Merge branch 'work' into 'master'

cleaner snakefile for workflow

See merge request susheel.busi/ont_pilot_gitlab!64

updated_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/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"]
+
+else:
+    raise Exception('You are not serious. No input data')
+
+
+rule all:
+    input:
+        TARGETS