Correct the paths for the aed output files

clinical-genomics-uppsala · Aug 21, 2023 · 9eabd82 · 9eabd82
1 parent 75e7970
commit 9eabd82
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/.tests/integration/config/output_list.json b/.tests/integration/config/output_list.json
@@ -5,6 +5,8 @@
   "results/{sample}/{sample}_snv_indels.filtered.vcf.gz.tbi": {"name": "_copy_snv_indels_filtered_tbi", "file": "vcf_final/{sample}_N.vep_annotated.filter.germline.vcf.gz.tbi", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.cnvpytor_filtered.vcf.gz": {"name": "_copy_cnvpytor_filtered_vcf", "file": "cnv_sv/cnvpytor/{sample}_N.filtered.vcf.gz", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.cnvpytor.vcf.gz": {"name": "_copy_cnvpytor_vcf", "file": "cnv_sv/cnvpytor/{sample}_N.vcf.gz", "types": ["N"]},
+  "results/{sample}/cnv_sv/{sample}.cnvpytor_filtered.aed": {"name": "_copy_cnvpytor_filtered_aed", "file": "cnv_sv/cnvpytor/{sample}_N_filtered.aed", "types": ["N"]},
+  "results/{sample}/cnv_sv/{sample}.cnvpytor.aed": {"name": "_copy_cnvpytor_aed", "file": "cnv_sv/cnvpytor/{sample}_N.aed", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.tiddit.vcf.gz": {"name": "_copy_tiddit_vcf", "file": "cnv_sv/tiddit/{sample}_N.vcf.gz", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.manta_diploidSV.vcf.gz": {"name": "_copy_manta_vcf", "file": "cnv_sv/manta_run_workflow_n/{sample}/results/variants/diploidSV.vcf.gz", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.svdb_merged.vcf.gz": {"name": "_copy_svdb_merged_vcf", "file": "cnv_sv/svdb_merge/{sample}_N.merged.vcf.gz", "types": ["N"]},

diff --git a/config/output_list.json b/config/output_list.json
@@ -5,8 +5,8 @@
   "results/{sample}/{sample}_snv_indels.filtered.vcf.gz.tbi": {"name": "_copy_snv_indels_filtered_tbi", "file": "vcf_final/{sample}_N.vep_annotated.filter.germline.vcf.gz.tbi", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.cnvpytor_filtered.vcf.gz": {"name": "_copy_cnvpytor_filtered_vcf", "file": "cnv_sv/cnvpytor/{sample}_N.filtered.vcf.gz", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.cnvpytor.vcf.gz": {"name": "_copy_cnvpytor_vcf", "file": "cnv_sv/cnvpytor/{sample}_N.vcf.gz", "types": ["N"]},
-  "results/{sample}/cnv_sv/{sample}.cnvpytor_filtered.aed": {"name": "_copy_cnvpytor_filtered_vcf", "file": "cnv_sv/cnvpytor/{sample}_N.filtered.aed", "types": ["N"]},
-  "results/{sample}/cnv_sv/{sample}.cnvpytor.aed": {"name": "_copy_cnvpytor_vcf", "file": "cnv_sv/cnvpytor/{sample}_N.aed", "types": ["N"]},
+  "results/{sample}/cnv_sv/{sample}.cnvpytor_filtered.aed": {"name": "_copy_cnvpytor_filtered_aed", "file": "cnv_sv/cnvpytor/{sample}_N_filtered.aed", "types": ["N"]},
+  "results/{sample}/cnv_sv/{sample}.cnvpytor.aed": {"name": "_copy_cnvpytor_aed", "file": "cnv_sv/cnvpytor/{sample}_N.aed", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.tiddit.vcf.gz": {"name": "_copy_tiddit_vcf", "file": "cnv_sv/tiddit/{sample}_N.vcf.gz", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.manta_diploidSV.vcf.gz": {"name": "_copy_manta_vcf", "file": "cnv_sv/manta_run_workflow_n/{sample}/results/variants/diploidSV.vcf.gz", "types": ["N"]},
   "results/{sample}/cnv_sv/{sample}.svdb_merged.vcf.gz": {"name": "_copy_svdb_merged_vcf", "file": "cnv_sv/svdb_merge/{sample}_N.merged.vcf.gz", "types": ["N"]},
@@ -25,4 +25,4 @@
   "results/{sample}/{sample}_N.cram.crai": {"name": "_copy_samtools_crai", "file": "compression/samtools_view/{sample}_N.cram.crai", "types": ["N"]},
   "results/{sample}/spring/{sample}_{type}_{flowcell}_{lane}_{barcode}.spring":  {"name": "_copy_spring", "file": "compression/spring/{sample}_{type}_{flowcell}_{lane}_{barcode}.spring", "types": ["N"]},
   "results/multiqc_DNA.html": {"name": "_copy_multiqc_html", "file": "qc/multiqc/multiqc_DNA.html", "types": ["N"]}
-}
+}
diff --git a/workflow/rules/vcf_to_aed.smk b/workflow/rules/vcf_to_aed.smk
@@ -28,13 +28,13 @@ rule vcf_to_aed:
     container:
         config.get("vcf_to_aed", {}).get("container", config["default_container"])
     message:
-        "{rule}: do stuff on {input.input1}"
+        "{rule}: convert {input.vcf} to AED format"
     script:
         "../scripts/cnvpytor_vcf_to_aed.py"
 
 
 use rule vcf_to_aed as vcf_to_aed_filtered with:
     input:
-        vcf="cnv_sv/cnvpytor/{sample}_{type}_filtered.vcf",
+        vcf="cnv_sv/cnvpytor/{sample}_{type}.filtered.vcf",
     output:
-        aed="cnv_sv/{sample}_{type}_filtered.aed",
+        aed="cnv_sv/cnvpytor/{sample}_{type}_filtered.aed",