update metadata and config for denmark

project/denmark/config/snakemake.yaml

@@ -0,0 +1,103 @@
+# Snakemake Configuration File
+
+# SQLITE Parameters
+sqlite_db : "yersinia_pestis_db.sqlite"
+sqlite_select_command_asm : SELECT
+                              AssemblyFTPGenbank
+                            FROM
+                              BioSample
+                            LEFT JOIN Assembly
+                              ON AssemblyBioSampleAccession = BioSampleAccession
+                            WHERE
+                              (BioSampleComment LIKE '%KEEP%Assembly%Modern%' AND
+                               length(AssemblyFTPGenbank) > 0)
+sqlite_select_command_sra : SELECT
+                              BioSampleAccession,
+                              SRARunAccession
+                            FROM
+                              BioSample
+                            LEFT JOIN SRA
+                              ON SRABioSampleAccession = BioSampleAccession
+                            WHERE
+                              (BioSampleComment LIKE '%KEEP%SRA%Ancient%' AND
+                               SRAComment NOT LIKE "%REMOVE%")
+sqlite_select_command_local : SELECT
+                              BioSampleAccession
+                            FROM
+                              BioSample
+                            WHERE
+                              (BioSampleComment LIKE '%Local%Denmark%')
+sqlite_select_command_ref : SELECT
+                              AssemblyFTPGenbank
+                            FROM
+                              BioSample
+                            LEFT JOIN Assembly
+                              ON AssemblyBioSampleAccession = BioSampleAccession
+                            WHERE
+                              (BioSampleComment LIKE '%Assembly%Modern%Reference%')
+
+# Dataset size
+max_datasets_assembly : 1000
+max_datasets_sra : 1000
+reads_origin :
+  - "assembly"
+  - "sra"
+  - "local"
+
+# misc filtering
+detect_repeats_threshold : 90
+detect_repeats_length : 50
+
+reference_locus : "AL590842"
+reference_locus_name : "chromosome"
+reference_locus_start : "0"
+reference_locus_end : "4653728"
+
+# Eager param
+eager_rev: "2.2.1"
+eager_clip_readlength : 35
+eager_bwaalnn : 0.01
+eager_bwaalnl : 16
+eager_other : '--mergedonly'
+organism : "Yersinia pestis"
+# Adapter Removal Defaults
+eager_forward_adapter : 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG'
+eager_reverse_adapter : 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
+
+# Snippy Parameters
+snippy_ctg_depth : 10
+snippy_bam_depth : 3
+snippy_base_qual : 20
+snippy_map_qual : 30
+snippy_min_frac : 0.9
+snippy_mask_char : "X"
+snippy_missing_data : 5
+snippy_snp_density : 10
+# Make this an empty string if removing singletons
+snippy_keep_singleton: ""
+#snippy_keep_singleton : "--keep-singleton"
+snippy_multi_plot_missing_data:
+  - 0
+  - 1
+  - 2
+  - 3
+  - 4
+  - 5
+  - 6
+  - 7
+  - 8
+  - 9
+  - 10
+
+# IQTREE
+#iqtree_model: "-m MFP"
+iqtree_model : "-m K3Pu+F+I"
+iqtree_seed : "47321424" # keeping it consistent in a config file allows for checkpointing
+# Outgroup Option #1: Reference
+#iqtree_outgroup : "Reference"
+# Outgroup Option #2: Basal modern clade
+#iqtree_outgroup : "GCA_000323485.1_ASM32348v1_genomic,GCA_000323845.1_ASM32384v1_genomic"
+# Outgroup Option #3: Basal ancient clade
+iqtree_outgroup : "SAMEA3541826,SAMEA3541827"
+iqtree_other : "--ufboot 1000"
+iqtree_runs : 10