nf-core · lindenb · Sep 11, 2024 · Sep 11, 2024 · Sep 11, 2024
diff --git a/data/genomics/sarscov2/genome/gff3/MT192765.1.gff3.gz b/data/genomics/sarscov2/genome/gff3/MT192765.1.gff3.gz
diff --git a/data/genomics/sarscov2/genome/gff3/MT192765.1.gff3.gz.tbi b/data/genomics/sarscov2/genome/gff3/MT192765.1.gff3.gz.tbi
diff --git a/data/genomics/sarscov2/genome/gff3/README.md b/data/genomics/sarscov2/genome/gff3/README.md
@@ -0,0 +1,2 @@
+gff3 file compatible with bcftools csq.
+see `data/genomics/sarscov2/wgsim/README.md`
diff --git a/data/genomics/sarscov2/genome/gtf/MT192765.1.gtf.gz b/data/genomics/sarscov2/genome/gtf/MT192765.1.gtf.gz
diff --git a/data/genomics/sarscov2/genome/gtf/MT192765.1.gtf.gz.tbi b/data/genomics/sarscov2/genome/gtf/MT192765.1.gtf.gz.tbi
diff --git a/data/genomics/sarscov2/genome/gtf/README.md b/data/genomics/sarscov2/genome/gtf/README.md
@@ -0,0 +1,2 @@
+valid gtf file
+see `data/genomics/sarscov2/wgsim/README.md`
diff --git a/data/genomics/sarscov2/wgsim/README.md b/data/genomics/sarscov2/wgsim/README.md
diff --git a/data/genomics/sarscov2/wgsim/SAMPLE_DEL.bam b/data/genomics/sarscov2/wgsim/SAMPLE_DEL.bam
diff --git a/data/genomics/sarscov2/wgsim/SAMPLE_DEL.bam.bai b/data/genomics/sarscov2/wgsim/SAMPLE_DEL.bam.bai
diff --git a/data/genomics/sarscov2/wgsim/SAMPLE_DUP.bam b/data/genomics/sarscov2/wgsim/SAMPLE_DUP.bam
diff --git a/data/genomics/sarscov2/wgsim/SAMPLE_DUP.bam.bai b/data/genomics/sarscov2/wgsim/SAMPLE_DUP.bam.bai
diff --git a/data/genomics/sarscov2/wgsim/SAMPLE_INV.bam b/data/genomics/sarscov2/wgsim/SAMPLE_INV.bam
diff --git a/data/genomics/sarscov2/wgsim/SAMPLE_INV.bam.bai b/data/genomics/sarscov2/wgsim/SAMPLE_INV.bam.bai
diff --git a/data/genomics/sarscov2/wgsim/SAMPLE_WT.bam b/data/genomics/sarscov2/wgsim/SAMPLE_WT.bam
diff --git a/data/genomics/sarscov2/wgsim/SAMPLE_WT.bam.bai b/data/genomics/sarscov2/wgsim/SAMPLE_WT.bam.bai
diff --git a/data/genomics/sarscov2/wgsim/vcf/bcftools/bcftools.annot.bcf b/data/genomics/sarscov2/wgsim/vcf/bcftools/bcftools.annot.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/bcftools/bcftools.annot.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/bcftools/bcftools.annot.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/bcftools/bcftools.call.bcf b/data/genomics/sarscov2/wgsim/vcf/bcftools/bcftools.call.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/bcftools/bcftools.call.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/bcftools/bcftools.call.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DEL.delly.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DEL.delly.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DEL.delly.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DEL.delly.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DEL.delly.gt.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DEL.delly.gt.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DEL.delly.gt.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DEL.delly.gt.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DUP.delly.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DUP.delly.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DUP.delly.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DUP.delly.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DUP.delly.gt.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DUP.delly.gt.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DUP.delly.gt.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_DUP.delly.gt.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_INV.delly.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_INV.delly.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_INV.delly.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_INV.delly.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_INV.delly.gt.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_INV.delly.gt.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_INV.delly.gt.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_INV.delly.gt.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_WT.delly.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_WT.delly.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_WT.delly.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_WT.delly.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_WT.delly.gt.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_WT.delly.gt.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_WT.delly.gt.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/SAMPLE_WT.delly.gt.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/delly.filter.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/delly.filter.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/delly.filter.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/delly.filter.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/delly.merge.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/delly.merge.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/delly.merge.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/delly.merge.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/delly.sites.bcf b/data/genomics/sarscov2/wgsim/vcf/delly/delly.sites.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/delly/delly.sites.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/delly/delly.sites.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/hapcaller/hapcaller.annot.bcf b/data/genomics/sarscov2/wgsim/vcf/hapcaller/hapcaller.annot.bcf
diff --git a/data/genomics/sarscov2/wgsim/vcf/hapcaller/hapcaller.annot.bcf.csi b/data/genomics/sarscov2/wgsim/vcf/hapcaller/hapcaller.annot.bcf.csi
diff --git a/data/genomics/sarscov2/wgsim/vcf/hapcaller/hapcaller.call.vcf.gz b/data/genomics/sarscov2/wgsim/vcf/hapcaller/hapcaller.call.vcf.gz
diff --git a/data/genomics/sarscov2/wgsim/vcf/hapcaller/hapcaller.call.vcf.gz.tbi b/data/genomics/sarscov2/wgsim/vcf/hapcaller/hapcaller.call.vcf.gz.tbi