Merge pull request #74 from Cristianetaniguti/add_poly

add tutorial examples
Cristianetaniguti · Mar 14, 2023 · d1f375c · d1f375c
2 parents b8d80a6 + 70bf577
commit d1f375c
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diff --git a/pipelines/EmpiricalMaps/EmpiricalMaps_inputs.json b/pipelines/EmpiricalMaps/EmpiricalMaps_inputs.json
@@ -0,0 +1,19 @@
+{
+  "Maps.ploidy": "4",
+  "Maps.dataset": {
+    "parent2": "P1",
+    "name": "roses",
+    "parent1": "P2",
+    "chromosome": "Chr04",
+    "cross": "F1",
+    "multiallelics": "false"
+  },
+  "Maps.max_cores": "2",
+  "Maps.gatk_mchap": "false",
+  "Maps.vcfs_counts_source": ["vcf"],
+  "Maps.vcfs_software": ["gatk"],
+  "Maps.filter_noninfo": "true",
+  "Maps.vcfs": ["gatk_Chr04_filt_example.vcf.gz"],
+  "Maps.replaceADbyMissing": "TRUE",
+  "Maps.prob_thres": 0.8
+}
diff --git a/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling_inputs.json b/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling_inputs.json
@@ -0,0 +1,21 @@
+{
+  "SNPCalling.max_cores": 2,
+  "SNPCalling.ploidy": 4,
+  "SNPCalling.rm_dupli": false,
+  "SNPCalling.run_gatk": true,
+  "SNPCalling.run_freebayes": true,
+  "SNPCalling.hardfilters": true,
+  "SNPCalling.n_chrom": 1,
+  "SNPCalling.chunk_size": 1,
+  "SNPCalling.samples_info": "samples_info.txt",
+  "SNPCalling.references": {
+    "ref_fasta": "Chr04_sub.fasta",
+    "ref_dict": "Chr04_sub.dict",
+    "ref_ann": "Chr04_sub.fasta.ann",
+    "ref_sa": "Chr04_sub.fasta.sa",
+    "ref_amb": "Chr04_sub.fasta.amb",
+    "ref_pac": "Chr04_sub.fasta.pac",
+    "ref_bwt": "Chr04_sub.fasta.bwt",
+    "ref_fasta_index": "Chr04_sub.fasta.fai"
+  }
+}
diff --git a/pipelines/EmpiricalSNPCalling/samples_info.txt b/pipelines/EmpiricalSNPCalling/samples_info.txt
@@ -0,0 +1,4 @@
+1.fastq.gz   1   1
+98.fastq.gz   98    98
+P1.fastq.gz   P1    P1
+P2.fastq.gz   P2    P2
diff --git a/tests/data/polyploid/fastq/1.sub.fastq.gz b/tests/data/polyploid/fastq/1.sub.fastq.gz
diff --git a/tests/data/polyploid/fastq/98.sub.fastq.gz b/tests/data/polyploid/fastq/98.sub.fastq.gz
diff --git a/tests/data/polyploid/fastq/P1.sub.fastq.gz b/tests/data/polyploid/fastq/P1.sub.fastq.gz
diff --git a/tests/data/polyploid/fastq/P2.sub.fastq.gz b/tests/data/polyploid/fastq/P2.sub.fastq.gz