Refactor align_single rule in align.smk

alsmith151 · Jan 3, 2024 · 7bd95af · 7bd95af
1 parent 9edb74a
commit 7bd95af
Showing 1 changed file with 26 additions and 20 deletions.
diff --git a/seqnado/workflow/rules/align.smk b/seqnado/workflow/rules/align.smk
@@ -1,6 +1,7 @@
 import seqnado.utils as utils
 
 if config["split_fastq"] == "False":
+
     rule align_paired:
         input:
             fq1="seqnado_output/trimmed/{sample}_1.fastq.gz",
@@ -22,6 +23,7 @@ if config["split_fastq"] == "False":
             mv {output.bam}_sorted {output.bam}
             """
 
+
 rule align_paired:
     input:
         fq1="seqnado_output/trimmed/{sample}_1.fastq.gz",
@@ -34,7 +36,7 @@ rule align_paired:
     threads: config["bowtie2"]["threads"]
     resources:
         mem_mb=4000,
-        time='0-04:00:00',
+        time="0-04:00:00",
     log:
         "seqnado_output/logs/align/{sample}.log",
     shell:
@@ -44,22 +46,26 @@ rule align_paired:
            mv {output.bam}_sorted {output.bam}
         """
 
-    # rule align_single:
-    #     input:
-    #         fq1="seqnado_output/trimmed/{sample}.fastq.gz",
-    #     params:
-    #         index=config["genome"]["indicies"],
-    #         options=config["bowtie2"]["options"],
-    #     output:
-    #         bam=temp("seqnado_output/aligned/raw/{sample}.bam"),
-    #     resources:
-    #         mem_mb=4000 // int(config["bowtie2"]["threads"])
-    #     threads: config["bowtie2"]["threads"]
-    #     log:
-    #         "seqnado_output/logs/align/{sample}.log",
-    #     shell:
-    #         """bowtie2 -p {threads} -x {params.index} -U {input.fq1} {params.options} 2> {log} |
-    #            samtools view -bS - > {output.bam} &&
-    #            samtools sort -@ {threads} -o {output.bam}_sorted {output.bam} &&
-    #            mv {output.bam}_sorted {output.bam}
-    #         """
+
+rule align_single:
+    input:
+        fq1="seqnado_output/trimmed/{sample}.fastq.gz",
+    params:
+        index=config["genome"]["indicies"],
+        options=utils.check_options(config["bowtie2"]["options"]),
+    output:
+        bam=temp("seqnado_output/aligned/raw/{sample}.bam"),
+    resources:
+        mem_mb=4000,
+    threads: config["bowtie2"]["threads"]
+    log:
+        "seqnado_output/logs/align/{sample}.log",
+    shell:
+        """bowtie2 -p {threads} -x {params.index} -U {input.fq1} {params.options} 2> {log} |
+            samtools view -bS - > {output.bam} &&
+            samtools sort -@ {threads} -o {output.bam}_sorted {output.bam} &&
+            mv {output.bam}_sorted {output.bam}
+        """
+
+
+ruleorder: align_paired > align_single