Merge branch 'work' into 'master'

included nanopolish indexing

See merge request susheel.busi/ont_pilot_gitlab!13

Snakefile

@@ -67,12 +67,11 @@ rule all:
     #input: expand(os.path.join(RESULTS_DIR, "mapping/sr/{mapper}/{sample}_reads-x-{barcode}-{assembler}_contigs.bam"), sample=SAMPLES, barcode=BARCODES, assembler=ASSEMBLERS, mapper=MAPPERS)
     #input: expand(os.path.join(RESULTS_DIR, "genomecov/sr/{mapper}/{sample}_reads-x-{barcode}-{assembler}_contigs.avg_cov.txt"), sample=SAMPLES, barcode=BARCODES, assembler=ASSEMBLERS, mapper=MAPPERS)
     #input: "assemble_and_coverage.done"
-    input: expand(os.path.join(RESULTS_DIR, "assembly/{assembler}/polished/medaka/round_{round}/lr/merged/{barcode}/assembly_polished.fna"), assembler=ASSEMBLERS, barcode=BARCODES, round="01")
-    
-    #### ADDITIONAL RULES TO BE RUN #####
-    input: "basecall_merge_qc.done"
-    input: "basecall_merge_qc_NO_MOD.done"
-    input: "coverage_of_references.done"
+    #input: expand(os.path.join(RESULTS_DIR, "assembly/{assembler}/polished/medaka/round_{round}/lr/merged/{barcode}/assembly_polished.fna"), assembler=ASSEMBLERS, barcode=BARCODES, round="01")
+    #input: "basecall_merge_qc.done"
+    #input: "basecall_merge_qc_NO_MOD.done"
+    #input: "coverage_of_references.done"
+    #input: expand(os.path.join(RESULTS_DIR, "basecalled/merged/{barcode}.fastq.gz.index.readdb"), barcode=BARCODES)
     input: "annotate.done"
     input: expand(os.path.join(RESULTS_DIR, "qc/lr/{run}/{barcode}/{barcode}NanoStats.txt"), run=RUNS, barcode=BARCODES)
     #input: expand(os.path.join(RESULTS_DIR, "qc/sr/fastqc/{sr_sample}/{sr_sample}_{suffix}.fastqc.zip"), sr_sample="NEB2_MG_S17",suffix=["R1_001.fastp", "R1_002.fastp"]))
@@ -84,7 +83,6 @@ rule all:
     #input: expand(os.path.join(RESULTS_DIR, "assembly/megahit/{sr_sample}/final.contigs.fna"), sr_sample="NEB2_MG_S17")
     #input: expand(os.path.join(RESULTS_DIR, "mapping/lr/bwa_mem/{barcode}_reads-x-{sr_sample}-{assembler}_contigs.bam"), barcode=BARCODES, assembler=ASSEMBLERS, sr_sample="NEB2_MG_S17")
     #input: expand(os.path.join(RESULTS_DIR, "annotation/nonpareil/{sr_sample}_R{orientation}_{suffix}.fastp.npo"), sr_sample="NEB2_MG_S17", orientation=["1", "2"], suffix="001")
-    #input: expand(os.path.join(RESULTS_DIR, "basecalled/merged/{barcode}.fastq.gz.index.readdb"), barcode=BARCODES)
     #input: expand(directory(os.path.join(RESULTS_DIR, "assembly/flye/polished/nanopolish/round_{round}/lr/merged/{barcode}/windows"), round="01", barcode=BARCODES))
     #input: expand(os.path.join(RESULTS_DIR, "assembly/{assembler}/polished/nanopolish/round_{round}/lr/merged/{barcode}/assembly_polished.fna"), assembler=ASSEMBLERS, round="01", barcode=BARCODES)
     #input: expand(os.path.join(RESULTS_DIR, "annotation/methylation/{assembler}/nanopolish/round_{round}/lr/merged/{barcode}/methylation_frequencies.tsv"), assembler=ASSEMBLERS, round="01", barcode=BARCODES)