Delete grid.smk

workflow/rules/Multi/Dereplicate/grid.smk

-rule GRID_summarize:
-    input:
-        grid=gather_multi_bins,
-        dastool=expand("Dereplication/{sample}/selected_DASTool_summary.txt",
-                 sample=samples.loc[[a and b for a,b in zip(samples.ass == 1,samples.rebinning == "yes")],"sample"])
-    output:
-        "Dereplication/dRep_multi/allSamples_bin_stats.tsv"
-    resources:
-        runtime = "12:00:00",
-        mem = MEMCORE
-    params:
-        sample = samples.loc[[a and b for a,b in zip(samples.ass == 1,samples.rebinning == "yes")],"sample"].tolist()
-    log: "logs/dereplication_GRID_summarize.log"
-    message: "GRID_summarize: Summarizing binning results."
-    threads: 1
-    conda: ENVDIR + "/IMP_binning.yaml"
-    script:
-        SRCDIR + "/multi_collect_GRID.R"
-    
-
-rule getMultiBins:
-    input: 
-        bins="Dereplication/{sample}/selected_DASTool_summary.txt",
-        indir="Dereplication/{sample}/selected_DASTool_bins"
-    output:
-        "status/dRep_multi_{sample}.dRep_multi.prepped"
-    resources:
-        runtime = "8:00:00",
-        mem = MEMCORE
-    threads: 1
-    message: "getMultiBins: Copying DAStool bins of {wildcards.sample} to common directory and to single directories."
-    run:
-        selected_bins=pd.read_csv(input.bins,sep="\t")
-        for BIN in selected_bins['bin']:
-            shell("cp {input.indir}/{BIN}.contigs.fa Dereplication/dRep_multi/{wildcards.sample}.{BIN}.contigs.fa")
-            shell("mkdir -p Dereplication/GRiD_multi/{wildcards.sample}.{BIN} && cp Dereplication/{wildcards.sample}/selected_DASTool_bins/{BIN}.contigs.fa Dereplication/GRiD_multi/{wildcards.sample}.{BIN}/contigs.fa")
-        shell("touch {output}")
-
-
-localrules: pre_grid
-checkpoint pre_grid:
-    input:
-       expand("status/dRep_multi_{sample}.dRep_multi.prepped",
-              sample=samples.loc[[a and b for a,b in zip(samples.ass == 1,samples.rebinning == "yes")],"sample"])
-    output:
-       touch("status/dereplication_GRiD_multi_grid.prepped")
-
-rule grid:
-    input:
-       "Dereplication/GRiD_multi/{clusterID}/contigs.fa",
-       "Dereplication/GRiD_multi/{clusterID}/reads.fastq.gz"
-    output:
-        "Dereplication/GRiD_multi/{clusterID}/grid/reads.GRiD.txt",
-        "Dereplication/GRiD_multi/{clusterID}/grid/reads.pdf"
-    params:
-        clusterInput= "Dereplication/GRiD_multi/{clusterID}",
-        outdir = "Dereplication/GRiD_multi/{clusterID}/grid"
-    resources:
-        runtime = "24:00:00",
-        mem = BIGMEMCORE
-    threads: 1
-    conda: ENVDIR + "/IMP_grid.yaml"
-    log: "logs/dereplication_grid.{clusterID}.log"
-    message: "grid: Running GRiD on {wildcards.clusterID}."
-    shell:
-        """
-        grid single -r {params.clusterInput} -e fastq.gz -o {params.outdir} -g {input[0]} > {log} 2>&1
-        """
-
-rule prepare_gridBed:
-    input:
-        "Dereplication/GRiD_multi/{clusterID}/contigs.fa"
-    output:
-        temporary("Dereplication/GRiD_multi/{clusterID}/contigs.bed")
-    resources:
-        runtime = "2:00:00",
-        mem = MEMCORE
-    threads: 1
-    log: "logs/dereplication_prepare_gridBed.{clusterID}.log"
-    message: "prepare_gridBed: Preparing .bed file for GRiD - {wildcards.clusterID}."
-    shell:
-        """
-        {SRCDIR}/fastaBed.pl {input} >> {output} 2> {log}
-        """
-
-rule prepare_gridReads:
-    input:
-        lambda wildcards: expand("{raw_directory}/Assembly/mg.reads.sorted.bam",
-                raw_directory=samples.path[wildcards.sample]),
-        "Dereplication/GRiD_multi/{sample}.{clusterID}/contigs.bed"
-    output:
-        temporary("Dereplication/GRiD_multi/{sample}.{clusterID}/reads.fastq.gz")
-    wildcard_constraints:
-        sample="[^.]*"
-    resources:
-        runtime = "12:00:00",
-        mem = BIGMEMCORE
-    threads: 1
-    log: "logs/dereplication_prepare_gridReads.{sample}.{clusterID}.log"
-    message: "prepare_gridReads: Preparing fastq file for GRiD - {wildcards.sample}{wildcards.clusterID}."
-    conda: ENVDIR + "/IMP_mapping.yaml"
-    shell:
-        """
-        samtools view -b -F 5 -L {input[1]} {input[0]} 2>> {log} | samtools fastq -n - > {output} 2>> {log} 
-        samtools view -b -f 65 -F 4 -L {input[1]} {input[0]} 2>> {log} | samtools fastq -n - >> {output} 2>> {log}
-        samtools view -b -f 129 -F 4 -L {input[1]} {input[0]} 2>> {log} | samtools fastq -n - >> {output} 2>> {log}
-        """