Merge branch 'main' of https://git.imp.fu-berlin.de/seehagec01/swp-workflows

project/workflow/rules/samtools.smk

@@ -11,22 +11,22 @@ rule samtool:
     shell:
         "samtools view --threads {threads} -f4 {input} > {output}"
 
-rule fastq:
+rule converts:
     input:
-        "results/unmapped/ERR4082860_unmapped.sam"
+        "results/unmapped/{sample}_unmapped.sam"
     output:
-        "results/unmapped_fastq/ERR4082860_1_unmapped.fastq",
-        "results/unmapped_fastq/ERR4082860_2_unmapped.fastq"
+        "results/unmapped_converts/{sample}_1_unmapped.fastq",
+        "results/unmapped_converts/{sample}_2_unmapped.fastq"
     log:
-        "workflow/report/fastq/ERR4082860.log"
+        "workflow/report/converts/{sample}.log"
     threads:4
     conda:
        "../envs/yourenv.yaml"
     shell:
         """
-        samtools view -S -b --threads={threads} {input} > ERR4082860_unmapped.bam
-        samtools sort -n ERR4082860_unmapped.bam -o ERR4082860_sorted.bam 
-        bedtools bamtofastq -i ERR4082860_sorted.bam -fq {output[0]} -fq2 {output[1]} 2> {log}
+        samtools view -S -b --threads={threads} {input} > {wildcards.sample}_unmapped.bam 2> {log}
+        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}
         """