sambam

project/workflow/rules/bowtie2.smk

@@ -26,7 +26,7 @@ rule map:
    threads:4
    conda:
        "../envs/yourenv.yaml"
-    wrapper:
+   wrapper:
         "v1.3.2/bio/bowtie2/align"
 
 

project/workflow/rules/samtools.smk

-rule samtool:
+rule fastq:
     input:
-        "results/sam/{sample}.sam"
+        "results/bam/{sample}.bam"
     output:
-        "results/unmapped/{sample}_unmapped.sam"
+        "results/unmapped_fastq/{sample}_1_unmapped.fastq",
+        "results/unmapped_fastq/{sample}_2_unmapped.fastq"
     log:
-        "workflow/report/samtools/{sample}.log"
-    threads:4
-    conda:
-       "../envs/yourenv.yaml"
-    shell:
-        "samtools view --threads {threads} -f4 {input} > {output}"
-
-rule converts:
-    input:
-        "results/unmapped/{sample}_unmapped.sam"
-    output:
-        "results/unmapped_converts/{sample}_1_unmapped.fastq",
-        "results/unmapped_converts/{sample}_2_unmapped.fastq"
-    log:
-        "workflow/report/converts/{sample}.log"
+        "workflow/report/fastq/{sample}.log"
     threads:4
     conda:
        "../envs/yourenv.yaml"
     shell:
         """
-        samtools view -S -b --threads={threads} {input} > {wildcards.sample}_unmapped.bam 2> {log}
+        samtools view --threads={threads} -b -f4 {input} > {wildcards.sample}_unmapped.bam 2> {log} #extract unmapped reads
         samtools sort -n {wildcards.sample}_unmapped.bam -o {wildcards.sample}_sorted.bam 2>> {log}
         bedtools bamtofastq -i {wildcards.sample}_sorted.bam -fq {output[0]} -fq2 {output[1]} 2>> {log}
         """