From 8f8e2fdd94af2a36365d883764ff6d1fc96c64c1 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 11:50:52 -0500 Subject: [PATCH 01/25] chore: mv tests/tools/input to tests/input --- tests/{tools => }/input/1scattered.interval_list | 0 .../{tools => }/input/Aligned.sortedByCoord.out.bam | 0 .../input/Aligned.sortedByCoord.out.bam.bai | 0 tests/{tools => }/input/GRCh38.chr1_chr19.dict | 0 tests/{tools => }/input/GRCh38.chr1_chr19.fa | 0 tests/{tools => }/input/GRCh38.chr1_chr19.fa.fai | 0 tests/{tools => }/input/GRCh38.chr9_chr22.fa.gz | 0 tests/{tools => }/input/GRCh38.chrY_chrM.fa.gz | 0 tests/{tools => }/input/GRCh38.tar.gz | 0 .../Homo_sapiens_assembly38.dbsnp138.top5000.vcf | 0 ...Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx | Bin ...Mills_and_1000G_gold_standard.indels.hg38.vcf.gz | 0 ...s_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi | Bin .../input/SJBT031344_D1.Exome.multiqc.tar.gz | 0 tests/{tools => }/input/bwa_db.tar.gz | 0 tests/{tools => }/input/chr1.interval_list | 0 tests/{tools => }/input/fusions.tsv | 0 .../{tools => }/input/gencode.v31.chr9_chr22.gtf.gz | 0 tests/{tools => }/input/genes.genelengths.txt | 0 tests/{tools => }/input/genes.gtf.gz | 0 .../{tools => }/input/kraken2_custom_library.tar.gz | 0 tests/{tools => }/input/kraken2_db.tar.gz | 0 tests/{tools => }/input/kraken2_taxonomy.tar.gz | 0 tests/{tools => }/input/pbmc_1k_v3.tar.gz | 0 tests/{tools => }/input/possorted_genome_bam.bam | 0 tests/{tools => }/input/star_db.tar.gz | 0 tests/{tools => }/input/test.bam | 0 tests/{tools => }/input/test.bam.bai | 0 tests/{tools => }/input/test.bwa_aln_pe.TPM.txt | 0 tests/{tools => }/input/test.bwa_aln_pe.bam | 0 tests/{tools => }/input/test.bwa_aln_pe.bam.bai | 0 .../input/test.bwa_aln_pe.feature-counts.txt | 0 .../input/test.bwa_aln_pe.readlength.txt | 0 tests/{tools => }/input/test.extra_RG.bam | 0 tests/{tools => }/input/test.fa | 0 tests/{tools => }/input/test.tar.gz | 0 tests/{tools => }/input/test.unaccounted_read.bam | 0 tests/{tools => }/input/test1.vcf.gz | 0 tests/{tools => }/input/test1.vcf.gz.tbi | Bin tests/{tools => }/input/test2.bam | 0 tests/{tools => }/input/test2.vcf.gz | 0 tests/{tools => }/input/test2.vcf.gz.tbi | Bin tests/{tools => }/input/test_R1.fq.gz | 0 tests/{tools => }/input/test_R2.fq.gz | 0 tests/{tools => }/input/test_rnaseq_variant.bam | 0 tests/{tools => }/input/test_rnaseq_variant.bam.bai | 0 .../{tools => }/input/test_rnaseq_variant.recal.txt | 0 .../input/wgs_calling_regions.hg38.interval_list | 0 48 files changed, 0 insertions(+), 0 deletions(-) rename tests/{tools => }/input/1scattered.interval_list (100%) rename tests/{tools => }/input/Aligned.sortedByCoord.out.bam (100%) rename tests/{tools => }/input/Aligned.sortedByCoord.out.bam.bai (100%) rename tests/{tools => }/input/GRCh38.chr1_chr19.dict (100%) rename tests/{tools => }/input/GRCh38.chr1_chr19.fa (100%) rename tests/{tools => }/input/GRCh38.chr1_chr19.fa.fai (100%) rename tests/{tools => }/input/GRCh38.chr9_chr22.fa.gz (100%) rename tests/{tools => }/input/GRCh38.chrY_chrM.fa.gz (100%) rename tests/{tools => }/input/GRCh38.tar.gz (100%) rename tests/{tools => }/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf (100%) rename tests/{tools => }/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx (100%) rename tests/{tools => }/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz (100%) rename tests/{tools => }/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi (100%) rename tests/{tools => }/input/SJBT031344_D1.Exome.multiqc.tar.gz (100%) rename tests/{tools => }/input/bwa_db.tar.gz (100%) rename tests/{tools => }/input/chr1.interval_list (100%) rename tests/{tools => }/input/fusions.tsv (100%) rename tests/{tools => }/input/gencode.v31.chr9_chr22.gtf.gz (100%) rename tests/{tools => }/input/genes.genelengths.txt (100%) rename tests/{tools => }/input/genes.gtf.gz (100%) rename tests/{tools => }/input/kraken2_custom_library.tar.gz (100%) rename tests/{tools => }/input/kraken2_db.tar.gz (100%) rename tests/{tools => }/input/kraken2_taxonomy.tar.gz (100%) rename tests/{tools => }/input/pbmc_1k_v3.tar.gz (100%) rename tests/{tools => }/input/possorted_genome_bam.bam (100%) rename tests/{tools => }/input/star_db.tar.gz (100%) rename tests/{tools => }/input/test.bam (100%) rename tests/{tools => }/input/test.bam.bai (100%) rename tests/{tools => }/input/test.bwa_aln_pe.TPM.txt (100%) rename tests/{tools => }/input/test.bwa_aln_pe.bam (100%) rename tests/{tools => }/input/test.bwa_aln_pe.bam.bai (100%) rename tests/{tools => }/input/test.bwa_aln_pe.feature-counts.txt (100%) rename tests/{tools => }/input/test.bwa_aln_pe.readlength.txt (100%) rename tests/{tools => }/input/test.extra_RG.bam (100%) rename tests/{tools => }/input/test.fa (100%) rename tests/{tools => }/input/test.tar.gz (100%) rename tests/{tools => }/input/test.unaccounted_read.bam (100%) rename tests/{tools => }/input/test1.vcf.gz (100%) rename tests/{tools => }/input/test1.vcf.gz.tbi (100%) rename tests/{tools => }/input/test2.bam (100%) rename tests/{tools => }/input/test2.vcf.gz (100%) rename tests/{tools => }/input/test2.vcf.gz.tbi (100%) rename tests/{tools => }/input/test_R1.fq.gz (100%) rename tests/{tools => }/input/test_R2.fq.gz (100%) rename tests/{tools => }/input/test_rnaseq_variant.bam (100%) rename tests/{tools => }/input/test_rnaseq_variant.bam.bai (100%) rename tests/{tools => }/input/test_rnaseq_variant.recal.txt (100%) rename tests/{tools => }/input/wgs_calling_regions.hg38.interval_list (100%) diff --git a/tests/tools/input/1scattered.interval_list b/tests/input/1scattered.interval_list similarity index 100% rename from tests/tools/input/1scattered.interval_list rename to tests/input/1scattered.interval_list diff --git a/tests/tools/input/Aligned.sortedByCoord.out.bam b/tests/input/Aligned.sortedByCoord.out.bam similarity index 100% rename from tests/tools/input/Aligned.sortedByCoord.out.bam rename to tests/input/Aligned.sortedByCoord.out.bam diff --git a/tests/tools/input/Aligned.sortedByCoord.out.bam.bai b/tests/input/Aligned.sortedByCoord.out.bam.bai similarity index 100% rename from tests/tools/input/Aligned.sortedByCoord.out.bam.bai rename to tests/input/Aligned.sortedByCoord.out.bam.bai diff --git a/tests/tools/input/GRCh38.chr1_chr19.dict b/tests/input/GRCh38.chr1_chr19.dict similarity index 100% rename from tests/tools/input/GRCh38.chr1_chr19.dict rename to tests/input/GRCh38.chr1_chr19.dict diff --git a/tests/tools/input/GRCh38.chr1_chr19.fa b/tests/input/GRCh38.chr1_chr19.fa similarity index 100% rename from tests/tools/input/GRCh38.chr1_chr19.fa rename to tests/input/GRCh38.chr1_chr19.fa diff --git a/tests/tools/input/GRCh38.chr1_chr19.fa.fai b/tests/input/GRCh38.chr1_chr19.fa.fai similarity index 100% rename from tests/tools/input/GRCh38.chr1_chr19.fa.fai rename to tests/input/GRCh38.chr1_chr19.fa.fai diff --git a/tests/tools/input/GRCh38.chr9_chr22.fa.gz b/tests/input/GRCh38.chr9_chr22.fa.gz similarity index 100% rename from tests/tools/input/GRCh38.chr9_chr22.fa.gz rename to tests/input/GRCh38.chr9_chr22.fa.gz diff --git a/tests/tools/input/GRCh38.chrY_chrM.fa.gz b/tests/input/GRCh38.chrY_chrM.fa.gz similarity index 100% rename from tests/tools/input/GRCh38.chrY_chrM.fa.gz rename to tests/input/GRCh38.chrY_chrM.fa.gz diff --git a/tests/tools/input/GRCh38.tar.gz b/tests/input/GRCh38.tar.gz similarity index 100% rename from tests/tools/input/GRCh38.tar.gz rename to tests/input/GRCh38.tar.gz diff --git a/tests/tools/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf b/tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf similarity index 100% rename from tests/tools/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf rename to tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf diff --git a/tests/tools/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx b/tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx similarity index 100% rename from tests/tools/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx rename to tests/input/Homo_sapiens_assembly38.dbsnp138.top5000.vcf.idx diff --git a/tests/tools/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz b/tests/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz similarity index 100% rename from tests/tools/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz rename to tests/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz diff --git a/tests/tools/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi b/tests/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi similarity index 100% rename from tests/tools/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi rename to tests/input/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi diff --git a/tests/tools/input/SJBT031344_D1.Exome.multiqc.tar.gz b/tests/input/SJBT031344_D1.Exome.multiqc.tar.gz similarity index 100% rename from tests/tools/input/SJBT031344_D1.Exome.multiqc.tar.gz rename to tests/input/SJBT031344_D1.Exome.multiqc.tar.gz diff --git a/tests/tools/input/bwa_db.tar.gz b/tests/input/bwa_db.tar.gz similarity index 100% rename from tests/tools/input/bwa_db.tar.gz rename to tests/input/bwa_db.tar.gz diff --git a/tests/tools/input/chr1.interval_list b/tests/input/chr1.interval_list similarity index 100% rename from tests/tools/input/chr1.interval_list rename to tests/input/chr1.interval_list diff --git a/tests/tools/input/fusions.tsv b/tests/input/fusions.tsv similarity index 100% rename from tests/tools/input/fusions.tsv rename to tests/input/fusions.tsv diff --git a/tests/tools/input/gencode.v31.chr9_chr22.gtf.gz b/tests/input/gencode.v31.chr9_chr22.gtf.gz similarity index 100% rename from tests/tools/input/gencode.v31.chr9_chr22.gtf.gz rename to tests/input/gencode.v31.chr9_chr22.gtf.gz diff --git a/tests/tools/input/genes.genelengths.txt b/tests/input/genes.genelengths.txt similarity index 100% rename from tests/tools/input/genes.genelengths.txt rename to tests/input/genes.genelengths.txt diff --git a/tests/tools/input/genes.gtf.gz b/tests/input/genes.gtf.gz similarity index 100% rename from tests/tools/input/genes.gtf.gz rename to tests/input/genes.gtf.gz diff --git a/tests/tools/input/kraken2_custom_library.tar.gz b/tests/input/kraken2_custom_library.tar.gz similarity index 100% rename from tests/tools/input/kraken2_custom_library.tar.gz rename to tests/input/kraken2_custom_library.tar.gz diff --git a/tests/tools/input/kraken2_db.tar.gz b/tests/input/kraken2_db.tar.gz similarity index 100% rename from tests/tools/input/kraken2_db.tar.gz rename to tests/input/kraken2_db.tar.gz diff --git a/tests/tools/input/kraken2_taxonomy.tar.gz b/tests/input/kraken2_taxonomy.tar.gz similarity index 100% rename from tests/tools/input/kraken2_taxonomy.tar.gz rename to tests/input/kraken2_taxonomy.tar.gz diff --git a/tests/tools/input/pbmc_1k_v3.tar.gz b/tests/input/pbmc_1k_v3.tar.gz similarity index 100% rename from tests/tools/input/pbmc_1k_v3.tar.gz rename to tests/input/pbmc_1k_v3.tar.gz diff --git a/tests/tools/input/possorted_genome_bam.bam b/tests/input/possorted_genome_bam.bam similarity index 100% rename from tests/tools/input/possorted_genome_bam.bam rename to tests/input/possorted_genome_bam.bam diff --git a/tests/tools/input/star_db.tar.gz b/tests/input/star_db.tar.gz similarity index 100% rename from tests/tools/input/star_db.tar.gz rename to tests/input/star_db.tar.gz diff --git a/tests/tools/input/test.bam b/tests/input/test.bam similarity index 100% rename from tests/tools/input/test.bam rename to tests/input/test.bam diff --git a/tests/tools/input/test.bam.bai b/tests/input/test.bam.bai similarity index 100% rename from tests/tools/input/test.bam.bai rename to tests/input/test.bam.bai diff --git a/tests/tools/input/test.bwa_aln_pe.TPM.txt b/tests/input/test.bwa_aln_pe.TPM.txt similarity index 100% rename from tests/tools/input/test.bwa_aln_pe.TPM.txt rename to tests/input/test.bwa_aln_pe.TPM.txt diff --git a/tests/tools/input/test.bwa_aln_pe.bam b/tests/input/test.bwa_aln_pe.bam similarity index 100% rename from tests/tools/input/test.bwa_aln_pe.bam rename to tests/input/test.bwa_aln_pe.bam diff --git a/tests/tools/input/test.bwa_aln_pe.bam.bai b/tests/input/test.bwa_aln_pe.bam.bai similarity index 100% rename from tests/tools/input/test.bwa_aln_pe.bam.bai rename to tests/input/test.bwa_aln_pe.bam.bai diff --git a/tests/tools/input/test.bwa_aln_pe.feature-counts.txt b/tests/input/test.bwa_aln_pe.feature-counts.txt similarity index 100% rename from tests/tools/input/test.bwa_aln_pe.feature-counts.txt rename to tests/input/test.bwa_aln_pe.feature-counts.txt diff --git a/tests/tools/input/test.bwa_aln_pe.readlength.txt b/tests/input/test.bwa_aln_pe.readlength.txt similarity index 100% rename from tests/tools/input/test.bwa_aln_pe.readlength.txt rename to tests/input/test.bwa_aln_pe.readlength.txt diff --git a/tests/tools/input/test.extra_RG.bam b/tests/input/test.extra_RG.bam similarity index 100% rename from tests/tools/input/test.extra_RG.bam rename to tests/input/test.extra_RG.bam diff --git a/tests/tools/input/test.fa b/tests/input/test.fa similarity index 100% rename from tests/tools/input/test.fa rename to tests/input/test.fa diff --git a/tests/tools/input/test.tar.gz b/tests/input/test.tar.gz similarity index 100% rename from tests/tools/input/test.tar.gz rename to tests/input/test.tar.gz diff --git a/tests/tools/input/test.unaccounted_read.bam b/tests/input/test.unaccounted_read.bam similarity index 100% rename from tests/tools/input/test.unaccounted_read.bam rename to tests/input/test.unaccounted_read.bam diff --git a/tests/tools/input/test1.vcf.gz b/tests/input/test1.vcf.gz similarity index 100% rename from tests/tools/input/test1.vcf.gz rename to tests/input/test1.vcf.gz diff --git a/tests/tools/input/test1.vcf.gz.tbi b/tests/input/test1.vcf.gz.tbi similarity index 100% rename from tests/tools/input/test1.vcf.gz.tbi rename to tests/input/test1.vcf.gz.tbi diff --git a/tests/tools/input/test2.bam b/tests/input/test2.bam similarity index 100% rename from tests/tools/input/test2.bam rename to tests/input/test2.bam diff --git a/tests/tools/input/test2.vcf.gz b/tests/input/test2.vcf.gz similarity index 100% rename from tests/tools/input/test2.vcf.gz rename to tests/input/test2.vcf.gz diff --git a/tests/tools/input/test2.vcf.gz.tbi b/tests/input/test2.vcf.gz.tbi similarity index 100% rename from tests/tools/input/test2.vcf.gz.tbi rename to tests/input/test2.vcf.gz.tbi diff --git a/tests/tools/input/test_R1.fq.gz b/tests/input/test_R1.fq.gz similarity index 100% rename from tests/tools/input/test_R1.fq.gz rename to tests/input/test_R1.fq.gz diff --git a/tests/tools/input/test_R2.fq.gz b/tests/input/test_R2.fq.gz similarity index 100% rename from tests/tools/input/test_R2.fq.gz rename to tests/input/test_R2.fq.gz diff --git a/tests/tools/input/test_rnaseq_variant.bam b/tests/input/test_rnaseq_variant.bam similarity index 100% rename from tests/tools/input/test_rnaseq_variant.bam rename to tests/input/test_rnaseq_variant.bam diff --git a/tests/tools/input/test_rnaseq_variant.bam.bai b/tests/input/test_rnaseq_variant.bam.bai similarity index 100% rename from tests/tools/input/test_rnaseq_variant.bam.bai rename to tests/input/test_rnaseq_variant.bam.bai diff --git a/tests/tools/input/test_rnaseq_variant.recal.txt b/tests/input/test_rnaseq_variant.recal.txt similarity index 100% rename from tests/tools/input/test_rnaseq_variant.recal.txt rename to tests/input/test_rnaseq_variant.recal.txt diff --git a/tests/tools/input/wgs_calling_regions.hg38.interval_list b/tests/input/wgs_calling_regions.hg38.interval_list similarity index 100% rename from tests/tools/input/wgs_calling_regions.hg38.interval_list rename to tests/input/wgs_calling_regions.hg38.interval_list From e18274b63e662a2c9e64b60d001155595717b414 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 11:55:09 -0500 Subject: [PATCH 02/25] fix: update test paths --- tests/tools/input_json/arriba.json | 6 ++--- tests/tools/input_json/bwa_aln.json | 4 +-- tests/tools/input_json/bwa_aln_pe.json | 6 ++--- tests/tools/input_json/bwa_mem.json | 4 +-- tests/tools/input_json/cellranger_count.json | 4 +-- tests/tools/input_json/gatk4_apply_bqsr.json | 6 ++--- .../input_json/gatk4_base_recalibrator.json | 18 ++++++------- .../input_json/gatk4_haplotype_caller.json | 16 ++++++------ .../input_json/gatk4_split_n_cigar_reads.json | 10 +++---- .../input_json/gatk4_variant_filtration.json | 10 +++---- tests/tools/input_json/kraken_build_db.json | 2 +- tests/tools/input_json/multiqc.json | 2 +- .../tools/input_json/ngsderive_encoding.json | 2 +- .../input_json/picard_merge_sam_files.json | 2 +- tests/tools/input_json/picard_merge_vcfs.json | 4 +-- tests/tools/input_json/sambamba_merge.json | 2 +- tests/tools/input_json/samtools_merge.json | 2 +- tests/tools/input_json/star_alignment.json | 6 ++--- tests/tools/test_arriba.yaml | 6 ++--- tests/tools/test_bwa.yaml | 2 +- tests/tools/test_cellranger.yaml | 2 +- tests/tools/test_deeptools.yaml | 2 +- tests/tools/test_estimate.yaml | 2 +- tests/tools/test_fastqc.yaml | 2 +- tests/tools/test_fq.yaml | 6 ++--- tests/tools/test_gatk4.yaml | 2 +- tests/tools/test_htseq.yaml | 4 +-- tests/tools/test_kraken2.yaml | 2 +- tests/tools/test_librarian.yaml | 2 +- tests/tools/test_md5sum.yaml | 2 +- tests/tools/test_mosdepth.yaml | 2 +- tests/tools/test_ngsderive.yaml | 10 +++---- tests/tools/test_picard.yaml | 26 +++++++++---------- tests/tools/test_qualimap.yaml | 4 +-- tests/tools/test_sambamba.yaml | 8 +++--- tests/tools/test_samtools.yaml | 20 +++++++------- tests/tools/test_star.yaml | 2 +- tests/tools/test_util.yaml | 16 ++++++------ 38 files changed, 114 insertions(+), 114 deletions(-) diff --git a/tests/tools/input_json/arriba.json b/tests/tools/input_json/arriba.json index 3cd5e6a06..109191322 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/bwa_aln.json b/tests/tools/input_json/bwa_aln.json index 768dfe347..07316b5a7 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/bwa_aln_pe.json b/tests/tools/input_json/bwa_aln_pe.json index 7e2f62b59..41b872388 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/bwa_mem.json b/tests/tools/input_json/bwa_mem.json index 74173562a..abe4fd5de 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/cellranger_count.json b/tests/tools/input_json/cellranger_count.json index 2793d73c9..ebb625092 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/gatk4_apply_bqsr.json b/tests/tools/input_json/gatk4_apply_bqsr.json index 31b1f9023..45ce2d595 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/gatk4_base_recalibrator.json b/tests/tools/input_json/gatk4_base_recalibrator.json index a9aa93f9c..2f814810c 100644 --- 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"] } \ No newline at end of file diff --git a/tests/tools/input_json/gatk4_haplotype_caller.json b/tests/tools/input_json/gatk4_haplotype_caller.json index 9cdc30918..99634e1b4 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/gatk4_split_n_cigar_reads.json b/tests/tools/input_json/gatk4_split_n_cigar_reads.json index 78602f4c4..57843b49b 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/gatk4_variant_filtration.json b/tests/tools/input_json/gatk4_variant_filtration.json index a88f4dd67..bb28edfb0 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/kraken_build_db.json b/tests/tools/input_json/kraken_build_db.json index 59a560bb9..f50dd116f 100644 --- 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"] } \ No newline at end of file diff --git a/tests/tools/input_json/multiqc.json b/tests/tools/input_json/multiqc.json index 55e64b814..fdf7954e5 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/ngsderive_encoding.json b/tests/tools/input_json/ngsderive_encoding.json index 526419c70..67a6d48bb 100644 --- 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 index eb80f99e9..dc353846d 100644 --- 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 index d6a09de52..1bf5e0ac3 100644 --- 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 index 5b763f1ca..f6411a6e4 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/samtools_merge.json b/tests/tools/input_json/samtools_merge.json index b939731be..4e1507e1f 100644 --- 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" } \ No newline at end of file diff --git a/tests/tools/input_json/star_alignment.json b/tests/tools/input_json/star_alignment.json index ea7ebffaa..1d855ebfc 100644 --- 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 index 881682010..c998e31b1 100644 --- 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 index 815ca73f9..71cf33d0a 100644 --- 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 index 421047ddf..98adac531 100644 --- 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 index 292ce1f91..5974242f8 100644 --- 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 index 3d38246ea..46febc352 100644 --- 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 index 377ebfaef..09594742c 100644 --- 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 index fe13be144..dd4a89e04 100644 --- 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 index 6f258881b..6e9541b97 100644 --- 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 index 2ebb8db16..f324a2131 100644 --- 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 index eaa735cec..023ab8f8f 100644 --- 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 index bf314b41d..f37e62958 100644 --- 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 index 8718df6de..90bfd08ba 100644 --- 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 index 5da1f068b..0bd658870 100644 --- 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 diff --git a/tests/tools/test_ngsderive.yaml b/tests/tools/test_ngsderive.yaml index 83792339a..3302db98a 100644 --- a/tests/tools/test_ngsderive.yaml +++ b/tests/tools/test_ngsderive.yaml @@ -3,7 +3,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task strandedness tools/ngsderive.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" bam_index="tests/tools/input/test.bwa_aln_pe.bam.bai" gene_model="tests/tools/input/genes.gtf.gz" + miniwdl run --verbose -d test-output/. --task strandedness tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" gene_model="tests/input/genes.gtf.gz" files: - path: test-output/out/strandedness_file/test.bwa_aln_pe.strandedness.tsv contains: @@ -14,7 +14,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task instrument tools/ngsderive.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task instrument tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/instrument_file/test.bwa_aln_pe.instrument.tsv contains: @@ -26,7 +26,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task read_length tools/ngsderive.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 read_length tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" files: - path: test-output/out/read_length_file/test.bwa_aln_pe.readlength.tsv contains: @@ -49,7 +49,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task junction_annotation tools/ngsderive.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" bam_index="tests/tools/input/test.bwa_aln_pe.bam.bai" gene_model="tests/tools/input/genes.gtf.gz" + miniwdl run --verbose -d test-output/. --task junction_annotation tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" gene_model="tests/input/genes.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 @@ -59,6 +59,6 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task endedness tools/ngsderive.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task endedness tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/endedness_file/test.bwa_aln_pe.endedness.tsv diff --git a/tests/tools/test_picard.yaml b/tests/tools/test_picard.yaml index 172f0d9a9..335461f47 100644 --- a/tests/tools/test_picard.yaml +++ b/tests/tools/test_picard.yaml @@ -3,7 +3,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task mark_duplicates tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task mark_duplicates tools/picard.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 @@ -15,7 +15,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task validate_bam tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task validate_bam tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/validate_report/test.bwa_aln_pe.ValidateSamFile.txt @@ -24,7 +24,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - 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 @@ -34,7 +34,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task sort tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" memory_gb=16 + miniwdl run --verbose -d test-output/. --task sort tools/picard.wdl bam="tests/input/test.bwa_aln_pe.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 @@ -44,7 +44,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task sort tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" memory_gb=16 sort_order="queryname" + miniwdl run --verbose -d test-output/. --task sort tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" memory_gb=16 sort_order="queryname" files: - path: test-output/out/sorted_bam/test.bwa_aln_pe.sorted.bam @@ -62,7 +62,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task clean_sam tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task clean_sam tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/cleaned_bam/test.bwa_aln_pe.cleaned.bam @@ -71,7 +71,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_wgs_metrics tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" reference_fasta="tests/tools/input/GRCh38.chrY_chrM.fa.gz" + miniwdl run --verbose -d test-output/. --task collect_wgs_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" reference_fasta="tests/input/GRCh38.chrY_chrM.fa.gz" files: - path: test-output/out/wgs_metrics/test.bwa_aln_pe.CollectWgsMetrics.txt @@ -80,7 +80,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_alignment_summary_metrics tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task collect_alignment_summary_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/alignment_metrics/test.bwa_aln_pe.CollectAlignmentSummaryMetrics.txt - path: test-output/out/alignment_metrics_pdf/test.bwa_aln_pe.CollectAlignmentSummaryMetrics.pdf @@ -90,7 +90,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_gc_bias_metrics tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" reference_fasta=tests/tools/input/GRCh38.chrY_chrM.fa.gz + miniwdl run --verbose -d test-output/. --task collect_gc_bias_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz files: - path: test-output/out/gc_bias_metrics/test.bwa_aln_pe.CollectGcBiasMetrics.txt - path: test-output/out/gc_bias_metrics_summary/test.bwa_aln_pe.CollectGcBiasMetrics.summary.txt @@ -101,7 +101,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_insert_size_metrics tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task collect_insert_size_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/insert_size_metrics/test.bwa_aln_pe.CollectInsertSizeMetrics.txt - path: test-output/out/insert_size_metrics_pdf/test.bwa_aln_pe.CollectInsertSizeMetrics.pdf @@ -111,7 +111,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task quality_score_distribution tools/picard.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task quality_score_distribution tools/picard.wdl bam="tests/input/test.bwa_aln_pe.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 @@ -130,7 +130,7 @@ - miniwdl - picard command: >- - miniwdl run -d test-output/. --task scatter_interval_list tools/picard.wdl interval_list="tests/tools/input/wgs_calling_regions.hg38.interval_list" scatter_count=3 + 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 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/tools/input/GRCh38.chrY_chrM.fa.gz" outfile_name="GRCh38.chrY_chrM.dict" + miniwdl run -d test-output/. --task create_sequence_dictionary tools/picard.wdl fasta="tests/input/GRCh38.chrY_chrM.fa.gz" outfile_name="GRCh38.chrY_chrM.dict" files: - path: test-output/out/dictionary/GRCh38.chrY_chrM.dict \ No newline at end of file diff --git a/tests/tools/test_qualimap.yaml b/tests/tools/test_qualimap.yaml index 87bc64017..a78b9a761 100644 --- a/tests/tools/test_qualimap.yaml +++ b/tests/tools/test_qualimap.yaml @@ -4,7 +4,7 @@ - qualimap - deprecated command: >- - miniwdl run --verbose -d test-output/. --task bamqc tools/qualimap.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task bamqc tools/qualimap.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/results/test.bwa_aln_pe.qualimap_bamqc_results.tar.gz @@ -13,7 +13,7 @@ - miniwdl - qualimap command: >- - miniwdl run --verbose -d test-output/. --task rnaseq tools/qualimap.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" gtf="tests/tools/input/genes.gtf.gz" + miniwdl run --verbose -d test-output/. --task rnaseq tools/qualimap.wdl bam="tests/input/test.bwa_aln_pe.bam" gtf="tests/input/genes.gtf.gz" files: - path: test-output/out/results/test.bwa_aln_pe.qualimap_rnaseq_results.tar.gz - path: test-output/out/raw_summary/rnaseq_qc_results.txt diff --git a/tests/tools/test_sambamba.yaml b/tests/tools/test_sambamba.yaml index 47fa4120b..18189bee5 100644 --- a/tests/tools/test_sambamba.yaml +++ b/tests/tools/test_sambamba.yaml @@ -3,7 +3,7 @@ - miniwdl - sambamba command: >- - miniwdl run -d test-output/. --task index tools/sambamba.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run -d test-output/. --task index tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/bam_index/test.bwa_aln_pe.bam.bai @@ -21,7 +21,7 @@ - miniwdl - sambamba command: >- - miniwdl run -d test-output/. --task sort tools/sambamba.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run -d test-output/. --task sort tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/sorted_bam/test.bwa_aln_pe.sorted.bam @@ -30,7 +30,7 @@ - miniwdl - sambamba command: >- - miniwdl run -d test-output/. --task flagstat tools/sambamba.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run -d test-output/. --task flagstat tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/flagstat_report/test.bwa_aln_pe.flagstat.txt @@ -39,7 +39,7 @@ - miniwdl - sambamba command: >- - miniwdl run -d test-output/. --task markdup tools/sambamba.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run -d test-output/. --task markdup tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.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 diff --git a/tests/tools/test_samtools.yaml b/tests/tools/test_samtools.yaml index c6559687e..28f9d3c85 100644 --- a/tests/tools/test_samtools.yaml +++ b/tests/tools/test_samtools.yaml @@ -3,7 +3,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task quickcheck tools/samtools.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task quickcheck tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" stdout: contains_regex: - "passed" @@ -13,7 +13,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task split tools/samtools.wdl bam="tests/tools/input/test.bam" + miniwdl run --verbose -d test-output/. --task split tools/samtools.wdl bam="tests/input/test.bam" files: - path: test-output/out/split_bams/0/test.1.bam - path: test-output/out/split_bams/1/test.2.bam @@ -23,7 +23,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task split tools/samtools.wdl bam="tests/tools/input/test.unaccounted_read.bam" + miniwdl run --verbose -d test-output/. --task split tools/samtools.wdl bam="tests/input/test.unaccounted_read.bam" exit_code: 21 - name: samtools_split_extra_RG @@ -31,7 +31,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task split tools/samtools.wdl bam="tests/tools/input/test.extra_RG.bam" + miniwdl run --verbose -d test-output/. --task split tools/samtools.wdl bam="tests/input/test.extra_RG.bam" exit_code: 42 - name: samtools_flagstat @@ -39,7 +39,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task flagstat tools/samtools.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task flagstat tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/flagstat_report/test.bwa_aln_pe.flagstat.txt contains: @@ -54,7 +54,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task index tools/samtools.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task index tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/bam_index/test.bwa_aln_pe.bam.bai @@ -81,7 +81,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task addreplacerg tools/samtools.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" read_group_id="test" + miniwdl run --verbose -d test-output/. --task addreplacerg tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" read_group_id="test" files: - path: test-output/out/tagged_bam/test.bwa_aln_pe.addreplacerg.bam @@ -90,7 +90,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task collate tools/samtools.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task collate tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: test-output/out/collated_bam/test.bwa_aln_pe.collated.bam @@ -99,7 +99,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/samtools.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" retain_collated_bam=true + miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.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 @@ -110,6 +110,6 @@ - miniwdl - samtools command: >- - miniwdl run -d test-output/. --task faidx tools/samtools.wdl fasta="tests/tools/input/test.fa" + miniwdl run -d test-output/. --task faidx tools/samtools.wdl fasta="tests/input/test.fa" files: - path: test-output/out/fasta_index/test.fa.fai diff --git a/tests/tools/test_star.yaml b/tests/tools/test_star.yaml index 783230e00..553bbacbe 100644 --- a/tests/tools/test_star.yaml +++ b/tests/tools/test_star.yaml @@ -4,7 +4,7 @@ - star - reference command: >- - miniwdl run --verbose -d test-output/. --task build_star_db tools/star.wdl reference_fasta=tests/tools/input/GRCh38.chrY_chrM.fa.gz gtf=tests/tools/input/genes.gtf.gz + miniwdl run --verbose -d test-output/. --task build_star_db tools/star.wdl reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz gtf=tests/input/genes.gtf.gz files: - path: test-output/out/star_db/star_db.tar.gz diff --git a/tests/tools/test_util.yaml b/tests/tools/test_util.yaml index c762aee66..3a084f6e1 100644 --- a/tests/tools/test_util.yaml +++ b/tests/tools/test_util.yaml @@ -44,7 +44,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task calc_gene_lengths tools/util.wdl gtf="tests/tools/input/genes.gtf.gz" + miniwdl run --verbose -d test-output/. --task calc_gene_lengths tools/util.wdl gtf="tests/input/genes.gtf.gz" files: - path: test-output/out/gene_lengths/genes.genelengths.txt contains: @@ -57,7 +57,7 @@ - util - deprecated command: >- - miniwdl run --verbose -d test-output/. --task qc_summary tools/util.wdl multiqc_tar_gz="tests/tools/input/SJBT031344_D1.Exome.multiqc.tar.gz" + miniwdl run --verbose -d test-output/. --task qc_summary tools/util.wdl multiqc_tar_gz="tests/input/SJBT031344_D1.Exome.multiqc.tar.gz" files: - path: "test-output/out/summary/SJBT031344_D1.Exome.qc_summary.json" @@ -66,7 +66,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task compression_integrity tools/util.wdl bgzipped_file="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task compression_integrity tools/util.wdl bgzipped_file="tests/input/test.bwa_aln_pe.bam" stdout: contains: - "passed" @@ -77,7 +77,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task add_to_bam_header tools/util.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" additional_header="@RG ID:3" + miniwdl run --verbose -d test-output/. --task add_to_bam_header tools/util.wdl bam="tests/input/test.bwa_aln_pe.bam" additional_header="@RG ID:3" files: - path: "test-output/out/reheadered_bam/test.bwa_aln_pe.reheader.bam" @@ -86,7 +86,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task unpack_tarball tools/util.wdl tarball="tests/tools/input/test.tar.gz" + miniwdl run --verbose -d test-output/. --task unpack_tarball tools/util.wdl tarball="tests/input/test.tar.gz" files: - path: "test-output/out/tarball_contents/0/a" - path: "test-output/out/tarball_contents/1/b" @@ -96,7 +96,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task make_coverage_regions_bed tools/util.wdl gtf="tests/tools/input/genes.gtf.gz" feature_type="exon" + miniwdl run --verbose -d test-output/. --task make_coverage_regions_bed tools/util.wdl gtf="tests/input/genes.gtf.gz" feature_type="exon" files: - path: "test-output/out/bed/genes.exon.bed" @@ -105,7 +105,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task global_phred_scores tools/util.wdl bam="tests/tools/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task global_phred_scores tools/util.wdl bam="tests/input/test.bwa_aln_pe.bam" files: - path: "test-output/out/phred_scores/test.bwa_aln_pe.global_PHRED_scores.tsv" @@ -114,6 +114,6 @@ - miniwdl - util command: >- - miniwdl run -d test-output/. --task split_fastq tools/util.wdl fastq="tests/tools/input/test_R1.fq.gz" prefix="test_R1." + miniwdl run -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" \ No newline at end of file From edad54e524534028e619a3bc4dae7b406f21f212 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 13:05:43 -0500 Subject: [PATCH 03/25] revise: rename star_db to include contigs --- .gitignore | 2 ++ tests/input/{star_db.tar.gz => star_db.chrY_chrM.tar.gz} | 0 tests/tools/input_json/star_alignment.json | 2 +- 3 files changed, 3 insertions(+), 1 deletion(-) rename tests/input/{star_db.tar.gz => star_db.chrY_chrM.tar.gz} (100%) diff --git a/.gitignore b/.gitignore index 4c6d3cedf..17fceec45 100644 --- a/.gitignore +++ b/.gitignore @@ -12,6 +12,8 @@ *.jar miniwdl_call_cache/ miniwdl_singularity_cache/ +_LAST +202*/ # Blacklist test directories test-output/ diff --git a/tests/input/star_db.tar.gz b/tests/input/star_db.chrY_chrM.tar.gz similarity index 100% rename from tests/input/star_db.tar.gz rename to tests/input/star_db.chrY_chrM.tar.gz diff --git a/tests/tools/input_json/star_alignment.json b/tests/tools/input_json/star_alignment.json index 1d855ebfc..1b3d85b51 100644 --- 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/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", + "star_db_tar_gz": "tests/input/star_db.chrY_chrM.tar.gz", "prefix": "test", "read_groups": "ID:test" } From 7dbe8ca4d0d5e801773fc009e029cbd97562c012 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 13:57:26 -0500 Subject: [PATCH 04/25] WIP --- .gitignore | 1 + docker/STAR/{2.7.11b-0 => 2.7.11b-1}/Dockerfile | 2 +- docker/STAR/{2.7.11b-0 => 2.7.11b-1}/sort_star_input.py | 0 tools/star.wdl | 4 ++-- 4 files changed, 4 insertions(+), 3 deletions(-) rename docker/STAR/{2.7.11b-0 => 2.7.11b-1}/Dockerfile (90%) rename docker/STAR/{2.7.11b-0 => 2.7.11b-1}/sort_star_input.py (100%) diff --git a/.gitignore b/.gitignore index 17fceec45..724d88fe2 100644 --- a/.gitignore +++ b/.gitignore @@ -17,6 +17,7 @@ _LAST # Blacklist test directories test-output/ +**/__pycache__ # Blacklist OS generated files .DS_Store diff --git a/docker/STAR/2.7.11b-0/Dockerfile b/docker/STAR/2.7.11b-1/Dockerfile similarity index 90% rename from docker/STAR/2.7.11b-0/Dockerfile rename to docker/STAR/2.7.11b-1/Dockerfile index eb3940796..616cdd7ac 100644 --- a/docker/STAR/2.7.11b-0/Dockerfile +++ b/docker/STAR/2.7.11b-1/Dockerfile @@ -4,7 +4,7 @@ RUN apt-get update \ && apt-get --yes install --no-install-recommends python3 \ && rm -rf /var/lib/apt/lists/* -FROM quay.io/biocontainers/star:2.7.11b--h43eeafb_0 +FROM quay.io/biocontainers/star:2.7.11b--h43eeafb_3 COPY --from=python /lib/x86_64-linux-gnu/libexpat.so.1 /lib/x86_64-linux-gnu/ COPY --from=python /lib/x86_64-linux-gnu/libz.so.1 /lib/x86_64-linux-gnu/ diff --git a/docker/STAR/2.7.11b-0/sort_star_input.py b/docker/STAR/2.7.11b-1/sort_star_input.py similarity index 100% rename from docker/STAR/2.7.11b-0/sort_star_input.py rename to docker/STAR/2.7.11b-1/sort_star_input.py diff --git a/tools/star.wdl b/tools/star.wdl index 44173bb3b..9d5402cb1 100755 --- a/tools/star.wdl +++ b/tools/star.wdl @@ -127,7 +127,7 @@ task build_star_db { cpu: ncpu memory: "~{memory_gb} GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/star:2.7.11b-0" + container: "ghcr.io/stjudecloud/star:2.7.11b-1" maxRetries: 1 } } @@ -814,7 +814,7 @@ task alignment { cpu: ncpu memory: "50 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/star:2.7.11b-0" + container: "ghcr.io/stjudecloud/star:2.7.11b-1" maxRetries: 1 } } From 9d849bedb4e2491057f0a2d0eb1a2c682d9f92f7 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 14:01:03 -0500 Subject: [PATCH 05/25] Update star.wdl --- tools/star.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/star.wdl b/tools/star.wdl index 9d5402cb1..c59ba3d7f 100755 --- a/tools/star.wdl +++ b/tools/star.wdl @@ -127,7 +127,7 @@ task build_star_db { cpu: ncpu memory: "~{memory_gb} GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/star:2.7.11b-1" + container: "ghcr.io/stjudecloud/star:branch-tests-2.7.11b-1" maxRetries: 1 } } @@ -814,7 +814,7 @@ task alignment { cpu: ncpu memory: "50 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/star:2.7.11b-1" + container: "ghcr.io/stjudecloud/star:branch-tests-2.7.11b-1" maxRetries: 1 } } From fde41d257dbcb1fb5d25c0fa851c324011282776 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 15:34:57 -0500 Subject: [PATCH 06/25] WIP --- tests/input/Aligned.sortedByCoord.chr9_chr22.bam | 3 +++ tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai | 3 +++ tests/input/Aligned.sortedByCoord.out.bam | 3 --- tests/input/Aligned.sortedByCoord.out.bam.bai | 3 --- tests/input/{genes.gtf.gz => genes.chrY_chrM.gtf.gz} | 0 tests/input/star_db.chrY_chrM.tar.gz | 4 ++-- tests/workflows/input_json/rnaseq-standard.json | 6 ++++++ tools/star.wdl | 9 ++++----- 8 files changed, 18 insertions(+), 13 deletions(-) create mode 100644 tests/input/Aligned.sortedByCoord.chr9_chr22.bam create mode 100644 tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai delete mode 100644 tests/input/Aligned.sortedByCoord.out.bam delete mode 100644 tests/input/Aligned.sortedByCoord.out.bam.bai rename tests/input/{genes.gtf.gz => genes.chrY_chrM.gtf.gz} (100%) create mode 100644 tests/workflows/input_json/rnaseq-standard.json diff --git a/tests/input/Aligned.sortedByCoord.chr9_chr22.bam b/tests/input/Aligned.sortedByCoord.chr9_chr22.bam new file mode 100644 index 000000000..5fbf7cdc9 --- /dev/null +++ b/tests/input/Aligned.sortedByCoord.chr9_chr22.bam @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6ea6012587b4e9444fdcabaa5e26522aaf8c651295198208f87859204b0adc13 +size 8221 diff --git a/tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai b/tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai new file mode 100644 index 000000000..0427afe56 --- /dev/null +++ b/tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bf5aadc2241ccf358a7120bae15262758f649c620ac8c10aa5a97597d007b04d +size 75432 diff --git a/tests/input/Aligned.sortedByCoord.out.bam b/tests/input/Aligned.sortedByCoord.out.bam deleted file mode 100644 index bbc8c4722..000000000 --- a/tests/input/Aligned.sortedByCoord.out.bam +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f327cbde3dac578b7a5137ed8dd6750e8b88c7582ea42774b32469023c6ccef1 -size 8055 diff --git a/tests/input/Aligned.sortedByCoord.out.bam.bai b/tests/input/Aligned.sortedByCoord.out.bam.bai deleted file mode 100644 index 7c812c23a..000000000 --- a/tests/input/Aligned.sortedByCoord.out.bam.bai +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:0ec29768e18799e82b82865b4aa2fc1df9aacf16b253be4edc67974efbba86a1 -size 75432 diff --git a/tests/input/genes.gtf.gz b/tests/input/genes.chrY_chrM.gtf.gz similarity index 100% rename from tests/input/genes.gtf.gz rename to tests/input/genes.chrY_chrM.gtf.gz diff --git a/tests/input/star_db.chrY_chrM.tar.gz b/tests/input/star_db.chrY_chrM.tar.gz index 499550435..435e1b3ee 100644 --- a/tests/input/star_db.chrY_chrM.tar.gz +++ b/tests/input/star_db.chrY_chrM.tar.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c6c240e6e37a1c3e4b3b71ae6184f5732d2a6e0e5d2eddef673e01f2817984f8 -size 604221552 +oid sha256:6dbc65ad89ee267e5bc2164124efd5e6f7a07e3986a5a5e19533d74f9ff5f07b +size 604222117 diff --git a/tests/workflows/input_json/rnaseq-standard.json b/tests/workflows/input_json/rnaseq-standard.json new file mode 100644 index 000000000..3160ec698 --- /dev/null +++ b/tests/workflows/input_json/rnaseq-standard.json @@ -0,0 +1,6 @@ +{ + "rnaseq_standard.bam": "tests/input/Aligned.sortedByCoord.out.addreplacerg.bam", + "rnaseq_standard.gtf": "tests/input/genes.chrY_chrM.gtf.gz", + "rnaseq_standard.star_db": "tests/input/star_db.chrY_chrM.tar.gz", + "rnaseq_standard.strandedness": "Unstranded" +} diff --git a/tools/star.wdl b/tools/star.wdl index c59ba3d7f..264ca3f88 100755 --- a/tools/star.wdl +++ b/tools/star.wdl @@ -116,7 +116,7 @@ task build_star_db { rm "$gtf_name" "$ref_fasta" - tar -czf ~{star_db_tar_gz} ~{db_name} + tar -C ~{db_name} -czf ~{star_db_tar_gz} . >>> output { @@ -615,8 +615,6 @@ task alignment { Int modify_disk_size_gb = 0 } - String star_db_dir = basename(star_db_tar_gz, ".tar.gz") - Float read_one_fastqs_size = size(read_one_fastqs_gz, "GiB") Float read_two_fastqs_size = size(read_two_fastqs_gz, "GiB") Float star_db_tar_gz_size = size(star_db_tar_gz, "GiB") @@ -635,7 +633,8 @@ task alignment { n_cores=$(nproc) fi - tar -xzf ~{star_db_tar_gz} + mkdir star_db + tar -xzf ~{star_db_tar_gz} -C star_db/ --no-same-owner # odd constructions a combination of needing white space properly parsed # and limitations of the WDL v1.1 spec @@ -655,7 +654,7 @@ task alignment { read -ra read_group_args < read_groups_sorted.txt STAR --readFilesIn "${read_one_args[@]}" "${read_two_args[@]}" \ --readFilesCommand "gunzip -c" \ - --genomeDir ~{star_db_dir} \ + --genomeDir star_db \ --runThreadN "$n_cores" \ --outSAMtype BAM Unsorted \ --outMultimapperOrder Random \ From 0f032a9e5b167ed3730fec68daf3a07473fc939b Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 15:49:17 -0500 Subject: [PATCH 07/25] WIP --- tests/tools/input_json/arriba.json | 2 +- tests/tools/test_arriba.yaml | 2 +- tests/workflows/input_json/rnaseq-standard.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/tools/input_json/arriba.json b/tests/tools/input_json/arriba.json index 109191322..b2329ca15 100644 --- a/tests/tools/input_json/arriba.json +++ b/tests/tools/input_json/arriba.json @@ -1,5 +1,5 @@ { - "bam": "tests/input/Aligned.sortedByCoord.out.bam", + "bam": "tests/input/Aligned.sortedByCoord.chr9_chr22.bam", "gtf": "tests/input/gencode.v31.chr9_chr22.gtf.gz", "reference_fasta_gz": "tests/input/GRCh38.chr9_chr22.fa.gz", "disable_filters": ["blacklist"], diff --git a/tests/tools/test_arriba.yaml b/tests/tools/test_arriba.yaml index c998e31b1..52cdf7fcf 100644 --- a/tests/tools/test_arriba.yaml +++ b/tests/tools/test_arriba.yaml @@ -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.out.bam" bam_index="tests/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.chr9_chr22.bam" bam_index="tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai" files: - path: test-output/out/fusion_bams/0/fusions_1.bam diff --git a/tests/workflows/input_json/rnaseq-standard.json b/tests/workflows/input_json/rnaseq-standard.json index 3160ec698..e338893e3 100644 --- a/tests/workflows/input_json/rnaseq-standard.json +++ b/tests/workflows/input_json/rnaseq-standard.json @@ -1,5 +1,5 @@ { - "rnaseq_standard.bam": "tests/input/Aligned.sortedByCoord.out.addreplacerg.bam", + "rnaseq_standard.bam": "tests/input/test.bwa_aln_pe.bam", "rnaseq_standard.gtf": "tests/input/genes.chrY_chrM.gtf.gz", "rnaseq_standard.star_db": "tests/input/star_db.chrY_chrM.tar.gz", "rnaseq_standard.strandedness": "Unstranded" From f387eb1a6d8d773f97549fde71428412d7ce18cf Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 15:49:34 -0500 Subject: [PATCH 08/25] fix: only grep for RG at start of line --- tools/util.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/util.wdl b/tools/util.wdl index a951b5acb..610a63ca9 100644 --- a/tools/util.wdl +++ b/tools/util.wdl @@ -81,13 +81,13 @@ task get_read_groups { if ~{format_for_star}; then samtools view -H ~{bam} \ - | grep "@RG" \ + | grep "^@RG" \ | cut -f 2- \ | sed -e 's/\t/ /g' \ | awk '{print}' ORS=' , ' \ | sed 's/ , $//' > read_groups.txt else - samtools view -H ~{bam} | grep "@RG" > read_groups.txt + samtools view -H ~{bam} | grep "^@RG" > read_groups.txt fi >>> From 8f671da95c2ca953e258ac28a212713a5ab1e246 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 15:52:47 -0500 Subject: [PATCH 09/25] fix: update paths --- tests/tools/test_htseq.yaml | 2 +- tests/tools/test_ngsderive.yaml | 4 ++-- tests/tools/test_qualimap.yaml | 2 +- tests/tools/test_star.yaml | 2 +- tests/tools/test_util.yaml | 4 ++-- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/tools/test_htseq.yaml b/tests/tools/test_htseq.yaml index f324a2131..7c09b69dc 100644 --- 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/input/test.bwa_aln_pe.bam" gtf="tests/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.chrY_chrM.gtf.gz" strandedness="no" files: - path: test-output/out/feature_counts/test.bwa_aln_pe.feature-counts.txt diff --git a/tests/tools/test_ngsderive.yaml b/tests/tools/test_ngsderive.yaml index 3302db98a..836c3d542 100644 --- a/tests/tools/test_ngsderive.yaml +++ b/tests/tools/test_ngsderive.yaml @@ -3,7 +3,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task strandedness tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" gene_model="tests/input/genes.gtf.gz" + miniwdl run --verbose -d test-output/. --task strandedness tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" gene_model="tests/input/genes.chrY_chrM.gtf.gz" files: - path: test-output/out/strandedness_file/test.bwa_aln_pe.strandedness.tsv contains: @@ -49,7 +49,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task junction_annotation tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" gene_model="tests/input/genes.gtf.gz" + miniwdl run --verbose -d test-output/. --task junction_annotation tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" gene_model="tests/input/genes.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 diff --git a/tests/tools/test_qualimap.yaml b/tests/tools/test_qualimap.yaml index a78b9a761..189c41b74 100644 --- a/tests/tools/test_qualimap.yaml +++ b/tests/tools/test_qualimap.yaml @@ -13,7 +13,7 @@ - miniwdl - qualimap command: >- - miniwdl run --verbose -d test-output/. --task rnaseq tools/qualimap.wdl bam="tests/input/test.bwa_aln_pe.bam" gtf="tests/input/genes.gtf.gz" + miniwdl run --verbose -d test-output/. --task rnaseq tools/qualimap.wdl bam="tests/input/test.bwa_aln_pe.bam" gtf="tests/input/genes.chrY_chrM.gtf.gz" files: - path: test-output/out/results/test.bwa_aln_pe.qualimap_rnaseq_results.tar.gz - path: test-output/out/raw_summary/rnaseq_qc_results.txt diff --git a/tests/tools/test_star.yaml b/tests/tools/test_star.yaml index 553bbacbe..f51fbea0a 100644 --- a/tests/tools/test_star.yaml +++ b/tests/tools/test_star.yaml @@ -4,7 +4,7 @@ - star - reference command: >- - miniwdl run --verbose -d test-output/. --task build_star_db tools/star.wdl reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz gtf=tests/input/genes.gtf.gz + miniwdl run --verbose -d test-output/. --task build_star_db tools/star.wdl reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz gtf=tests/input/genes.chrY_chrM.gtf.gz files: - path: test-output/out/star_db/star_db.tar.gz diff --git a/tests/tools/test_util.yaml b/tests/tools/test_util.yaml index 3a084f6e1..8d2a1551f 100644 --- a/tests/tools/test_util.yaml +++ b/tests/tools/test_util.yaml @@ -44,7 +44,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task calc_gene_lengths tools/util.wdl gtf="tests/input/genes.gtf.gz" + miniwdl run --verbose -d test-output/. --task calc_gene_lengths tools/util.wdl gtf="tests/input/genes.chrY_chrM.gtf.gz" files: - path: test-output/out/gene_lengths/genes.genelengths.txt contains: @@ -96,7 +96,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task make_coverage_regions_bed tools/util.wdl gtf="tests/input/genes.gtf.gz" feature_type="exon" + miniwdl run --verbose -d test-output/. --task make_coverage_regions_bed tools/util.wdl gtf="tests/input/genes.chrY_chrM.gtf.gz" feature_type="exon" files: - path: "test-output/out/bed/genes.exon.bed" From 51254f4f7afbab0395c9d1e4546c589e8077db97 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 16:00:00 -0500 Subject: [PATCH 10/25] revise: rename things --- ... => gencode.v31.chrY_chrM.genelengths.txt} | 0 ...rM.gtf.gz => gencode.v31.chrY_chrM.gtf.gz} | 0 ...n_pe.bam => test.bwa_aln_pe.chrY_chrM.bam} | 0 ....bai => test.bwa_aln_pe.chrY_chrM.bam.bai} | 0 .../tools/input_json/ngsderive_encoding.json | 2 +- .../input_json/picard_merge_sam_files.json | 2 +- tests/tools/input_json/sambamba_merge.json | 2 +- tests/tools/input_json/samtools_merge.json | 2 +- tests/tools/test_deeptools.yaml | 2 +- tests/tools/test_fastqc.yaml | 2 +- tests/tools/test_gatk4.yaml | 2 +- tests/tools/test_htseq.yaml | 4 ++-- tests/tools/test_md5sum.yaml | 2 +- tests/tools/test_mosdepth.yaml | 2 +- tests/tools/test_ngsderive.yaml | 10 ++++----- tests/tools/test_picard.yaml | 22 +++++++++---------- tests/tools/test_qualimap.yaml | 4 ++-- tests/tools/test_sambamba.yaml | 8 +++---- tests/tools/test_samtools.yaml | 12 +++++----- tests/tools/test_star.yaml | 2 +- tests/tools/test_util.yaml | 10 ++++----- .../workflows/input_json/rnaseq-standard.json | 4 ++-- 22 files changed, 47 insertions(+), 47 deletions(-) rename tests/input/{genes.genelengths.txt => gencode.v31.chrY_chrM.genelengths.txt} (100%) rename tests/input/{genes.chrY_chrM.gtf.gz => gencode.v31.chrY_chrM.gtf.gz} (100%) rename tests/input/{test.bwa_aln_pe.bam => test.bwa_aln_pe.chrY_chrM.bam} (100%) rename tests/input/{test.bwa_aln_pe.bam.bai => test.bwa_aln_pe.chrY_chrM.bam.bai} (100%) diff --git a/tests/input/genes.genelengths.txt b/tests/input/gencode.v31.chrY_chrM.genelengths.txt similarity index 100% rename from tests/input/genes.genelengths.txt rename to tests/input/gencode.v31.chrY_chrM.genelengths.txt diff --git a/tests/input/genes.chrY_chrM.gtf.gz b/tests/input/gencode.v31.chrY_chrM.gtf.gz similarity index 100% rename from tests/input/genes.chrY_chrM.gtf.gz rename to tests/input/gencode.v31.chrY_chrM.gtf.gz diff --git a/tests/input/test.bwa_aln_pe.bam b/tests/input/test.bwa_aln_pe.chrY_chrM.bam similarity index 100% rename from tests/input/test.bwa_aln_pe.bam rename to tests/input/test.bwa_aln_pe.chrY_chrM.bam diff --git a/tests/input/test.bwa_aln_pe.bam.bai b/tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai similarity index 100% rename from tests/input/test.bwa_aln_pe.bam.bai rename to tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai diff --git a/tests/tools/input_json/ngsderive_encoding.json b/tests/tools/input_json/ngsderive_encoding.json index 67a6d48bb..e2271d0cf 100644 --- a/tests/tools/input_json/ngsderive_encoding.json +++ b/tests/tools/input_json/ngsderive_encoding.json @@ -1,4 +1,4 @@ { - "ngs_files": ["tests/input/test.bwa_aln_pe.bam"], + "ngs_files": ["tests/input/test.bwa_aln_pe.chrY_chrM.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 index dc353846d..e7e22a02c 100644 --- 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/input/possorted_genome_bam.bam", "tests/input/test.bwa_aln_pe.bam"], + "bams": ["tests/input/possorted_genome_bam.bam", "tests/input/test.bwa_aln_pe.chrY_chrM.bam"], "prefix": "test" } diff --git a/tests/tools/input_json/sambamba_merge.json b/tests/tools/input_json/sambamba_merge.json index f6411a6e4..3afd4f3cc 100644 --- a/tests/tools/input_json/sambamba_merge.json +++ b/tests/tools/input_json/sambamba_merge.json @@ -1,4 +1,4 @@ { - "bams": ["tests/input/possorted_genome_bam.bam", "tests/input/test.bwa_aln_pe.bam"], + "bams": ["tests/input/possorted_genome_bam.bam", "tests/input/test.bwa_aln_pe.chrY_chrM.bam"], "prefix": "test" } \ No newline at end of file diff --git a/tests/tools/input_json/samtools_merge.json b/tests/tools/input_json/samtools_merge.json index 4e1507e1f..656e99d9c 100644 --- a/tests/tools/input_json/samtools_merge.json +++ b/tests/tools/input_json/samtools_merge.json @@ -1,4 +1,4 @@ { - "bams": ["tests/input/test2.bam", "tests/input/test.bwa_aln_pe.bam"], + "bams": ["tests/input/test2.bam", "tests/input/test.bwa_aln_pe.chrY_chrM.bam"], "prefix": "test" } \ No newline at end of file diff --git a/tests/tools/test_deeptools.yaml b/tests/tools/test_deeptools.yaml index 5974242f8..dc318ca12 100644 --- 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/input/test.bwa_aln_pe.bam" bam_index="tests/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.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 diff --git a/tests/tools/test_fastqc.yaml b/tests/tools/test_fastqc.yaml index 09594742c..653c6cf0a 100644 --- 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/input/test.bwa_aln_pe.bam" + 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 diff --git a/tests/tools/test_gatk4.yaml b/tests/tools/test_gatk4.yaml index 6e9541b97..7a1f64056 100644 --- 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/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.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 diff --git a/tests/tools/test_htseq.yaml b/tests/tools/test_htseq.yaml index 7c09b69dc..dab3e6fc4 100644 --- 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/input/test.bwa_aln_pe.bam" gtf="tests/input/genes.chrY_chrM.gtf.gz" strandedness="no" + 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 @@ -12,6 +12,6 @@ - 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/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/gencode.v31.chrY_chrM.genelengths.txt" files: - path: test-output/out/tpm_file/test.bwa_aln_pe.TPM.txt diff --git a/tests/tools/test_md5sum.yaml b/tests/tools/test_md5sum.yaml index 90bfd08ba..2ff793543 100644 --- 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/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.chrY_chrM.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 index 0bd658870..23b5237dc 100644 --- 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/input/test.bwa_aln_pe.bam" bam_index="tests/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.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 diff --git a/tests/tools/test_ngsderive.yaml b/tests/tools/test_ngsderive.yaml index 836c3d542..3fd7482f8 100644 --- a/tests/tools/test_ngsderive.yaml +++ b/tests/tools/test_ngsderive.yaml @@ -3,7 +3,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task strandedness tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" gene_model="tests/input/genes.chrY_chrM.gtf.gz" + 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 contains: @@ -14,7 +14,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task instrument tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 contains: @@ -26,7 +26,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task read_length tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" + 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 contains: @@ -49,7 +49,7 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task junction_annotation tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" bam_index="tests/input/test.bwa_aln_pe.bam.bai" gene_model="tests/input/genes.chrY_chrM.gtf.gz" + 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 @@ -59,6 +59,6 @@ - miniwdl - ngsderive command: >- - miniwdl run --verbose -d test-output/. --task endedness tools/ngsderive.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 diff --git a/tests/tools/test_picard.yaml b/tests/tools/test_picard.yaml index 335461f47..339821c5a 100644 --- a/tests/tools/test_picard.yaml +++ b/tests/tools/test_picard.yaml @@ -3,7 +3,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task mark_duplicates tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 @@ -15,7 +15,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task validate_bam tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 @@ -24,7 +24,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - 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 @@ -34,7 +34,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task sort tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" memory_gb=16 + 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 @@ -44,7 +44,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task sort tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" memory_gb=16 sort_order="queryname" + 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 @@ -62,7 +62,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task clean_sam tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task clean_sam tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - path: test-output/out/cleaned_bam/test.bwa_aln_pe.cleaned.bam @@ -71,7 +71,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_wgs_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" reference_fasta="tests/input/GRCh38.chrY_chrM.fa.gz" + miniwdl run --verbose -d test-output/. --task collect_wgs_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" reference_fasta="tests/input/GRCh38.chrY_chrM.fa.gz" files: - path: test-output/out/wgs_metrics/test.bwa_aln_pe.CollectWgsMetrics.txt @@ -80,7 +80,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_alignment_summary_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task collect_alignment_summary_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - path: test-output/out/alignment_metrics/test.bwa_aln_pe.CollectAlignmentSummaryMetrics.txt - path: test-output/out/alignment_metrics_pdf/test.bwa_aln_pe.CollectAlignmentSummaryMetrics.pdf @@ -90,7 +90,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_gc_bias_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz + miniwdl run --verbose -d test-output/. --task collect_gc_bias_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz files: - path: test-output/out/gc_bias_metrics/test.bwa_aln_pe.CollectGcBiasMetrics.txt - path: test-output/out/gc_bias_metrics_summary/test.bwa_aln_pe.CollectGcBiasMetrics.summary.txt @@ -101,7 +101,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_insert_size_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task collect_insert_size_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - path: test-output/out/insert_size_metrics/test.bwa_aln_pe.CollectInsertSizeMetrics.txt - path: test-output/out/insert_size_metrics_pdf/test.bwa_aln_pe.CollectInsertSizeMetrics.pdf @@ -111,7 +111,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task quality_score_distribution tools/picard.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 diff --git a/tests/tools/test_qualimap.yaml b/tests/tools/test_qualimap.yaml index 189c41b74..75fac084b 100644 --- a/tests/tools/test_qualimap.yaml +++ b/tests/tools/test_qualimap.yaml @@ -4,7 +4,7 @@ - qualimap - deprecated command: >- - miniwdl run --verbose -d test-output/. --task bamqc tools/qualimap.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 @@ -13,7 +13,7 @@ - miniwdl - qualimap command: >- - miniwdl run --verbose -d test-output/. --task rnaseq tools/qualimap.wdl bam="tests/input/test.bwa_aln_pe.bam" gtf="tests/input/genes.chrY_chrM.gtf.gz" + 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/raw_summary/rnaseq_qc_results.txt diff --git a/tests/tools/test_sambamba.yaml b/tests/tools/test_sambamba.yaml index 18189bee5..ee75e4cd2 100644 --- a/tests/tools/test_sambamba.yaml +++ b/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.bam" + 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 @@ -21,7 +21,7 @@ - miniwdl - sambamba command: >- - miniwdl run -d test-output/. --task sort tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 @@ -30,7 +30,7 @@ - miniwdl - sambamba command: >- - miniwdl run -d test-output/. --task flagstat tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 @@ -39,7 +39,7 @@ - miniwdl - sambamba command: >- - miniwdl run -d test-output/. --task markdup tools/sambamba.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 diff --git a/tests/tools/test_samtools.yaml b/tests/tools/test_samtools.yaml index 28f9d3c85..3229b86ee 100644 --- a/tests/tools/test_samtools.yaml +++ b/tests/tools/test_samtools.yaml @@ -3,7 +3,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task quickcheck tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task quickcheck tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" stdout: contains_regex: - "passed" @@ -39,7 +39,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task flagstat tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 contains: @@ -54,7 +54,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task index tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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 @@ -81,7 +81,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task addreplacerg tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" read_group_id="test" + 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 @@ -90,7 +90,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task collate tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task collate tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - path: test-output/out/collated_bam/test.bwa_aln_pe.collated.bam @@ -99,7 +99,7 @@ - miniwdl - samtools command: >- - miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.bam" retain_collated_bam=true + 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 diff --git a/tests/tools/test_star.yaml b/tests/tools/test_star.yaml index f51fbea0a..1e85bf74d 100644 --- a/tests/tools/test_star.yaml +++ b/tests/tools/test_star.yaml @@ -4,7 +4,7 @@ - star - reference command: >- - miniwdl run --verbose -d test-output/. --task build_star_db tools/star.wdl reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz gtf=tests/input/genes.chrY_chrM.gtf.gz + miniwdl run --verbose -d test-output/. --task build_star_db tools/star.wdl reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz gtf=tests/input/gencode.v31.chrY_chrM.gtf.gz files: - path: test-output/out/star_db/star_db.tar.gz diff --git a/tests/tools/test_util.yaml b/tests/tools/test_util.yaml index 8d2a1551f..3e04b3f95 100644 --- a/tests/tools/test_util.yaml +++ b/tests/tools/test_util.yaml @@ -44,7 +44,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task calc_gene_lengths tools/util.wdl gtf="tests/input/genes.chrY_chrM.gtf.gz" + miniwdl run --verbose -d test-output/. --task calc_gene_lengths tools/util.wdl gtf="tests/input/gencode.v31.chrY_chrM.gtf.gz" files: - path: test-output/out/gene_lengths/genes.genelengths.txt contains: @@ -66,7 +66,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task compression_integrity tools/util.wdl bgzipped_file="tests/input/test.bwa_aln_pe.bam" + miniwdl run --verbose -d test-output/. --task compression_integrity tools/util.wdl bgzipped_file="tests/input/test.bwa_aln_pe.chrY_chrM.bam" stdout: contains: - "passed" @@ -77,7 +77,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task add_to_bam_header tools/util.wdl bam="tests/input/test.bwa_aln_pe.bam" additional_header="@RG ID:3" + 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" @@ -96,7 +96,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task make_coverage_regions_bed tools/util.wdl gtf="tests/input/genes.chrY_chrM.gtf.gz" feature_type="exon" + miniwdl run --verbose -d test-output/. --task make_coverage_regions_bed tools/util.wdl gtf="tests/input/gencode.v31.chrY_chrM.gtf.gz" feature_type="exon" files: - path: "test-output/out/bed/genes.exon.bed" @@ -105,7 +105,7 @@ - miniwdl - util command: >- - miniwdl run --verbose -d test-output/. --task global_phred_scores tools/util.wdl bam="tests/input/test.bwa_aln_pe.bam" + 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" diff --git a/tests/workflows/input_json/rnaseq-standard.json b/tests/workflows/input_json/rnaseq-standard.json index e338893e3..a45724177 100644 --- a/tests/workflows/input_json/rnaseq-standard.json +++ b/tests/workflows/input_json/rnaseq-standard.json @@ -1,6 +1,6 @@ { - "rnaseq_standard.bam": "tests/input/test.bwa_aln_pe.bam", - "rnaseq_standard.gtf": "tests/input/genes.chrY_chrM.gtf.gz", + "rnaseq_standard.bam": "tests/input/test.bwa_aln_pe.chrY_chrM.bam", + "rnaseq_standard.gtf": "tests/input/gencode.v31.chrY_chrM.gtf.gz", "rnaseq_standard.star_db": "tests/input/star_db.chrY_chrM.tar.gz", "rnaseq_standard.strandedness": "Unstranded" } From 1303a34c2088ad24c23f75d05b18ae2c5f854bc6 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 17:13:03 -0500 Subject: [PATCH 11/25] WIP --- tests/input/GRCh38.chrY_chrM.dict | 3 +++ tests/input/GRCh38.chrY_chrM.fa | 3 +++ tests/input/GRCh38.chrY_chrM.fa.fai | 2 ++ tests/input/GRCh38.chrY_chrM.fa.gz | 3 --- tests/workflows/input_json/dnaseq-standard.json | 4 ++++ tests/workflows/input_json/qc-standard.json | 5 +++++ workflows/dnaseq/dnaseq-standard.wdl | 4 ++-- workflows/qc/quality-check-standard.wdl | 6 +++--- 8 files changed, 22 insertions(+), 8 deletions(-) create mode 100644 tests/input/GRCh38.chrY_chrM.dict create mode 100644 tests/input/GRCh38.chrY_chrM.fa create mode 100644 tests/input/GRCh38.chrY_chrM.fa.fai delete mode 100644 tests/input/GRCh38.chrY_chrM.fa.gz create mode 100644 tests/workflows/input_json/dnaseq-standard.json create mode 100644 tests/workflows/input_json/qc-standard.json diff --git a/tests/input/GRCh38.chrY_chrM.dict b/tests/input/GRCh38.chrY_chrM.dict new file mode 100644 index 000000000..13c64ee61 --- /dev/null +++ b/tests/input/GRCh38.chrY_chrM.dict @@ -0,0 +1,3 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chrY LN:57227415 M5:ce3e31103314a704255f3cd90369ecce UR:file:///Users/afrantz/workflows/tests/input/GRCh38.chrY_chrM.fa.gz +@SQ SN:chrM LN:16569 M5:c68f52674c9fb33aef52dcf399755519 UR:file:///Users/afrantz/workflows/tests/input/GRCh38.chrY_chrM.fa.gz diff --git a/tests/input/GRCh38.chrY_chrM.fa b/tests/input/GRCh38.chrY_chrM.fa new file mode 100644 index 000000000..26d8494c7 --- /dev/null +++ b/tests/input/GRCh38.chrY_chrM.fa @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1d6d51aee25e5c8005a655d6165f8de3db9422ec7c0b5ea87f529a900e622f42 +size 58062025 diff --git a/tests/input/GRCh38.chrY_chrM.fa.fai b/tests/input/GRCh38.chrY_chrM.fa.fai new file mode 100644 index 000000000..fb6ea39ed --- /dev/null +++ b/tests/input/GRCh38.chrY_chrM.fa.fai @@ -0,0 +1,2 @@ +chrY 57227415 147 70 71 +chrM 16569 58045219 70 71 diff --git a/tests/input/GRCh38.chrY_chrM.fa.gz b/tests/input/GRCh38.chrY_chrM.fa.gz deleted file mode 100644 index 482bf460f..000000000 --- a/tests/input/GRCh38.chrY_chrM.fa.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:1b5073d1ac4509609573a275566f9cf0b3d28682abb635d79ef8a524615e455c -size 7060411 diff --git a/tests/workflows/input_json/dnaseq-standard.json b/tests/workflows/input_json/dnaseq-standard.json new file mode 100644 index 000000000..dec3d6ab3 --- /dev/null +++ b/tests/workflows/input_json/dnaseq-standard.json @@ -0,0 +1,4 @@ +{ + "dnaseq_standard_experimental.bam": "tests/input/test.bwa_aln_pe.chrY_chrM.bam", + "dnaseq_standard_experimental.bwa_db": "tests/input/bwa_db.tar.gz" +} diff --git a/tests/workflows/input_json/qc-standard.json b/tests/workflows/input_json/qc-standard.json new file mode 100644 index 000000000..924ca8ed9 --- /dev/null +++ b/tests/workflows/input_json/qc-standard.json @@ -0,0 +1,5 @@ +{ + "quality_check.bam": "tests/input/test.bwa_aln_pe.chrY_chrM.bam", + "quality_check.bam_index": "tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai", + "quality_check.kraken_db": "tests/input/kraken2_db.tar.gz" +} \ No newline at end of file diff --git a/workflows/dnaseq/dnaseq-standard.wdl b/workflows/dnaseq/dnaseq-standard.wdl index 259495669..cd6b1e44e 100644 --- a/workflows/dnaseq/dnaseq-standard.wdl +++ b/workflows/dnaseq/dnaseq-standard.wdl @@ -21,7 +21,7 @@ workflow dnaseq_standard_experimental { parameter_meta { bam: "Input BAM to realign" bwa_db: "Gzipped tar archive of the bwa reference files. Files should be at the root of the archive." - reads_per_file: "Controls the number of reads per FASTQ file for internal split to run BWA in parallel." + sample_override: "Value to override the SM field of *every* read group." prefix: "Prefix for the BAM file. The extension `.bam` will be added." aligner: { description: "BWA aligner to use", @@ -32,8 +32,8 @@ workflow dnaseq_standard_experimental { } validate_input: "Ensure input BAM is well-formed before beginning harmonization?" use_all_cores: "Use all cores? Recommended for cloud environments." + reads_per_file: "Controls the number of reads per FASTQ file for internal split to run BWA in parallel." subsample_n_reads: "Only process a random sampling of `n` reads. Any `n`<=`0` for processing entire input." - sample_override: "Value to override the SM field of *every* read group." } input { diff --git a/workflows/qc/quality-check-standard.wdl b/workflows/qc/quality-check-standard.wdl index 17f255682..5e308dddc 100644 --- a/workflows/qc/quality-check-standard.wdl +++ b/workflows/qc/quality-check-standard.wdl @@ -80,12 +80,12 @@ workflow quality_check { bam: "Input BAM format file to quality check" bam_index: "BAM index file corresponding to the input BAM" kraken_db: "Kraken2 database. Can be generated with `../reference/make-qc-reference.wdl`. Must be a tarball without a root directory." + coverage_beds: "An array of 3 column BEDs which are passed to the `-b` flag of mosdepth, in order to restrict coverage analysis to select regions. Any regional analysis enabled by this option is _in addition_ to whole genome coverage, which is calculated regardless of this setting. An exon BED and a Coding Sequence BED are examples of regions you may wish to restrict coverage analysis to. Those two BEDs can be created with the workflow in `../reference/make-qc-reference.wdl`." + gtf: "GTF features file. Gzipped or uncompressed. **Required** for RNA-Seq data." standard_filter: "Filter to apply to the input BAM while converting to FASTQ, before running Kraken2 and `librarian` (if `run_librarian == true`). This is a `FlagFilter` object (see ../../data_structures/flag_filter.wdl for more information). By default, it will **remove secondary and supplementary reads** from the created FASTQs. **WARNING:** These filters can be tricky to configure; please read documentation thoroughly before changing the defaults. **WARNING:** If you have set `run_librarian` to `true`, we **strongly** recommend leaving this filter at the default value. `librarian` is trained on a specific set of reads, and changing this filter may produce nonsensical results." comparative_filter: "Filter to apply to the input BAM while performing a second FASTQ conversion, before running Kraken2 another time. This is a `FlagFilter` object (see ../../data_structures/flag_filter.wdl for more information). By default, it will **remove unmapped, secondary, and supplementary reads** from the created FASTQs. **WARNING** These filters can be tricky to configure; please read documentation thoroughly before changing the defaults." - gtf: "GTF features file. Gzipped or uncompressed. **Required** for RNA-Seq data." multiqc_config: "YAML file for configuring MultiQC" extra_multiqc_inputs: "An array of additional files to pass directly into MultiQC" - coverage_beds: "An array of 3 column BEDs which are passed to the `-b` flag of mosdepth, in order to restrict coverage analysis to select regions. Any regional analysis enabled by this option is _in addition_ to whole genome coverage, which is calculated regardless of this setting. An exon BED and a Coding Sequence BED are examples of regions you may wish to restrict coverage analysis to. Those two BEDs can be created with the workflow in `../reference/make-qc-reference.wdl`." coverage_labels: "An array of equal length to `coverage_beds` which determines the prefix label applied to the output files. If omitted, defaults of `regions1`, `regions2`, etc. will be used. If using the BEDs created by `../reference/make-qc-reference.wdl`, the labels [\"exon\", \"CDS\"] are appropriate. Make sure to provide the coverage BEDs **in the same order** as the labels." prefix: "Prefix for all results files" rna: "Is the sequenced molecule RNA? Enabling this option adds RNA-Seq specific analyses to the workflow. If `true`, a GTF file must be provided. If `false`, the GTF file is ignored." @@ -106,12 +106,12 @@ workflow quality_check { File bam File bam_index File kraken_db + Array[File]+ coverage_beds File? gtf #@ except: LineWidth File multiqc_config = "https://raw.githubusercontent.com/stjudecloud/workflows/main/workflows/qc/inputs/multiqc_config_hg38.yaml" Array[File] extra_multiqc_inputs = [] - Array[File] coverage_beds = [] Array[String] coverage_labels = [] FlagFilter standard_filter = { "include_if_all": "0x0", From fa97539396abc02a167efd4b398dd07f13f3b570 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 17:19:49 -0500 Subject: [PATCH 12/25] WIP --- tests/input/gencode.v31.chrY_chrM.gene.bed | 604 ++++++++++++++++++++ tests/workflows/input_json/qc-standard.json | 5 +- 2 files changed, 608 insertions(+), 1 deletion(-) create mode 100644 tests/input/gencode.v31.chrY_chrM.gene.bed diff --git a/tests/input/gencode.v31.chrY_chrM.gene.bed b/tests/input/gencode.v31.chrY_chrM.gene.bed new file mode 100644 index 000000000..cc0861c13 --- /dev/null +++ b/tests/input/gencode.v31.chrY_chrM.gene.bed @@ -0,0 +1,604 @@ +chrM 576 647 +chrM 647 1601 +chrM 1601 1670 +chrM 1670 3229 +chrM 3229 3304 +chrM 3306 4262 +chrM 4262 4331 +chrM 4328 4400 +chrM 4401 4469 +chrM 4469 5511 +chrM 5511 5579 +chrM 5586 5655 +chrM 5656 5729 +chrM 5760 5826 +chrM 5825 5891 +chrM 5903 7445 +chrM 7445 7514 +chrM 7517 7585 +chrM 7585 8269 +chrM 8294 8364 +chrM 8365 8572 +chrM 8526 9207 +chrM 9206 9990 +chrM 9990 10058 +chrM 10058 10404 +chrM 10404 10469 +chrM 10469 10766 +chrM 10759 12137 +chrM 12137 12206 +chrM 12206 12265 +chrM 12265 12336 +chrM 12336 14148 +chrM 14148 14673 +chrM 14673 14742 +chrM 14746 15887 +chrM 15887 15953 +chrM 15955 16023 +chrY 253742 255091 +chrY 276321 303356 +chrY 304528 318819 +chrY 320989 321851 +chrY 333962 386955 +chrY 386979 405579 +chrY 388099 388389 +chrY 419156 421980 +chrY 523774 524102 +chrY 545235 545352 +chrY 624343 659411 +chrY 990220 994365 +chrY 1008502 1010101 +chrY 1187548 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23762837 23765583 +chrY 23771231 23798150 +chrY 23808820 23809059 +chrY 23855521 23857091 +chrY 23917240 23917723 +chrY 23919904 23921510 +chrY 23934952 23940101 +chrY 23936726 23941622 +chrY 23945926 23952293 +chrY 23946617 23946771 +chrY 23956568 23960218 +chrY 23967563 23970694 +chrY 23972779 23995081 +chrY 24006910 24007237 +chrY 24045228 24048019 +chrY 24049877 24051487 +chrY 24077798 24079812 +chrY 24081703 24090346 +chrY 24104106 24106018 +chrY 24142357 24157843 +chrY 24168186 24174494 +chrY 24179315 24183505 +chrY 24182476 24183071 +chrY 24183433 24187231 +chrY 24186508 24191870 +chrY 24196517 24206132 +chrY 24209566 24215581 +chrY 24210957 24211216 +chrY 24232825 24238984 +chrY 24276244 24277026 +chrY 24278336 24281140 +chrY 24283061 24283230 +chrY 24362334 24362409 +chrY 24396603 24403526 +chrY 24485331 24486463 +chrY 24494708 24495583 +chrY 24500262 24501505 +chrY 24570201 24607025 +chrY 24607559 24639207 +chrY 24650807 24651534 +chrY 24659336 24660406 +chrY 24683656 24684935 +chrY 24691790 24692932 +chrY 24763068 24813492 +chrY 24833842 24907040 +chrY 24977175 24978317 +chrY 24985200 24986476 +chrY 25009699 25010769 +chrY 25018498 25019303 +chrY 25030900 25062548 +chrY 25063082 25099892 +chrY 25168598 25169841 +chrY 25174519 25175237 +chrY 25182276 25213389 +chrY 25266583 25273531 +chrY 25307728 25307803 +chrY 25378299 25394719 +chrY 25388991 25391811 +chrY 25393153 25394056 +chrY 25431155 25437315 +chrY 25454560 25460572 +chrY 25458925 25459184 +chrY 25464005 25473621 +chrY 25478268 25483630 +chrY 25482907 25486705 +chrY 25486639 25487322 +chrY 25487283 25487662 +chrY 25495650 25501958 +chrY 25512300 25527786 +chrY 25564121 25566033 +chrY 25579789 25588444 +chrY 25590322 25592345 +chrY 25618643 25620253 +chrY 25622161 25624902 +chrY 25662899 25663226 +chrY 25675059 25697346 +chrY 25699450 25702562 +chrY 25709907 25713557 +chrY 25723015 25724186 +chrY 25723341 25723495 +chrY 25728489 25733388 +chrY 25730010 25735160 +chrY 25748595 25750206 +chrY 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57214397 diff --git a/tests/workflows/input_json/qc-standard.json b/tests/workflows/input_json/qc-standard.json index 924ca8ed9..0ac5a0ddf 100644 --- a/tests/workflows/input_json/qc-standard.json +++ b/tests/workflows/input_json/qc-standard.json @@ -1,5 +1,8 @@ { "quality_check.bam": "tests/input/test.bwa_aln_pe.chrY_chrM.bam", "quality_check.bam_index": "tests/input/test.bwa_aln_pe.chrY_chrM.bam.bai", - "quality_check.kraken_db": "tests/input/kraken2_db.tar.gz" + "quality_check.kraken_db": "tests/input/kraken2_db.tar.gz", + "quality_check.coverage_beds": [ + "tests/input/gencode.v31.chrY_chrM.gene.bed" + ] } \ No newline at end of file From 971d3bbd5d07f000032d76a8db47700389f7494b Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 18:12:18 -0500 Subject: [PATCH 13/25] fix: --- tests/input/test.bwa_aln_pe.readlength.txt | 2 +- tests/tools/input_json/multiqc.json | 2 +- .../tools/input_json/ngsderive_encoding.json | 2 +- tests/tools/test_deeptools.yaml | 2 +- tests/tools/test_estimate.yaml | 4 ++-- tests/tools/test_fastqc.yaml | 2 +- tests/tools/test_gatk4.yaml | 6 +++--- tests/tools/test_htseq.yaml | 6 +++--- tests/tools/test_md5sum.yaml | 2 +- tests/tools/test_mosdepth.yaml | 4 ++-- tests/tools/test_multiqc.yaml | 2 +- tests/tools/test_ngsderive.yaml | 14 ++++++------- tests/tools/test_picard.py | 2 +- tests/tools/test_picard.yaml | 20 +++++++++---------- tests/tools/test_qualimap.yaml | 4 ++-- tests/tools/test_sambamba.yaml | 12 +++++------ tests/tools/test_samtools.py | 4 ++-- tests/tools/test_samtools.yaml | 10 +++++----- tests/tools/test_util.yaml | 4 ++-- .../input_json/rnaseq-variant-calling.json | 16 +++++++++++++++ 20 files changed, 68 insertions(+), 52 deletions(-) create mode 100644 tests/workflows/input_json/rnaseq-variant-calling.json diff --git a/tests/input/test.bwa_aln_pe.readlength.txt b/tests/input/test.bwa_aln_pe.readlength.txt index f3fa86d4e..47e55dc37 100644 --- a/tests/input/test.bwa_aln_pe.readlength.txt +++ b/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 diff --git a/tests/tools/input_json/multiqc.json b/tests/tools/input_json/multiqc.json index fdf7954e5..9de83e9ea 100644 --- a/tests/tools/input_json/multiqc.json +++ b/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" } \ No newline at end of file diff --git a/tests/tools/input_json/ngsderive_encoding.json b/tests/tools/input_json/ngsderive_encoding.json index e2271d0cf..5a3cccf7d 100644 --- a/tests/tools/input_json/ngsderive_encoding.json +++ b/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" } diff --git a/tests/tools/test_deeptools.yaml b/tests/tools/test_deeptools.yaml index dc318ca12..e5dd47eb1 100644 --- a/tests/tools/test_deeptools.yaml +++ b/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 diff --git a/tests/tools/test_estimate.yaml b/tests/tools/test_estimate.yaml index 46febc352..6b3f56418 100644 --- 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/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 diff --git a/tests/tools/test_fastqc.yaml b/tests/tools/test_fastqc.yaml index 653c6cf0a..60a95c722 100644 --- a/tests/tools/test_fastqc.yaml +++ b/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 diff --git a/tests/tools/test_gatk4.yaml b/tests/tools/test_gatk4.yaml index 7a1f64056..b8244bbb4 100644 --- a/tests/tools/test_gatk4.yaml +++ b/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 \ No newline at end of file + - 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 \ No newline at end of file diff --git a/tests/tools/test_htseq.yaml b/tests/tools/test_htseq.yaml index dab3e6fc4..8b2b401d7 100644 --- a/tests/tools/test_htseq.yaml +++ b/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 diff --git a/tests/tools/test_md5sum.yaml b/tests/tools/test_md5sum.yaml index 2ff793543..a648dcb9c 100644 --- a/tests/tools/test_md5sum.yaml +++ b/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" diff --git a/tests/tools/test_mosdepth.yaml b/tests/tools/test_mosdepth.yaml index 23b5237dc..76c6da11c 100644 --- a/tests/tools/test_mosdepth.yaml +++ b/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 diff --git a/tests/tools/test_multiqc.yaml b/tests/tools/test_multiqc.yaml index 542e3e9a9..4b1219f41 100644 --- a/tests/tools/test_multiqc.yaml +++ b/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 diff --git a/tests/tools/test_ngsderive.yaml b/tests/tools/test_ngsderive.yaml index 3fd7482f8..b9e828508 100644 --- a/tests/tools/test_ngsderive.yaml +++ b/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 diff --git a/tests/tools/test_picard.py b/tests/tools/test_picard.py index 6d1eacacc..4f6de9782 100644 --- a/tests/tools/test_picard.py +++ b/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 \ No newline at end of file diff --git a/tests/tools/test_picard.yaml b/tests/tools/test_picard.yaml index 339821c5a..1fcf2ed4f 100644 --- a/tests/tools/test_picard.yaml +++ b/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: diff --git a/tests/tools/test_qualimap.yaml b/tests/tools/test_qualimap.yaml index 75fac084b..b37eadf6f 100644 --- a/tests/tools/test_qualimap.yaml +++ b/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 diff --git a/tests/tools/test_sambamba.yaml b/tests/tools/test_sambamba.yaml index ee75e4cd2..c893a503d 100644 --- a/tests/tools/test_sambamba.yaml +++ b/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 \ No newline at end of file + - 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 \ No newline at end of file diff --git a/tests/tools/test_samtools.py b/tests/tools/test_samtools.py index a58bf4603..a870cc83a 100644 --- a/tests/tools/test_samtools.py +++ b/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") diff --git a/tests/tools/test_samtools.yaml b/tests/tools/test_samtools.yaml index 3229b86ee..5c06dd2a7 100644 --- a/tests/tools/test_samtools.yaml +++ b/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: diff --git a/tests/tools/test_util.yaml b/tests/tools/test_util.yaml index 3e04b3f95..611e57187 100644 --- a/tests/tools/test_util.yaml +++ b/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: diff --git a/tests/workflows/input_json/rnaseq-variant-calling.json b/tests/workflows/input_json/rnaseq-variant-calling.json new file mode 100644 index 000000000..ada5628b3 --- /dev/null +++ b/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" +} From d2d33d938ae600672ee4df38e0874aa999ece2e1 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 18:16:47 -0500 Subject: [PATCH 14/25] fix --- ...{test.bwa_aln_pe.TPM.txt => test.bwa_aln_pe.chrY_chrM.TPM.txt} | 0 ...re-counts.txt => test.bwa_aln_pe.chrY_chrM.feature-counts.txt} | 0 ...pe.readlength.txt => test.bwa_aln_pe.chrY_chrM.readlength.txt} | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename tests/input/{test.bwa_aln_pe.TPM.txt => test.bwa_aln_pe.chrY_chrM.TPM.txt} (100%) rename tests/input/{test.bwa_aln_pe.feature-counts.txt => test.bwa_aln_pe.chrY_chrM.feature-counts.txt} (100%) rename tests/input/{test.bwa_aln_pe.readlength.txt => test.bwa_aln_pe.chrY_chrM.readlength.txt} (100%) diff --git a/tests/input/test.bwa_aln_pe.TPM.txt b/tests/input/test.bwa_aln_pe.chrY_chrM.TPM.txt similarity index 100% rename from tests/input/test.bwa_aln_pe.TPM.txt rename to tests/input/test.bwa_aln_pe.chrY_chrM.TPM.txt diff --git a/tests/input/test.bwa_aln_pe.feature-counts.txt b/tests/input/test.bwa_aln_pe.chrY_chrM.feature-counts.txt similarity index 100% rename from tests/input/test.bwa_aln_pe.feature-counts.txt rename to tests/input/test.bwa_aln_pe.chrY_chrM.feature-counts.txt diff --git a/tests/input/test.bwa_aln_pe.readlength.txt b/tests/input/test.bwa_aln_pe.chrY_chrM.readlength.txt similarity index 100% rename from tests/input/test.bwa_aln_pe.readlength.txt rename to tests/input/test.bwa_aln_pe.chrY_chrM.readlength.txt From 9966797129656dd5e0ae44ace286552b117e3f2a Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 18:19:48 -0500 Subject: [PATCH 15/25] Update test_fastqc.yaml --- tests/tools/test_fastqc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/tools/test_fastqc.yaml b/tests/tools/test_fastqc.yaml index 60a95c722..dc0ed642e 100644 --- a/tests/tools/test_fastqc.yaml +++ b/tests/tools/test_fastqc.yaml @@ -5,5 +5,5 @@ command: >- 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/raw_data/test.bwa_aln_pe.chrM_chrY_fastqc.zip - path: test-output/out/results/test.bwa_aln_pe.chrY_chrM.fastqc_results.tar.gz From a3f0a2523ae57bb83f7bda945ff84ba1f3950ea4 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 18:23:55 -0500 Subject: [PATCH 16/25] Update test_fastqc.yaml --- tests/tools/test_fastqc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/tools/test_fastqc.yaml b/tests/tools/test_fastqc.yaml index dc0ed642e..d9a6d10bb 100644 --- a/tests/tools/test_fastqc.yaml +++ b/tests/tools/test_fastqc.yaml @@ -5,5 +5,5 @@ command: >- 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.chrM_chrY_fastqc.zip + - path: test-output/out/raw_data/test.bwa_aln_pe.chrY_chrM_fastqc.zip - path: test-output/out/results/test.bwa_aln_pe.chrY_chrM.fastqc_results.tar.gz From 0e15ff936acdac9a4e11e55503faf019a3a89507 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Mon, 25 Nov 2024 18:31:07 -0500 Subject: [PATCH 17/25] Update multiqc.json --- tests/tools/input_json/multiqc.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/tools/input_json/multiqc.json b/tests/tools/input_json/multiqc.json index 9de83e9ea..46ac12563 100644 --- a/tests/tools/input_json/multiqc.json +++ b/tests/tools/input_json/multiqc.json @@ -1,4 +1,4 @@ { "files": ["tests/input/test.bwa_aln_pe.chrY_chrM.readlength.txt"], - "prefix": "test.bwa_aln_pe" + "prefix": "test.bwa_aln_pe.chrY_chrM" } \ No newline at end of file From 615787cba17d7cb92d5bf7cf2922b7fb45cd7f71 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Tue, 26 Nov 2024 09:23:12 -0500 Subject: [PATCH 18/25] fix: more renaming --- tests/tools/test_samtools.py | 2 +- tests/tools/test_samtools.yaml | 4 ++-- tests/tools/test_util.yaml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/tools/test_samtools.py b/tests/tools/test_samtools.py index a870cc83a..a06f4ed3b 100644 --- a/tests/tools/test_samtools.py +++ b/tests/tools/test_samtools.py @@ -34,7 +34,7 @@ def test_samtools_merge(workflow_dir): @pytest.mark.workflow('samtools_collate', 'samtools_collate_to_fastq') def test_samtools_collate(workflow_dir): - bam = pathlib.Path(workflow_dir, 'test-output/out/collated_bam/test.bwa_aln_pe.collated.bam') + bam = pathlib.Path(workflow_dir, 'test-output/out/collated_bam/test.bwa_aln_pe.chrY_chrM.collated.bam') samfile = pysam.AlignmentFile(bam, "rb") reads = list(samfile.fetch(until_eof=True)) diff --git a/tests/tools/test_samtools.yaml b/tests/tools/test_samtools.yaml index 5c06dd2a7..e5652b2a0 100644 --- a/tests/tools/test_samtools.yaml +++ b/tests/tools/test_samtools.yaml @@ -92,7 +92,7 @@ command: >- miniwdl run --verbose -d test-output/. --task collate tools/samtools.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - - path: test-output/out/collated_bam/test.bwa_aln_pe.collated.bam + - path: test-output/out/collated_bam/test.bwa_aln_pe.chrY_chrM.collated.bam - name: samtools_bam_to_fastq tags: @@ -101,7 +101,7 @@ command: >- 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/collated_bam/test.bwa_aln_pe.chrY_chrM.collated.bam - 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 diff --git a/tests/tools/test_util.yaml b/tests/tools/test_util.yaml index 611e57187..53014bd17 100644 --- a/tests/tools/test_util.yaml +++ b/tests/tools/test_util.yaml @@ -98,7 +98,7 @@ command: >- miniwdl run --verbose -d test-output/. --task make_coverage_regions_bed tools/util.wdl gtf="tests/input/gencode.v31.chrY_chrM.gtf.gz" feature_type="exon" files: - - path: "test-output/out/bed/genes.exon.bed" + - path: "test-output/out/bed/gencode.v31.chrY_chrM.exon.bed" - name: global_phred_scores tags: From 8cfbfaafbe396f097b18cbed8a7e7172307b288e Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Tue, 26 Nov 2024 09:41:43 -0500 Subject: [PATCH 19/25] Update test_samtools.py --- tests/tools/test_samtools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/tools/test_samtools.py b/tests/tools/test_samtools.py index a06f4ed3b..d9b16efb1 100644 --- a/tests/tools/test_samtools.py +++ b/tests/tools/test_samtools.py @@ -30,7 +30,7 @@ def test_samtools_merge(workflow_dir): read_groups = [read_group['ID'] for read_group in bam_header.get('RG', []) if 'ID' in read_group] assert len(read_groups) == 2 assert read_groups[0] == "test2" - assert read_groups[1] == "test.bwa_aln_pe" + assert read_groups[1] == "test.bwa_aln_pe.chrY_chrM" @pytest.mark.workflow('samtools_collate', 'samtools_collate_to_fastq') def test_samtools_collate(workflow_dir): From e9286fb3d1819d9fa2426177907d9ce390bf907d Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Tue, 26 Nov 2024 09:45:13 -0500 Subject: [PATCH 20/25] Update test_util.yaml --- tests/tools/test_util.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/tools/test_util.yaml b/tests/tools/test_util.yaml index 53014bd17..64ee98499 100644 --- a/tests/tools/test_util.yaml +++ b/tests/tools/test_util.yaml @@ -46,7 +46,7 @@ command: >- miniwdl run --verbose -d test-output/. --task calc_gene_lengths tools/util.wdl gtf="tests/input/gencode.v31.chrY_chrM.gtf.gz" files: - - path: test-output/out/gene_lengths/genes.genelengths.txt + - path: test-output/out/gene_lengths/gencode.v31.chrY_chrM.genelengths.txt contains: - "AL954722.1" From 44eb77f77df72826345a5a1f1208cfab3e6bedc8 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Tue, 26 Nov 2024 09:57:57 -0500 Subject: [PATCH 21/25] Update test_picard.yaml --- tests/tools/test_picard.yaml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/tests/tools/test_picard.yaml b/tests/tools/test_picard.yaml index 1fcf2ed4f..7abf805cc 100644 --- a/tests/tools/test_picard.yaml +++ b/tests/tools/test_picard.yaml @@ -26,8 +26,8 @@ command: >- miniwdl run --verbose -d test-output/. --task bam_to_fastq tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - - 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: picard_sort tags: @@ -64,7 +64,7 @@ command: >- miniwdl run --verbose -d test-output/. --task clean_sam tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - - path: test-output/out/cleaned_bam/test.bwa_aln_pe.cleaned.bam + - path: test-output/out/cleaned_bam/test.bwa_aln_pe.chrY_chrM.cleaned.bam - name: picard_collect_wgs_metrics tags: @@ -73,7 +73,7 @@ command: >- miniwdl run --verbose -d test-output/. --task collect_wgs_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" reference_fasta="tests/input/GRCh38.chrY_chrM.fa.gz" files: - - path: test-output/out/wgs_metrics/test.bwa_aln_pe.CollectWgsMetrics.txt + - path: test-output/out/wgs_metrics/test.bwa_aln_pe.chrY_chrM.CollectWgsMetrics.txt - name: picard_collect_alignment_summary_metrics tags: @@ -82,8 +82,8 @@ command: >- miniwdl run --verbose -d test-output/. --task collect_alignment_summary_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - - path: test-output/out/alignment_metrics/test.bwa_aln_pe.CollectAlignmentSummaryMetrics.txt - - path: test-output/out/alignment_metrics_pdf/test.bwa_aln_pe.CollectAlignmentSummaryMetrics.pdf + - path: test-output/out/alignment_metrics/test.bwa_aln_pe.chrY_chrM.CollectAlignmentSummaryMetrics.txt + - path: test-output/out/alignment_metrics_pdf/test.bwa_aln_pe.chrY_chrM.CollectAlignmentSummaryMetrics.pdf - name: picard_collect_gc_bias_metrics tags: @@ -92,9 +92,9 @@ command: >- miniwdl run --verbose -d test-output/. --task collect_gc_bias_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz files: - - path: test-output/out/gc_bias_metrics/test.bwa_aln_pe.CollectGcBiasMetrics.txt - - path: test-output/out/gc_bias_metrics_summary/test.bwa_aln_pe.CollectGcBiasMetrics.summary.txt - - path: test-output/out/gc_bias_metrics_pdf/test.bwa_aln_pe.CollectGcBiasMetrics.pdf + - path: test-output/out/gc_bias_metrics/test.bwa_aln_pe.chrY_chrM.CollectGcBiasMetrics.txt + - path: test-output/out/gc_bias_metrics_summary/test.bwa_aln_pe.chrY_chrM.CollectGcBiasMetrics.summary.txt + - path: test-output/out/gc_bias_metrics_pdf/test.bwa_aln_pe.chrY_chrM.CollectGcBiasMetrics.pdf - name: picard_collect_insert_size_metrics tags: @@ -103,8 +103,8 @@ command: >- miniwdl run --verbose -d test-output/. --task collect_insert_size_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - - path: test-output/out/insert_size_metrics/test.bwa_aln_pe.CollectInsertSizeMetrics.txt - - path: test-output/out/insert_size_metrics_pdf/test.bwa_aln_pe.CollectInsertSizeMetrics.pdf + - path: test-output/out/insert_size_metrics/test.bwa_aln_pe.chrY_chrMCollectInsertSizeMetrics.txt + - path: test-output/out/insert_size_metrics_pdf/test.bwa_aln_pe.chrY_chrM.CollectInsertSizeMetrics.pdf - name: picard_quality_score_distribution tags: From 6c61689a7f0178dceb37e6875e268d8367c20434 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Tue, 26 Nov 2024 10:03:24 -0500 Subject: [PATCH 22/25] Update test_picard.yaml --- tests/tools/test_picard.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/tools/test_picard.yaml b/tests/tools/test_picard.yaml index 7abf805cc..593d3a0fe 100644 --- a/tests/tools/test_picard.yaml +++ b/tests/tools/test_picard.yaml @@ -71,7 +71,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_wgs_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" reference_fasta="tests/input/GRCh38.chrY_chrM.fa.gz" + miniwdl run --verbose -d test-output/. --task collect_wgs_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" reference_fasta="tests/input/GRCh38.chrY_chrM.fa" files: - path: test-output/out/wgs_metrics/test.bwa_aln_pe.chrY_chrM.CollectWgsMetrics.txt @@ -90,7 +90,7 @@ - miniwdl - picard command: >- - miniwdl run --verbose -d test-output/. --task collect_gc_bias_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" reference_fasta=tests/input/GRCh38.chrY_chrM.fa.gz + miniwdl run --verbose -d test-output/. --task collect_gc_bias_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" reference_fasta=tests/input/GRCh38.chrY_chrM.fa files: - path: test-output/out/gc_bias_metrics/test.bwa_aln_pe.chrY_chrM.CollectGcBiasMetrics.txt - path: test-output/out/gc_bias_metrics_summary/test.bwa_aln_pe.chrY_chrM.CollectGcBiasMetrics.summary.txt @@ -103,7 +103,7 @@ command: >- miniwdl run --verbose -d test-output/. --task collect_insert_size_metrics tools/picard.wdl bam="tests/input/test.bwa_aln_pe.chrY_chrM.bam" files: - - path: test-output/out/insert_size_metrics/test.bwa_aln_pe.chrY_chrMCollectInsertSizeMetrics.txt + - path: test-output/out/insert_size_metrics/test.bwa_aln_pe.chrY_chrM.CollectInsertSizeMetrics.txt - path: test-output/out/insert_size_metrics_pdf/test.bwa_aln_pe.chrY_chrM.CollectInsertSizeMetrics.pdf - name: picard_quality_score_distribution @@ -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.gz" outfile_name="GRCh38.chrY_chrM.dict" + 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" files: - path: test-output/out/dictionary/GRCh38.chrY_chrM.dict \ No newline at end of file From f7059208b8928b8f107a5509c8dfed72711135e7 Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Tue, 26 Nov 2024 10:13:11 -0500 Subject: [PATCH 23/25] Update lint-check.yaml --- .github/workflows/lint-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/lint-check.yaml b/.github/workflows/lint-check.yaml index 6124d2551..96d19a6b7 100644 --- a/.github/workflows/lint-check.yaml +++ b/.github/workflows/lint-check.yaml @@ -71,6 +71,6 @@ jobs: EXITCODE=2 ;; esac - done < <(awk '/docker: .*stjudecloud/' < "$file") + done < <(awk '/container: .*stjudecloud/' < "$file") done exit $EXITCODE From 0e796ea4deb8637f08d100c7469abfea0ab2d66c Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Tue, 26 Nov 2024 10:17:51 -0500 Subject: [PATCH 24/25] fix: bump to latest util image --- data_structures/flag_filter.wdl | 2 +- tools/htseq.wdl | 2 +- tools/md5sum.wdl | 2 +- workflows/qc/quality-check-standard.wdl | 2 +- workflows/rnaseq/rnaseq-standard.wdl | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/data_structures/flag_filter.wdl b/data_structures/flag_filter.wdl index 9e9bd762e..3b7e4d542 100644 --- a/data_structures/flag_filter.wdl +++ b/data_structures/flag_filter.wdl @@ -118,7 +118,7 @@ task validate_string_is_12bit_oct_dec_or_hex { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.3.0" + container: "ghcr.io/stjudecloud/util:1.4.0" maxRetries: 1 } } diff --git a/tools/htseq.wdl b/tools/htseq.wdl index d6e90d673..f00679089 100755 --- a/tools/htseq.wdl +++ b/tools/htseq.wdl @@ -209,7 +209,7 @@ task calc_tpm { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.3.0" + container: "ghcr.io/stjudecloud/util:1.4.0" maxRetries: 1 } } diff --git a/tools/md5sum.wdl b/tools/md5sum.wdl index d7e98386d..fa58f984c 100755 --- a/tools/md5sum.wdl +++ b/tools/md5sum.wdl @@ -36,7 +36,7 @@ task compute_checksum { runtime { memory: "4 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/util:1.3.0" + container: "ghcr.io/stjudecloud/util:1.4.0" maxRetries: 1 } } diff --git a/workflows/qc/quality-check-standard.wdl b/workflows/qc/quality-check-standard.wdl index 5e308dddc..3daa31600 100644 --- a/workflows/qc/quality-check-standard.wdl +++ b/workflows/qc/quality-check-standard.wdl @@ -556,7 +556,7 @@ task parse_input { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.3.0" + container: "ghcr.io/stjudecloud/util:1.4.0" maxRetries: 1 } } diff --git a/workflows/rnaseq/rnaseq-standard.wdl b/workflows/rnaseq/rnaseq-standard.wdl index 35c110f0c..ea4cdd906 100755 --- a/workflows/rnaseq/rnaseq-standard.wdl +++ b/workflows/rnaseq/rnaseq-standard.wdl @@ -179,7 +179,7 @@ task parse_input { runtime { memory: "4 GB" disks: "10 GB" - container: "ghcr.io/stjudecloud/util:1.3.0" + container: "ghcr.io/stjudecloud/util:1.4.0" maxRetries: 1 } } From 22487945b9df56cbefbfc8e1694e8d8ffa94b18b Mon Sep 17 00:00:00 2001 From: Andrew Frantz Date: Tue, 26 Nov 2024 10:25:30 -0500 Subject: [PATCH 25/25] chore: don't use branch image --- tools/star.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/star.wdl b/tools/star.wdl index 264ca3f88..bade225c3 100755 --- a/tools/star.wdl +++ b/tools/star.wdl @@ -127,7 +127,7 @@ task build_star_db { cpu: ncpu memory: "~{memory_gb} GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/star:branch-tests-2.7.11b-1" + container: "ghcr.io/stjudecloud/star:2.7.11b-1" maxRetries: 1 } } @@ -813,7 +813,7 @@ task alignment { cpu: ncpu memory: "50 GB" disks: "~{disk_size_gb} GB" - container: "ghcr.io/stjudecloud/star:branch-tests-2.7.11b-1" + container: "ghcr.io/stjudecloud/star:2.7.11b-1" maxRetries: 1 } }