From d503d965d9528d5b6874ea2257c178200b62aa19 Mon Sep 17 00:00:00 2001 From: Lia Obinu Date: Thu, 4 Jan 2024 11:27:54 +0000 Subject: [PATCH] delete samtools rule --- workflow/rules/samtools.smk | 22 ---------------------- 1 file changed, 22 deletions(-) delete mode 100644 workflow/rules/samtools.smk diff --git a/workflow/rules/samtools.smk b/workflow/rules/samtools.smk deleted file mode 100644 index ab80e57..0000000 --- a/workflow/rules/samtools.smk +++ /dev/null @@ -1,22 +0,0 @@ -# This rule uses samtools and shell commands to extract the name of the fastq reads aligning to organelles fasta for their subsequent removal - -rule run_samtools: - input: - mito = "results/minimap2/aln.mito.sam", - pltd = "results/minimap2/aln.pltd.sam" - output: - mito_bam = "results/samtools/mito.sorted.bam", - pltd_bam = "results/samtools/pltd.sorted.bam", - mito_reads = "results/samtools/mapped.mito.reads.txt", - pltd_reads = "results/samtools/mapped.pltd.reads.txt", - organelles = "results/samtools/organelles.reads.txt" - conda: - "../envs/samtools.yaml" - shell: - """ - samtools view -Sb {input.mito} | samtools sort -o {output.mito_bam} - samtools view -Sb {input.pltd} | samtools sort -o {output.pltd_bam} - samtools view -F 4 {output.mito_bam} | cut -f1 > {output.mito_reads} - samtools view -F 4 {output.pltd_bam} | cut -f1 > {output.pltd_reads} - cat {output.mito_reads} {output.pltd_reads} | sort | uniq > {output.organelles} - """ \ No newline at end of file