chore: update output_files to yaml

clinical-genomics-uppsala · Oct 21, 2024 · ab1ab54 · ab1ab54
1 parent c65b167
commit ab1ab54
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Showing 10 changed files with 480 additions and 171 deletions.
diff --git a/.tests/integration/config.yaml b/.tests/integration/config.yaml
@@ -1,4 +1,4 @@
-output: "../../config/output_files.json"
+output: "../../config/output_files.yaml"
 
 reference:
   design_bed: "reference/homo_sapiens.wgs.bed"

diff --git a/.tests/integration/input/HD829-T_S3_R1.fq.gz b/.tests/integration/input/HD829-T_S3_R1.fq.gz
diff --git a/.tests/integration/input/HD829-T_S3_R2.fq.gz b/.tests/integration/input/HD829-T_S3_R2.fq.gz
diff --git a/.tests/integration/samples.tsv b/.tests/integration/samples.tsv
@@ -1,2 +1,3 @@
 sample	tumor_content	sex
-NA12878	1.0	O
+NA12878	1.0	K
+HD829	1.0	O
diff --git a/.tests/integration/units.tsv b/.tests/integration/units.tsv
@@ -2,3 +2,4 @@ sample	type	platform	machine	flowcell	lane	barcode	fastq1	fastq2	adapter
 NA12878	T	illumina	NovaSeq	1FLOWCELL	L001	ACGGAACA	input/NA12878-T_S2_R1.fq.gz	input/NA12878-T_S2_R2.fq.gz	AAAA,TTTT
 NA12878	N	illumina	NovaSeq	1FLOWCELL	L001	ACGGAACA	input/NA12878-N_S1_R1.fq.gz	input/NA12878-N_S1_R2.fq.gz	CCCC,GGGG
 NA12878	R	illumina	NovaSeq	1FLOWCELL	L001	ACGGAACA	input/NA12878-R_S10_R1.fq.gz	input/NA12878-R_S10_R2.fq.gz	CCCC,GGGG
+HD829	T	illumina	NovaSeq	1FLOWCELL	L001	ACGGAACA	input/HD829-T_S3_R1.fq.gz	input/HD829-T_S3_R2.fq.gz	AAAA,TTTT
diff --git a/config/config.yaml b/config/config.yaml
@@ -1,7 +1,7 @@
 resources: "resources.yaml"
 samples: "samples.tsv"
 units: "units.tsv"
-output: "config/output_files.json"
+output: "config/output_files.yaml"
 
 aligner: "bwa_gpu" # bwa_gpu or bwa_sentieon
 

diff --git a/config/output_files.json b/config/output_files.json