updated the overal snakefiles including the with the ANALYSIS_RULES

2019_GDB/checkpoint_SNAKEFILE

+# File for running ONT analyses
+
+# default configuration file
+configfile:"config/CONFIG.yaml"
+
+# default executable for snakmake
+shell.executable("bash")
+
+# input settings
+RUNS=config['runs']['first']
+STEPS=config['steps']
+
+# include rules for the workflows based on "steps" in the CONFIG.yaml file
+# ONT analyses workflow
+TARGETS = []
+
+if 'assembly_annotation' in STEPS:
+        include: "workflows/checkpoint_assembly_annotation.smk"
+        TARGETS += ["assemble_and_coverage.done",
+                    "annotate.done",
+                    "basecall_merge_qc.done",
+                    "coverage_of_references.done",
+                    "prodigal_gene_call.done",
+                    "diamond_proteins.done"]
+
+if 'mmseq' in STEPS:
+        include: "workflows/mmseq.smk"
+        TARGETS += ["mmseq_comparison_for_ont.done"]
+
+if 'metaT' in STEPS:
+        include: "workflows/metat.smk"
+        TARGETS += ["metaT_mapping_for_ONT.done"]
+
+if 'mapping' in STEPS:
+        include: "workflows/mapping.smk"
+        TARGETS += ["mapping_for_binning.done"]
+
+if 'binning' in STEPS:
+        include: "workflows/binning.smk"
+        TARGETS += ["binning_for_ont.done"]
+
+if 'taxonomy' in STEPS:
+        include: "workflows/taxonomy.smk"
+        TARGETS += ["taxonomy_for_ont.done"]
+
+if 'analysis' in STEPS:
+        include: "workflows/analysis.smk"
+        TARGETS += ["analysis.done"]
+
+#else:
+#    raise Exception('You are not serious. No input data')
+#        print("No input data provided")
+
+
+rule all:
+    input:
+        TARGETS

2019_GDB/config/CONFIG.yaml

-# steps: "assembly_annotation mapping metaT mmseq binning taxonomy"
-steps: "mapping metaT mmseq binning taxonomy"
+# steps: "assembly_annotation mapping metaT mmseq binning taxonomy analysis"
+steps: "binning taxonomy"
 data_dir: "data"
 results_dir: "results"
 db_dir: "dbs"

2019_GDB/updated_SNAKEFILE

@@ -43,9 +43,13 @@ if 'taxonomy' in STEPS:
         include: "workflows/taxonomy.smk"
         TARGETS += ["taxonomy_for_ont.done"]
 
-else:
-     #   raise Exception('You are not serious. No input data')
-        print("No input data provided")
+if 'analysis' in STEPS:
+        include: "workflows/analysis.smk"
+        TARGETS += ["analysis.done"]
+
+#else:
+#    raise Exception('You are not serious. No input data')
+#        print("No input data provided")
 
 
 rule all:

checkpoint_SNAKEFILE

@@ -43,6 +43,10 @@ if 'taxonomy' in STEPS:
         include: "workflows/taxonomy.smk"
         TARGETS += ["taxonomy_for_ont.done"]
 
+if 'analysis' in STEPS:
+        include: "workflows/analysis.smk"
+        TARGETS += ["analysis.done"]
+
 #else:
 #    raise Exception('You are not serious. No input data')
 #        print("No input data provided")

config/CONFIG.yaml

+# steps: "assembly_annotation mapping metaT mmseq binning taxonomy analysis"
+steps: "binning taxonomy"
+data_dir: "data"
+results_dir: "results"
+db_dir: "dbs"
+runs:
+    first: "S1_SizeSelected"
+    second: "S3_Gtube"
+#    third: "20181108_0827_test"
+assemblers: ["flye"]
+p7zip:
+    bin: "/home/users/claczny/apps/software/p7zip_16.02/bin/7za"
+    threads: 4
+ont_fast5_api:
+    single_to_multi_fast5:
+        bin: "single_to_multi_fast5"
+        batch: 8000
+        threads: 8
+flowcell: "FLO-MIN106"
+kit: "SQK-LSK109"
+#barcodes: ["barcode06", "barcode07", "barcode08", "barcode09", "barcode10"]
+barcodes: ["no_barcode"]
+guppy_cpu:
+    path: "/scratch/users/claczny/ont/apps/software/ont-guppy-cpu-3.1.5_linux64/bin"
+    bin: "/scratch/users/claczny/ont/apps/software/ont-guppy-cpu-3.1.5_linux64/bin/guppy_basecaller"
+    version: "cpu-3.1.5"
+    config: "dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg"
+    cpu_threads: 28
+guppy_gpu:
+    path: "/home/users/sbusi/apps/ont-guppy/bin"
+    bin: "set +u; source ~/.bashrc; set -u; ml compiler/LLVM system/CUDA && /home/users/sbusi/apps/ont-guppy/bin/guppy_basecaller"
+    version: "3.6.0+98ff765"
+    config: "dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg"
+    hac_config: "dna_r9.4.1_450bps_hac.cfg"
+    records_per_fastq: 8000
+    chunk_size: 1000
+    chunks_per_runner: 1000
+    num_callers: 4
+    runners_per_device: 2
+    gpu_device: "cuda:0"
+    cpu_threads: 28
+guppy_barcoder:
+    path: "/home/users/sbusi/apps/ont-guppy/bin"
+    bin: "set +u; source ~/.bashrc; set -u; ml compiler/LLVM system/CUDA && /home/users/sbusi/apps/ont-guppy/bin/guppy_barcoder"
+    version: "3.4.5+fb1fbfb"
+    records_per_fastq: 8000
+    threads: 8
+nanostats:
+short_reads_prefix: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/data/raw/short_reads"
+#short_reads_prefix: "/mnt/isilon/projects/lcsb_sequencing/transfer/bioecosystem/Rashi/2019/Apr/fastq"
+metaT_prefix: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/data/metaT"
+fastp:
+    min_length: 40
+minimap2:
+    threads: 16
+igc:
+    uri: "parrot.genomics.cn/gigadb/pub/10.5524/100001_101000/100064/1.GeneCatalogs/IGC.fa.gz"
+hg38:
+    uri: "ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.fna.gz"
+genomecov:
+    bin: "bedtools genomecov"
+compute_avg_coverage:
+    bin: "scripts/coverage.awk"
+bwa:
+    threads: 24
+    long_reads_index:
+        opts: "-aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5"
+samtools:
+    sort:
+        threads: 4
+        chunk_size: "4G"
+    view:
+        threads: 4
+flye:
+    bin: "flye"
+    threads: 27
+    genome_size: "1g"
+operams:
+    bin: "set +u; source ~/.bashrc; set -u; ml lang/Perl lang/R && perl /scratch/users/claczny/ont/apps/software/OPERA-MS/OPERA-MS.pl"
+    threads: 28
+megahit:
+    threads: 28
+nonpareil:
+    memory: 4096
+    threads: 14
+medaka:
+    threads: 28
+racon:
+    threads: 28 
+rebaler:
+    threads: 28
+diamond:
+    threads: 28
+    db: "/mnt/isilon/projects/ecosystem_biology/NOMIS/DIAMOND/new_nr.dmnd"
+metaspades:
+    threads: 28
+mmseq2:
+    threads: 24
+# Define sample names
+#samples: ["flye", "megahit", "metaspades_hybrid"]
+# samples: ["flye", "megahit"]
+# samples: ["metaspades_hybrid"]
+binning_samples: ["flye", "megahit", "bwa_sr_metaspades_hybrid", "bwa_lr_metaspades_hybrid", "bwa_merged_metaspades_hybrid", "mmi_sr_metaspades_hybrid", "mmi_lr_metaspades_hybrid", "mmi_merged_metaspades_hybrid"]
+
+# Hybrid assembler
+hybrid_assembler: "metaspades_hybrid"
+
+# Directory where fastq files are
+#data_dir: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/Binning"
+
+# Directory to save the output to
+#results_dir: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/Binning"
+
+# Number of cpus or threads to use
+threads: 28
+
+# Path to the the 140GB Kraken2 database
+kraken2_database: "/scratch/users/bkunath/Kraken2/maxikraken2_1903_140GB/"
+
+# Path to DAS_Tool
+DAS_Tool:
+        path: "/home/users/sbusi/apps/DAS_Tool-master"
+        bin: "/home/users/sbusi/apps/DAS_Tool-master/src/"
+
+# Path to DAS_Tool database
+dastool_database: "/home/users/sbusi/apps/DAS_Tool-master/db/"
+
+# Mapping options
+bwa:
+    threads: 24
+    long_reads_index:
+        opts: "-aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5"
+samtools:
+    sort:
+        threads: 4
+        chunk_size: "4G"
+    view:
+        threads: 4
+minimap2:
+    threads: 24
+
+# Path to GTDBTK database
+GTDBTK:
+    DATA: "/home/users/sbusi/apps/db/gtdbtk/release89"
+
+# Rscript path
+Rscript: "/home/users/sbusi/apps/miniconda3/envs/dastool/bin/"
+
+mmseqs:
+     path: "/home/users/sbusi/apps/mmseqs/bin"
+     createdb: "/home/users/sbusi/apps/mmseqs/bin/mmseqs createdb"
+     rbh: "/home/users/sbusi/apps/mmseqs/bin/mmseqs rbh"
+     convertalis: "/home/users/sbusi/apps/mmseqs/bin/mmseqs convertalis"

config/CONFIG_original.yaml

+steps: "assembly_annotation metaT"
+# steps: "assembly_annotation mmseq metaT mapping binning taxonomy"
+data_dir: "data"
+results_dir: "results"
+db_dir: "dbs"
+runs:
+    first: "S1_SizeSelected"
+    second: "S3_Gtube"
+#    third: "20181108_0827_test"
+barcodes: ["barcode06", "barcode07", "barcode08", "barcode09", "barcode10"]
+assemblers: ["flye"]
+p7zip:
+    bin: "/home/users/claczny/apps/software/p7zip_16.02/bin/7za"
+    threads: 4
+ont_fast5_api:
+    single_to_multi_fast5:
+        bin: "single_to_multi_fast5"
+        batch: 8000
+        threads: 8
+flowcell: "FLO-MIN106"
+kit: "SQK-LSK109"
+#barcodes: ["barcode06", "barcode07", "barcode08", "barcode09", "barcode10"]
+barcodes: ["barcode07"]
+guppy_cpu:
+    path: "/scratch/users/claczny/ont/apps/software/ont-guppy-cpu-3.1.5_linux64/bin"
+    bin: "/scratch/users/claczny/ont/apps/software/ont-guppy-cpu-3.1.5_linux64/bin/guppy_basecaller"
+    version: "cpu-3.1.5"
+    config: "dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg"
+    cpu_threads: 28
+guppy_gpu:
+    path: "/home/users/sbusi/apps/ont-guppy/bin"
+    bin: "set +u; source ~/.bashrc; set -u; ml compiler/LLVM system/CUDA && /home/users/sbusi/apps/ont-guppy/bin/guppy_basecaller"
+    version: "3.6.0+98ff765"
+    config: "dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg"
+    hac_config: "dna_r9.4.1_450bps_hac.cfg"
+    records_per_fastq: 8000
+    chunk_size: 1000
+    chunks_per_runner: 1000
+    num_callers: 4
+    runners_per_device: 2
+    gpu_device: "cuda:0"
+    cpu_threads: 28
+guppy_barcoder:
+    path: "/home/users/sbusi/apps/ont-guppy/bin"
+    bin: "set +u; source ~/.bashrc; set -u; ml compiler/LLVM system/CUDA && /home/users/sbusi/apps/ont-guppy/bin/guppy_barcoder"
+    version: "3.4.5+fb1fbfb"
+    records_per_fastq: 8000
+    threads: 8
+nanostats:
+short_reads_prefix: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/data/raw/short_reads"
+#short_reads_prefix: "/mnt/isilon/projects/lcsb_sequencing/transfer/bioecosystem/Rashi/2019/Apr/fastq"
+metaT_prefix: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/data/metaT"
+fastp:
+    min_length: 40
+minimap2:
+    threads: 16
+igc:
+    uri: "parrot.genomics.cn/gigadb/pub/10.5524/100001_101000/100064/1.GeneCatalogs/IGC.fa.gz"
+hg38:
+    uri: "ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.fna.gz"
+genomecov:
+    bin: "bedtools genomecov"
+compute_avg_coverage:
+    bin: "scripts/coverage.awk"
+bwa:
+    threads: 24
+    long_reads_index:
+        opts: "-aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5"
+samtools:
+    sort:
+        threads: 4
+        chunk_size: "4G"
+    view:
+        threads: 4
+flye:
+    bin: "flye"
+    threads: 27
+    genome_size: "1g"
+operams:
+    bin: "set +u; source ~/.bashrc; set -u; ml lang/Perl lang/R && perl /scratch/users/claczny/ont/apps/software/OPERA-MS/OPERA-MS.pl"
+    threads: 28
+megahit:
+    threads: 28
+nonpareil:
+    memory: 4096
+    threads: 14
+medaka:
+    threads: 28
+racon:
+    threads: 28 
+rebaler:
+    threads: 28
+diamond:
+    threads: 28
+    db: "/mnt/isilon/projects/ecosystem_biology/NOMIS/DIAMOND/new_nr.dmnd"
+metaspades:
+    threads: 28
+mmseq2:
+    threads: 24
+# Define sample names
+#samples: ["flye", "megahit", "metaspades_hybrid"]
+# samples: ["flye", "megahit"]
+# samples: ["metaspades_hybrid"]
+binning_samples: ["flye", "megahit", "bwa_sr_metaspades_hybrid", "bwa_lr_metaspades_hybrid", "bwa_merged_metaspades_hybrid", "mmi_sr_metaspades_hybrid", "mmi_lr_metaspades_hybrid", "mmi_merged_metaspades_hybrid"]
+
+# Hybrid assembler
+hybrid_assembler: "metaspades_hybrid"
+
+# Directory where fastq files are
+#data_dir: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/Binning"
+
+# Directory to save the output to
+#results_dir: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/Binning"
+
+# Number of cpus or threads to use
+threads: 28
+
+# Path to the the 140GB Kraken2 database
+kraken2_database: "/scratch/users/bkunath/Kraken2/maxikraken2_1903_140GB/"
+
+# Path to DAS_Tool
+DAS_Tool:
+        path: "/home/users/sbusi/apps/DAS_Tool-master"
+        bin: "/home/users/sbusi/apps/DAS_Tool-master/src/"
+
+# Path to DAS_Tool database
+dastool_database: "/home/users/sbusi/apps/DAS_Tool-master/db/"
+
+# Mapping options
+bwa:
+    threads: 24
+    long_reads_index:
+        opts: "-aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5"
+samtools:
+    sort:
+        threads: 4
+        chunk_size: "4G"
+    view:
+        threads: 4
+minimap2:
+    threads: 24
+
+# Path to GTDBTK database
+GTDBTK:
+    DATA: "/home/users/sbusi/apps/db/gtdbtk/release89"
+
+# Rscript path
+Rscript: "/home/users/sbusi/apps/miniconda3/envs/dastool/bin/"

updated_SNAKEFILE

@@ -43,8 +43,13 @@ if 'taxonomy' in STEPS:
         include: "workflows/taxonomy.smk"
         TARGETS += ["taxonomy_for_ont.done"]
 
-else:
-    raise Exception('You are not serious. No input data')
+if 'analysis' in STEPS:
+        include: "workflows/analysis.smk"
+        TARGETS += ["analysis.done"]
+
+#else:
+#    raise Exception('You are not serious. No input data')
+#        print("No input data provided")
 
 
 rule all: