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Commit 10886ebb authored by ahb-ufz's avatar ahb-ufz
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eukdetect redundancy with mapping

parent b348fd19
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              workflow/rules/Taxonomy/eukdetect.smk
              View file @ 10886ebb
              ...@@ -225,22 +225,23 @@ rule ED_rmsort: ...@@ -225,22 +225,23 @@ rule ED_rmsort:
              samtools sort -o {output} {input} &>> {log} samtools sort -o {output} {input} &>> {log}
              """ """
              rule ED_index: if not 'assembly' in IMP_STEPS and not 'analysis' in IMP_STEPS:
              input: rule ED_index:
              bam = "Analysis/taxonomy/EukDetect/filtering/{sample}_aln_q30_lenfilter_complexityfilter_dupfilter.sorted.bam" input:
              output: bam = "Analysis/taxonomy/EukDetect/filtering/{sample}_aln_q30_lenfilter_complexityfilter_dupfilter.sorted.bam"
              bai = "Analysis/taxonomy/EukDetect/filtering/{sample}_aln_q30_lenfilter_complexityfilter_dupfilter.sorted.bam.bai" output:
              threads: 1 bai = "Analysis/taxonomy/EukDetect/filtering/{sample}_aln_q30_lenfilter_complexityfilter_dupfilter.sorted.bam.bai"
              resources: threads: 1
              runtime = "12:00:00", resources:
              mem = MEMCORE runtime = "12:00:00",
              log: "logs/analysis_eukdetect_index.{sample}.log" mem = MEMCORE
              message: "index: Indexing bam for eukdetect on {wildcards.sample} reads." log: "logs/analysis_eukdetect_index.{sample}.log"
              conda: ENVDIR + "/eukdetect.yaml" message: "index: Indexing bam for eukdetect on {wildcards.sample} reads."
              shell: conda: ENVDIR + "/eukdetect.yaml"
              """ shell:
              samtools index {input.bam} {output.bai} &>> {log} """
              """ samtools index {input.bam} {output.bai} &>> {log}
              """
              rule ED_countreads: rule ED_countreads:
              input: input:
              ......
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