fix:

tests/input/test.bwa_aln_pe.readlength.txt

@@ -1,2 +1,2 @@
 File	Evidence	MajorityPctDetected	ConsensusReadLength
-test.bwa_aln_pe.bam	150=20000	1.0	150
+test.bwa_aln_pe.chrY_chrM.bam	150=20000	1.0	150

tests/tools/input_json/multiqc.json

@@ -1,4 +1,4 @@
 {
-    "files": ["tests/input/test.bwa_aln_pe.readlength.txt"],
+    "files": ["tests/input/test.bwa_aln_pe.chrY_chrM.readlength.txt"],
     "prefix": "test.bwa_aln_pe"
 }

tests/tools/input_json/ngsderive_encoding.json

@@ -1,4 +1,4 @@
 {
     "ngs_files": ["tests/input/test.bwa_aln_pe.chrY_chrM.bam"],
-    "outfile_name": "test.bwa_aln_pe.encoding.tsv"
+    "outfile_name": "test.bwa_aln_pe.chrY_chrM.encoding.tsv"
 }

tests/tools/test_deeptools.yaml

@@ -5,4 +5,4 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task bam_coverage tools/deeptools.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" bam_index="tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai"
   files:
-    - path: test-output/out/bigwig/test.bwa_aln_pe.bw
+    - path: test-output/out/bigwig/test.bwa_aln_pe.chrY_chrM.bw

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/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.chrY_chrM.TPM.txt"
   files:
-    - path: test-output/out/estimate_file/test.bwa_aln_pe.ESTIMATE.gct
+    - path: test-output/out/estimate_file/test.bwa_aln_pe.chrY_chrM.ESTIMATE.gct

tests/tools/test_fastqc.yaml

@@ -6,4 +6,4 @@
     miniwdl run --verbose -d test-output/. --task fastqc tools/fastqc.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.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
+    - path: test-output/out/results/test.bwa_aln_pe.chrY_chrM.fastqc_results.tar.gz

tests/tools/test_gatk4.yaml

@@ -55,6 +55,6 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task mark_duplicates_spark tools/gatk4.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.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
-    - path: test-output/out/mark_duplicates_metrics/test.bwa_aln_pe.MarkDuplicates.metrics.txt
+    - path: test-output/out/duplicate_marked_bam/test.bwa_aln_pe.chrY_chrM.MarkDuplicates.bam
+    - path: test-output/out/duplicate_marked_bam_index/test.bwa_aln_pe.chrY_chrM.MarkDuplicates.bam.bai
+    - path: test-output/out/mark_duplicates_metrics/test.bwa_aln_pe.chrY_chrM.MarkDuplicates.metrics.txt

tests/tools/test_htseq.yaml

@@ -5,13 +5,13 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task count tools/htseq.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" gtf="tests/input/gencode.v31.chrY_chrM.gtf.gz" strandedness="no"
   files:
-    - path: test-output/out/feature_counts/test.bwa_aln_pe.feature-counts.txt
+    - path: test-output/out/feature_counts/test.bwa_aln_pe.chrY_chrM.feature-counts.txt
 
 - name: calc_tpm
   tags:
     - miniwdl
     - htseq
   command: >-
-    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/gencode.v31.chrY_chrM.genelengths.txt"
+    miniwdl run --verbose -d test-output/. --task calc_tpm tools/htseq.wdl counts="tests/input/test.bwa_aln_pe.chrY_chrM.feature-counts.txt" gene_lengths="tests/input/gencode.v31.chrY_chrM.genelengths.txt"
   files:
-    - path: test-output/out/tpm_file/test.bwa_aln_pe.TPM.txt
+    - path: test-output/out/tpm_file/test.bwa_aln_pe.chrY_chrM.TPM.txt

tests/tools/test_md5sum.yaml

@@ -5,6 +5,6 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task compute_checksum tools/md5sum.wdl file="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: test-output/out/md5sum/test.bwa_aln_pe.bam.md5
+    - path: test-output/out/md5sum/test.bwa_aln_pe.chrY_chrM.bam.md5
       contains:
         - "77fa2f59b0083202c73b0c80b60b24f6"

tests/tools/test_mosdepth.yaml

@@ -5,5 +5,5 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task coverage tools/mosdepth.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" bam_index="tests/input/test.bwa_aln_pe.chrY_chrM.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
+    - path: test-output/out/summary/test.bwa_aln_pe.chrY_chrM.mosdepth.summary.txt
+    - path: test-output/out/global_dist/test.bwa_aln_pe.chrY_chrM.mosdepth.global.dist.txt

tests/tools/test_multiqc.yaml

@@ -5,4 +5,4 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task multiqc -i tests/tools/input_json/multiqc.json tools/multiqc.wdl
   files:
-    - path: test-output/out/multiqc_report/test.bwa_aln_pe.tar.gz
+    - path: test-output/out/multiqc_report/test.bwa_aln_pe.chrY_chrM.tar.gz

tests/tools/test_ngsderive.yaml

@@ -5,7 +5,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task strandedness tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" bam_index="tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai" gene_model="tests/input/gencode.v31.chrY_chrM.gtf.gz"
   files:
-    - path: test-output/out/strandedness_file/test.bwa_aln_pe.strandedness.tsv
+    - path: test-output/out/strandedness_file/test.bwa_aln_pe.chrY_chrM.strandedness.tsv
       contains:
         - "Unstranded"
 
@@ -16,7 +16,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task instrument tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: test-output/out/instrument_file/test.bwa_aln_pe.instrument.tsv
+    - path: test-output/out/instrument_file/test.bwa_aln_pe.chrY_chrM.instrument.tsv
       contains:
         - "multiple instruments"
         - "unknown confidence"
@@ -28,7 +28,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task read_length tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" bam_index="tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai"
   files:
-    - path: test-output/out/read_length_file/test.bwa_aln_pe.readlength.tsv
+    - path: test-output/out/read_length_file/test.bwa_aln_pe.chrY_chrM.readlength.tsv
       contains:
         - "150=20000"
 
@@ -39,7 +39,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task encoding -i tests/tools/input_json/ngsderive_encoding.json tools/ngsderive.wdl
   files:
-    - path: test-output/out/encoding_file/test.bwa_aln_pe.encoding.tsv
+    - path: test-output/out/encoding_file/test.bwa_aln_pe.chrY_chrM.encoding.tsv
       contains:
         - "ASCII range: 74-74"
         - "Illumina 1.3"
@@ -51,8 +51,8 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task junction_annotation tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" bam_index="tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai" gene_model="tests/input/gencode.v31.chrY_chrM.gtf.gz"
   files:
-    - path: test-output/out/junction_summary/test.bwa_aln_pe.junction_summary.tsv
-    - path: test-output/out/junctions/test.bwa_aln_pe.junctions.tsv.gz
+    - path: test-output/out/junction_summary/test.bwa_aln_pe.chrY_chrM.junction_summary.tsv
+    - path: test-output/out/junctions/test.bwa_aln_pe.chrY_chrM.junctions.tsv.gz
 
 - name: endedness
   tags:
@@ -61,4 +61,4 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task endedness tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: test-output/out/endedness_file/test.bwa_aln_pe.endedness.tsv
+    - path: test-output/out/endedness_file/test.bwa_aln_pe.chrY_chrM.endedness.tsv

tests/tools/test_picard.py

@@ -3,5 +3,5 @@
 
 @pytest.mark.workflow('picard_sort_queryname')
 def test_picard_sort_queryname(workflow_dir):
-    exists = pathlib.Path(workflow_dir, 'test-output/out/sorted_bam_index/test.bwa_aln_pe.sorted.bam.bai').exists()
+    exists = pathlib.Path(workflow_dir, 'test-output/out/sorted_bam_index/test.bwa_aln_pe.chrY_chrM.sorted.bam.bai').exists()
     assert exists is False

tests/tools/test_picard.yaml

@@ -5,10 +5,10 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task mark_duplicates tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.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
-    - path: test-output/out/duplicate_marked_bam_md5/test.bwa_aln_pe.MarkDuplicates.bam.md5
-    - path: test-output/out/mark_duplicates_metrics/test.bwa_aln_pe.MarkDuplicates.metrics.txt
+    - path: test-output/out/duplicate_marked_bam/test.bwa_aln_pe.chrY_chrM.MarkDuplicates.bam
+    - path: test-output/out/duplicate_marked_bam_index/test.bwa_aln_pe.chrY_chrM.MarkDuplicates.bam.bai
+    - path: test-output/out/duplicate_marked_bam_md5/test.bwa_aln_pe.chrY_chrM.MarkDuplicates.bam.md5
+    - path: test-output/out/mark_duplicates_metrics/test.bwa_aln_pe.chrY_chrM.MarkDuplicates.metrics.txt
 
 - name: picard_validate_bam
   tags:
@@ -17,7 +17,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task validate_bam tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: test-output/out/validate_report/test.bwa_aln_pe.ValidateSamFile.txt
+    - path: test-output/out/validate_report/test.bwa_aln_pe.chrY_chrM.ValidateSamFile.txt
 
 - name: picard_bam_to_fastq
   tags:
@@ -36,8 +36,8 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task sort tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" memory_gb=16
   files:
-    - path: test-output/out/sorted_bam/test.bwa_aln_pe.sorted.bam
-    - path: test-output/out/sorted_bam_index/test.bwa_aln_pe.sorted.bam.bai
+    - path: test-output/out/sorted_bam/test.bwa_aln_pe.chrY_chrM.sorted.bam
+    - path: test-output/out/sorted_bam_index/test.bwa_aln_pe.chrY_chrM.sorted.bam.bai
 
 - name: picard_sort_queryname
   tags:
@@ -46,7 +46,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task sort tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" memory_gb=16 sort_order="queryname"
   files:
-    - path: test-output/out/sorted_bam/test.bwa_aln_pe.sorted.bam
+    - path: test-output/out/sorted_bam/test.bwa_aln_pe.chrY_chrM.sorted.bam
 
 - name: picard_merge_sam_files
   tags:
@@ -113,8 +113,8 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task quality_score_distribution tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: test-output/out/quality_score_distribution_txt/test.bwa_aln_pe.QualityScoreDistribution.txt
-    - path: test-output/out/quality_score_distribution_pdf/test.bwa_aln_pe.QualityScoreDistribution.pdf
+    - path: test-output/out/quality_score_distribution_txt/test.bwa_aln_pe.chrY_chrM.QualityScoreDistribution.txt
+    - path: test-output/out/quality_score_distribution_pdf/test.bwa_aln_pe.chrY_chrM.QualityScoreDistribution.pdf
 
 - name: picard_merge_vcfs
   tags:

tests/tools/test_qualimap.yaml

@@ -6,7 +6,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task bamqc tools/qualimap.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: test-output/out/results/test.bwa_aln_pe.qualimap_bamqc_results.tar.gz
+    - path: test-output/out/results/test.bwa_aln_pe.chrY_chrM.qualimap_bamqc_results.tar.gz
 
 - name: qualimap_rnaseq
   tags:
@@ -15,6 +15,6 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task rnaseq tools/qualimap.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" gtf="tests/input/gencode.v31.chrY_chrM.gtf.gz"
   files:
-    - path: test-output/out/results/test.bwa_aln_pe.qualimap_rnaseq_results.tar.gz
+    - path: test-output/out/results/test.bwa_aln_pe.chrY_chrM.qualimap_rnaseq_results.tar.gz
     - path: test-output/out/raw_summary/rnaseq_qc_results.txt
     - path: test-output/out/raw_coverage/coverage_profile_along_genes_(total).txt

tests/tools/test_sambamba.yaml

@@ -5,7 +5,7 @@
   command: >-
     miniwdl run -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.bam.bai
+    - path: test-output/out/bam_index/test.bwa_aln_pe.chrY_chrM.bam.bai
 
 - name: sambamba_merge
   tags:
@@ -23,7 +23,7 @@
   command: >-
     miniwdl run -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.sorted.bam
+    - path: test-output/out/sorted_bam/test.bwa_aln_pe.chrY_chrM.sorted.bam
 
 - name: sambamba_flagstat
   tags:
@@ -32,7 +32,7 @@
   command: >-
     miniwdl run -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.flagstat.txt
+    - path: test-output/out/flagstat_report/test.bwa_aln_pe.chrY_chrM.flagstat.txt
 
 - name: sambamba_markdup
   tags:
@@ -41,6 +41,6 @@
   command: >-
     miniwdl run -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.markdup.bam
-    - path: test-output/out/duplicate_marked_bam_index/test.bwa_aln_pe.markdup.bam.bai
-    - path: test-output/out/markdup_log/test.bwa_aln_pe.markdup_log.txt
+    - 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
+    - path: test-output/out/markdup_log/test.bwa_aln_pe.chrY_chrM.markdup_log.txt

tests/tools/test_samtools.py

@@ -44,8 +44,8 @@ def test_samtools_collate(workflow_dir):
 
 @pytest.mark.workflow('samtools_bam_to_fastq', 'samtools_collate_to_fastq')
 def test_samtools_bam_to_fastq(workflow_dir):
-    fq1 = fastq.read(pathlib.Path(workflow_dir, 'test-output/out/read_one_fastq_gz/test.bwa_aln_pe.R1.fastq.gz'))
-    fq2 = fastq.read(pathlib.Path(workflow_dir, 'test-output/out/read_two_fastq_gz/test.bwa_aln_pe.R2.fastq.gz'))
+    fq1 = fastq.read(pathlib.Path(workflow_dir, 'test-output/out/read_one_fastq_gz/test.bwa_aln_pe.chrY_chrM.R1.fastq.gz'))
+    fq2 = fastq.read(pathlib.Path(workflow_dir, 'test-output/out/read_two_fastq_gz/test.bwa_aln_pe.chrY_chrM.R2.fastq.gz'))
 
     for r1, r2 in zip(fq1, fq2):
         assert r1.head.removesuffix("/1") == r2.head.removesuffix("/2")

tests/tools/test_samtools.yaml

@@ -41,7 +41,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task flagstat tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: test-output/out/flagstat_report/test.bwa_aln_pe.flagstat.txt
+    - path: test-output/out/flagstat_report/test.bwa_aln_pe.chrY_chrM.flagstat.txt
       contains:
         - "20000"
         - "0 + 0 secondary"
@@ -56,7 +56,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task index tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: test-output/out/bam_index/test.bwa_aln_pe.bam.bai
+    - path: test-output/out/bam_index/test.bwa_aln_pe.chrY_chrM.bam.bai
 
 - name: samtools_subsample
   tags:
@@ -83,7 +83,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task addreplacerg tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" read_group_id="test"
   files:
-    - path: test-output/out/tagged_bam/test.bwa_aln_pe.addreplacerg.bam
+    - path: test-output/out/tagged_bam/test.bwa_aln_pe.chrY_chrM.addreplacerg.bam
 
 - name: samtools_collate
   tags:
@@ -102,8 +102,8 @@
     miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" retain_collated_bam=true
   files:
     - path: test-output/out/collated_bam/test.bwa_aln_pe.collated.bam
-    - path: test-output/out/read_one_fastq_gz/test.bwa_aln_pe.R1.fastq.gz
-    - path: test-output/out/read_two_fastq_gz/test.bwa_aln_pe.R2.fastq.gz
+    - path: test-output/out/read_one_fastq_gz/test.bwa_aln_pe.chrY_chrM.R1.fastq.gz
+    - path: test-output/out/read_two_fastq_gz/test.bwa_aln_pe.chrY_chrM.R2.fastq.gz
 
 - name: samtools_faidx
   tags:

tests/tools/test_util.yaml

@@ -79,7 +79,7 @@
   command: >-
       miniwdl run --verbose -d test-output/. --task add_to_bam_header tools/util.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" additional_header="@RG	ID:3"
   files:
-    - path: "test-output/out/reheadered_bam/test.bwa_aln_pe.reheader.bam"
+    - path: "test-output/out/reheadered_bam/test.bwa_aln_pe.chrY_chrM.reheader.bam"
 
 - name: unpack_tarball
   tags:
@@ -107,7 +107,7 @@
   command: >-
     miniwdl run --verbose -d test-output/. --task global_phred_scores tools/util.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam"
   files:
-    - path: "test-output/out/phred_scores/test.bwa_aln_pe.global_PHRED_scores.tsv"
+    - path: "test-output/out/phred_scores/test.bwa_aln_pe.chrY_chrM.global_PHRED_scores.tsv"
 
 - name: split_fastq
   tags:

tests/workflows/input_json/rnaseq-variant-calling.json

@@ -0,0 +1,16 @@
+{
+    "rnaseq_variant_calling.bam": "tests/input/test.bwa_aln_pe.chrY_chrM.bam",
+    "rnaseq_variant_calling.bam_index": "tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai",
+    "rnaseq_variant_calling.fasta": "tests/input/GRCh38.chrY_chrM.fa",
+    "rnaseq_variant_calling.fasta_index": "tests/input/GRCh38.chrY_chrM.fa.fai",
+    "rnaseq_variant_calling.dict": "tests/input/GRCh38.chrY_chrM.dict",
+    "rnaseq_variant_calling.calling_interval_list": "tests/input/wgs_calling_regions.hg38.interval_list",
+    "rnaseq_variant_calling.known_vcfs": [
+        "tests/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
+    ],
+    "rnaseq_variant_calling.known_vcf_indexes": [
+        "tests/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi"
+    ],
+    "rnaseq_variant_calling.dbSNP_vcf": "tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf",
+    "rnaseq_variant_calling.dbSNP_vcf_index": "tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx"
+}