From 570a357c8c025dfd7c6435195e3dd04eea53a598 Mon Sep 17 00:00:00 2001 From: Rike Date: Mon, 18 Jul 2022 17:32:44 +0200 Subject: [PATCH] update paths in test files --- tests/test_bam_remap.yml | 2 +- tests/test_default.yml | 8 ++++---- tests/test_markduplicates.yml | 16 ++++++++-------- tests/test_split_fastq.yml | 8 ++++---- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml index 9e91c19342..f49d42d9a8 100644 --- a/tests/test_bam_remap.yml +++ b/tests/test_bam_remap.yml @@ -11,7 +11,7 @@ - path: results/csv/recalibrated.csv - path: results/multiqc/multiqc_report.html - path: results/pipeline_info - - path: results/preprocessing/test + - path: results/preprocessing/ - path: results/reports - path: results/samtools - path: results/collate diff --git a/tests/test_default.yml b/tests/test_default.yml index 80f7288aba..c52b174a08 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -82,7 +82,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools/test/test.md.cram.stats - path: results/reports/samtools/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz + - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz + - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates.yml index a136c9cfb2..44b326bf03 100644 --- a/tests/test_markduplicates.yml +++ b/tests/test_markduplicates.yml @@ -24,10 +24,10 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools/test/test.md.cram.stats - path: results/reports/samtools/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz + - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz + - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi - name: Run Mark Duplicates starting from CRAM command: nextflow run main.nf -profile test,markduplicates_cram,docker --tools strelka @@ -55,7 +55,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools/test/test.md.cram.stats - path: results/reports/samtools/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz + - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz + - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi diff --git a/tests/test_split_fastq.yml b/tests/test_split_fastq.yml index c00b9cb470..bd3602ad25 100644 --- a/tests/test_split_fastq.yml +++ b/tests/test_split_fastq.yml @@ -3,7 +3,7 @@ tags: - split_fastq files: - - path: results/preprocessing/test/fastp/0001.test-test_L1_1.fastp.fastq.gz - - path: results/preprocessing/test/fastp/0001.test-test_L1_2.fastp.fastq.gz - - path: results/preprocessing/test/fastp/0002.test-test_L1_1.fastp.fastq.gz - - path: results/preprocessing/test/fastp/0002.test-test_L1_2.fastp.fastq.gz + - path: results/preprocessing/fastp/test/0001.test-test_L1_1.fastp.fastq.gz + - path: results/preprocessing/fastp/test/0001.test-test_L1_2.fastp.fastq.gz + - path: results/preprocessing/fastp/test/0002.test-test_L1_1.fastp.fastq.gz + - path: results/preprocessing/fastp/test/0002.test-test_L1_2.fastp.fastq.gz