picard_merge_vcfs.json b/tests/tools/input_json/picard_merge_vcfs.json
@@ -1,5 +1,5 @@
 {
-    "vcfs": ["tests/tools/input/test1.vcf.gz", "tests/tools/input/test2.vcf.gz"],
-    "vcfs_indexes": ["tests/tools/input/test1.vcf.gz.tbi", "tests/tools/input/test2.vcf.gz.tbi"],
+    "vcfs": ["tests/input/test1.vcf.gz", "tests/input/test2.vcf.gz"],
+    "vcfs_indexes": ["tests/input/test1.vcf.gz.tbi", "tests/input/test2.vcf.gz.tbi"],
     "output_vcf_name": "test.vcf.gz"
 }
diff --git a/tests/tools/input_json/sambamba_merge.json b/tests/tools/input_json/sambamba_merge.json
@@ -1,4 +1,4 @@
 {
-    "bams": ["tests/tools/input/possorted_genome_bam.bam", "tests/tools/input/test.bwa_aln_pe.bam"],
+    "bams": ["tests/input/possorted_genome_bam.bam", "tests/input/test.bwa_aln_pe.bam"],
     "prefix": "test"
 }
diff --git a/tests/tools/input_json/samtools_merge.json b/tests/tools/input_json/samtools_merge.json
@@ -1,4 +1,4 @@
 {
-    "bams": ["tests/tools/input/test2.bam", "tests/tools/input/test.bwa_aln_pe.bam"],
+    "bams": ["tests/input/test2.bam", "tests/input/test.bwa_aln_pe.bam"],
     "prefix": "test"
 }
diff --git a/tests/tools/input_json/star_alignment.json b/tests/tools/input_json/star_alignment.json
@@ -1,7 +1,7 @@
 {
-    "read_one_fastqs_gz": ["tests/tools/input/test_R1.fq.gz"],
-    "read_two_fastqs_gz": ["tests/tools/input/test_R2.fq.gz"],
-    "star_db_tar_gz": "tests/tools/input/star_db.tar.gz",
+    "read_one_fastqs_gz": ["tests/input/test_R1.fq.gz"],
+    "read_two_fastqs_gz": ["tests/input/test_R2.fq.gz"],
+    "star_db_tar_gz": "tests/input/star_db.tar.gz",
     "prefix": "test",
     "read_groups": "ID:test"
 }
diff --git a/tests/tools/test_arriba.yaml b/tests/tools/test_arriba.yaml
@@ -13,7 +13,7 @@
     - miniwdl
     - arriba
   command: >-
-    miniwdl run -d test-output/. --task arriba_tsv_to_vcf tools/arriba.wdl fusions="tests/tools/input/fusions.tsv" reference_fasta="tests/tools/input/GRCh38.chr9_chr22.fa.gz"
+    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"
   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/tools/input/fusions.tsv" bam="tests/tools/input/Aligned.sortedByCoord.out.bam" bam_index="tests/tools/input/Aligned.sortedByCoord.out.bam.bai"
+    miniwdl run -d test-output/. --task arriba_extract_fusion_supporting_alignments tools/arriba.wdl fusions="tests/input/fusions.tsv" bam="tests/input/Aligned.sortedByCoord.out.bam" bam_index="tests/input/Aligned.sortedByCoord.out.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/tools/input/fusions.tsv" gtf="tests/tools/input/gencode.v31.chr9_chr22.gtf.gz"
+    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"
   files:
     - path: test-output/out/fusion_tsv/fusions.annotated.tsv
diff --git a/tests/tools/test_bwa.yaml b/tests/tools/test_bwa.yaml
@@ -31,6 +31,6 @@
     - bwa
     - reference
   command: >-
-    miniwdl run --verbose -d test-output/. --task build_bwa_db tools/bwa.wdl reference_fasta="tests/tools/input/GRCh38.chrY_chrM.fa.gz"
+    miniwdl run --verbose -d test-output/. --task build_bwa_db tools/bwa.wdl reference_fasta="tests/input/GRCh38.chrY_chrM.fa.gz"
   files:
     - path: test-output/out/bwa_db_tar_gz/bwa_db.tar.gz
diff --git a/tests/tools/test_cellranger.yaml b/tests/tools/test_cellranger.yaml
@@ -25,7 +25,7 @@
     - miniwdl
     - cellranger
   command: >-
-    miniwdl run --verbose -d test-output/. --task bamtofastq tools/cellranger.wdl bam="tests/tools/input/possorted_genome_bam.bam"
+    miniwdl run --verbose -d test-output/. --task bamtofastq tools/cellranger.wdl bam="tests/input/possorted_genome_bam.bam"
   files:
     - path: test-output/out/fastqs/0/bamtofastq_S1_L001_R1_001.fastq.gz
     - path: test-output/out/fastqs/1/bamtofastq_S1_L001_R2_001.fastq.gz

diff --git a/tests/tools/test_deeptools.yaml b/tests/tools/test_deeptools.yaml
@@ -3,6 +3,6 @@
     - miniwdl
     - deeptools
   command: >-
-    miniwdl run --verbose -d test-output/. --task bam_coverage tools/deeptools.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" bam_index="tests/tools/input/test.bwa_aln_pe.bam.bai"
+    miniwdl run --verbose -d test-output/. --task bam_coverage tools/deeptools.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai"
   files:
     - path: test-output/out/bigwig/test.bwa_aln_pe.bw
diff --git a/tests/tools/test_estimate.yaml b/tests/tools/test_estimate.yaml
@@ -5,6 +5,6 @@
     - estimate
     - deprecated
   command: >-
-    miniwdl run --verbose -d test-output/. --task run_estimate tools/estimate.wdl gene_expression_file="tests/tools/input/test.bwa_aln_pe.TPM.txt"
+    miniwdl run --verbose -d test-output/. --task run_estimate tools/estimate.wdl gene_expression_file="tests/input/test.bwa_aln_pe.TPM.txt"
   files:
     - path: test-output/out/estimate_file/test.bwa_aln_pe.ESTIMATE.gct
diff --git a/tests/tools/test_fastqc.yaml b/tests/tools/test_fastqc.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - fastqc
   command: >-
-    miniwdl run --verbose -d test-output/. --task fastqc tools/fastqc.wdl bam="tests/tools/input/test.bwa_aln_pe.bam"
+    miniwdl run --verbose -d test-output/. --task fastqc tools/fastqc.wdl bam="tests/input/test.bwa_aln_pe.bam"
   files:
     - path: test-output/out/raw_data/test.bwa_aln_pe_fastqc.zip
     - path: test-output/out/results/test.bwa_aln_pe.fastqc_results.tar.gz
diff --git a/tests/tools/test_fq.yaml b/tests/tools/test_fq.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - fq
   command: >-
-    miniwdl run --verbose -d test-output/. --task fqlint tools/fq.wdl read_one_fastq=tests/tools/input/test_R1.fq.gz read_two_fastq=tests/tools/input/test_R2.fq.gz
+    miniwdl run --verbose -d test-output/. --task fqlint tools/fq.wdl read_one_fastq=tests/input/test_R1.fq.gz read_two_fastq=tests/input/test_R2.fq.gz
   stdout:
     contains_regex:
       - "passed"
@@ -13,7 +13,7 @@
     - miniwdl
     - fq
   command: >-
-    miniwdl run --verbose -d test-output/. --task subsample tools/fq.wdl read_one_fastq=tests/tools/input/test_R1.fq.gz read_two_fastq=tests/tools/input/test_R2.fq.gz record_count=1000
+    miniwdl run --verbose -d test-output/. --task subsample tools/fq.wdl read_one_fastq=tests/input/test_R1.fq.gz read_two_fastq=tests/input/test_R2.fq.gz record_count=1000
   files:
     - path: test-output/out/subsampled_read1/test_R1.subsampled.fastq.gz
     - path: test-output/out/subsampled_read2/test_R2.subsampled.fastq.gz
@@ -23,7 +23,7 @@
     - miniwdl
     - fq
   command: >-
-    miniwdl run --verbose -d test-output/. --task subsample tools/fq.wdl read_one_fastq=tests/tools/input/test_R1.fq.gz read_two_fastq=tests/tools/input/test_R2.fq.gz probability=0.01
+    miniwdl run --verbose -d test-output/. --task subsample tools/fq.wdl read_one_fastq=tests/input/test_R1.fq.gz read_two_fastq=tests/input/test_R2.fq.gz probability=0.01
   files:
     - path: test-output/out/subsampled_read1/test_R1.subsampled.fastq.gz
     - path: test-output/out/subsampled_read2/test_R2.subsampled.fastq.gz
diff --git a/tests/tools/test_gatk4.yaml b/tests/tools/test_gatk4.yaml
@@ -53,7 +53,7 @@
     - miniwdl
     - gatk4
   command: >-
-    miniwdl run --verbose -d test-output/. --task mark_duplicates_spark tools/gatk4.wdl bam="tests/tools/input/test.bwa_aln_pe.bam"
+    miniwdl run --verbose -d test-output/. --task mark_duplicates_spark tools/gatk4.wdl bam="tests/input/test.bwa_aln_pe.bam"
   files:
     - path: test-output/out/duplicate_marked_bam/test.bwa_aln_pe.MarkDuplicates.bam
     - path: test-output/out/duplicate_marked_bam_index/test.bwa_aln_pe.MarkDuplicates.bam.bai

diff --git a/tests/tools/test_htseq.yaml b/tests/tools/test_htseq.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - htseq
   command: >-
-    miniwdl run --verbose -d test-output/. --task count tools/htseq.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" gtf="tests/tools/input/genes.gtf.gz" strandedness="no"
+    miniwdl run --verbose -d test-output/. --task count tools/htseq.wdl bam="tests/input/test.bwa_aln_pe.bam" gtf="tests/input/genes.gtf.gz" strandedness="no"
   files:
     - path: test-output/out/feature_counts/test.bwa_aln_pe.feature-counts.txt
 
@@ -12,6 +12,6 @@
     - miniwdl
     - htseq
   command: >-
-    miniwdl run --verbose -d test-output/. --task calc_tpm tools/htseq.wdl counts="tests/tools/input/test.bwa_aln_pe.feature-counts.txt" gene_lengths="tests/tools/input/genes.genelengths.txt"
+    miniwdl run --verbose -d test-output/. --task calc_tpm tools/htseq.wdl counts="tests/input/test.bwa_aln_pe.feature-counts.txt" gene_lengths="tests/input/genes.genelengths.txt"
   files:
     - path: test-output/out/tpm_file/test.bwa_aln_pe.TPM.txt
diff --git a/tests/tools/test_kraken2.yaml b/tests/tools/test_kraken2.yaml
@@ -43,6 +43,6 @@
     - miniwdl
     - kraken
   command: >-
-    miniwdl run --verbose -d test-output/. --task kraken tools/kraken2.wdl read_one_fastq_gz="tests/tools/input/test_R1.fq.gz" read_two_fastq_gz="tests/tools/input/test_R2.fq.gz" db="tests/tools/input/kraken2_db.tar.gz"
+    miniwdl run --verbose -d test-output/. --task kraken tools/kraken2.wdl read_one_fastq_gz="tests/input/test_R1.fq.gz" read_two_fastq_gz="tests/input/test_R2.fq.gz" db="tests/input/kraken2_db.tar.gz"
   files:
     - path: test-output/out/report/test.kraken2.txt
diff --git a/tests/tools/test_librarian.yaml b/tests/tools/test_librarian.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - librarian
   command: >-
-    miniwdl run --verbose -d test-output/. --task librarian tools/librarian.wdl read_one_fastq="tests/tools/input/test_R1.fq.gz"
+    miniwdl run --verbose -d test-output/. --task librarian tools/librarian.wdl read_one_fastq="tests/input/test_R1.fq.gz"
   files:
     - path: test-output/out/report/test.librarian.tar.gz
     - path: test-output/out/raw_data/librarian_heatmap.txt
diff --git a/tests/tools/test_md5sum.yaml b/tests/tools/test_md5sum.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - md5sum
   command: >-
-    miniwdl run --verbose -d test-output/. --task compute_checksum tools/md5sum.wdl file="tests/tools/input/test.bwa_aln_pe.bam"
+    miniwdl run --verbose -d test-output/. --task compute_checksum tools/md5sum.wdl file="tests/input/test.bwa_aln_pe.bam"
   files:
     - path: test-output/out/md5sum/test.bwa_aln_pe.bam.md5
       contains:

diff --git a/tests/tools/test_mosdepth.yaml b/tests/tools/test_mosdepth.yaml
@@ -3,7 +3,7 @@
     - miniwdl
     - mosdepth
   command: >-
-    miniwdl run --verbose -d test-output/. --task coverage tools/mosdepth.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" bam_index="tests/tools/input/test.bwa_aln_pe.bam.bai"
+    miniwdl run --verbose -d test-output/. --task coverage tools/mosdepth.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai"
   files:
     - path: test-output/out/summary/test.bwa_aln_pe.mosdepth.summary.txt
     - path: test-output/out/global_dist/test.bwa_aln_pe.mosdepth.global.dist.txt