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Commit d1a9ddb7 authored by Susheel Busi's avatar Susheel Busi
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Snakefile updated

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Snakefile
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......@@ -38,17 +38,17 @@ rule all:
#input: expand("{data_dir}/multifast5/{run}", data_dir=DATA_DIR, run=RUNS)
#input: expand(os.path.join(RESULTS_DIR, "basecalled/guppy/cpu/{run}/basecalling.done"), run=RUNS)
#input: expand(os.path.join(RESULTS_DIR, "basecalled/{run}/basecalling.done"), run=RUNS)
input: expand(os.path.join(RESULTS_DIR, "basecalled_NO_MOD/{run}/NO_MOD_basecalling.done"), run=RUNS)
#input: expand(os.path.join(RESULTS_DIR, "basecalled_NO_MOD/{run}/NO_MOD_basecalling.done"), run=RUNS)
#input: expand(os.path.join(RESULTS_DIR, "basecalled/{run}/demux.done"), run=RUNS)
input: expand(os.path.join(RESULTS_DIR, "basecalled_NO_MOD/{run}/demux_NO_MOD.done"), run=RUNS)
#input: expand(os.path.join(RESULTS_DIR, "basecalled_NO_MOD/{run}/demux_NO_MOD.done"), run=RUNS)
#input: expand(os.path.join(RESULTS_DIR, "basecalled/{run}/{barcode}/{barcode}.fastq.gz"), run=RUNS, barcode=BARCODES)
input: expand(os.path.join(RESULTS_DIR, "basecalled_NO_MOD/{run}/{barcode}/{barcode}.fastq.gz"), run=RUNS, barcode=BARCODES)
#input: expand(os.path.join(RESULTS_DIR, "basecalled_NO_MOD/{run}/{barcode}/{barcode}.fastq.gz"), run=RUNS, barcode=BARCODES)
#input: expand(os.path.join(RESULTS_DIR, "basecalled/merged/{barcode}.fastq.gz"), barcode=BARCODES)
input: expand(os.path.join(RESULTS_DIR, "basecalled_NO_MOD/merged/{barcode}.fastq.gz"), barcode=BARCODES)
#input: expand(os.path.join(RESULTS_DIR, "basecalled_NO_MOD/merged/{barcode}.fastq.gz"), barcode=BARCODES)
#input: expand(os.path.join(RESULTS_DIR, "qc/lr/merged/{barcode}/{barcode}NanoStats.txt"), barcode=BARCODES)
input: expand(os.path.join(RESULTS_DIR, "qc/lr/merged/{barcode}/{barcode}NanoStats_NO_MOD.txt"), barcode=BARCODES)
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/lr/{run}/{barcode}/{barcode}NanoStats_NO_MOD.txt"), run=RUNS, barcode=BARCODES)
#input: expand(os.path.join(RESULTS_DIR, "qc/lr/merged/{barcode}/{barcode}NanoStats_NO_MOD.txt"), barcode=BARCODES)
#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/lr/{run}/{barcode}/{barcode}NanoStats_NO_MOD.txt"), run=RUNS, barcode=BARCODES)
#input: expand(os.path.join(RESULTS_DIR, "mapping/guppy/gpu/{barcode}/{barcode}-long_reads_on_short_reads.sam"), barcode=BARCODES) # checked with CCL. not required (legacy)
#input: expand(os.path.join(RESULTS_DIR, "mapping/lr/merged/{barcode}/{barcode}-x-igc.bam"), barcode=BARCODES)
#input: expand(os.path.join(RESULTS_DIR, "mapping/lr/merged/{barcode}/{barcode}-x-hg38.bam"), barcode=BARCODES)
......@@ -67,10 +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"))
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: "annotate.done"
input: expand(os.path.join(RESULTS_DIR, "qc/lr/{run}/{barcode}/{barcode}NanoStats.txt"), run=RUNS, barcode=BARCODES)
......@@ -389,6 +390,7 @@ rule nanostat:
NanoStat --fastq {input} --outdir $(dirname {output}) --prefix {wildcards.barcode} -n $(basename -s "" {output}) &&\
date) 2> >(tee {log}.stderr) > >(tee {log}.stdout)
"""
rule nanostat_NO_MOD:
input: rules.get_single_fastq_per_barcode_NO_MOD.output
output: os.path.join(RESULTS_DIR, "qc/lr/merged/{barcode}/{barcode}NanoStats_NO_MOD.txt")
......@@ -413,6 +415,7 @@ rule nanostat_per_run:
NanoStat --fastq {input} --outdir $(dirname {output}) --prefix {wildcards.barcode} -n $(basename -s "" {output})
date
"""
rule nanostat_per_run_NO_MOD:
input: os.path.join(RESULTS_DIR, "basecalled_NO_MOD/{run}/{barcode}/{barcode}.fastq.gz")
output: os.path.join(RESULTS_DIR, "qc/lr/{run}/{barcode}/{barcode}NanoStats_NO_MOD.txt")
......
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