fix bamtofastq_pairs

tools/bedtools/bamtofastq_pairs/Snakefile

@@ -7,9 +7,11 @@ rule bedtools_bamtofastq_pairs:
     input:
         __bedtools_bamtofastq_pairs_input
     output:
-        forward = __bedtools_bamtofastq_pairs_output_forward,
-        reverse = __bedtools_bamtofastq_pairs_output_reverse
+        forward = f"{__bedtools_bamtofastq_pairs_output_forward_name}.fq.gz",
+        reverse = f"{__bedtools_bamtofastq_pairs_output_reverse_name}.fq.gz"
     params:
+        forward_name = __bedtools_bamtofastq_pairs_output_forward_name,
+        reverse_name = __bedtools_bamtofastq_pairs_output_reverse_name,
         exec_command = __bedtools_bamtofastq_pairs_bedtools_exec_command,
         modules = __bedtools_bamtofastq_pairs_modules
     run:
@@ -17,8 +19,8 @@ rule bedtools_bamtofastq_pairs:
         if params.modules:
         	command.append("module load {params.modules}")
         command.append(
-            "{params.exec_command} bamtofastq -i {input} -fq {output.forward}.fastq -fq2 {output.reverse}.fastq"
+            "{params.exec_command} bamtofastq -i {input} -fq {params.forward_name}.fq -fq2 {params.reverse_name}.fq"
         )
-        command.append("gunzip {output}_1.fastq")
-        command.append("gunzip {output}_2.fastq")
+        command.append("gzip {params.forward_name}.fq")
+        command.append("gzip {params.reverse_name}.fq")
         shell(" && ".join(command))
\ No newline at end of file

tools/bedtools/bamtofastq_pairs/example_usage/Snakefile

@@ -12,8 +12,15 @@ __input_dir = config.get('input_dir', 'data')
 # ==== Bedtools bamtofastq ====
 __bedtools_bamtofastq_pairs_output_dir = f"{__main_output_dir}/bedtools_bamtofastq_pairs"
 __bedtools_bamtofastq_pairs_input = "{dir}/{{sample}}.bam".format(dir=__input_dir, sample="{sample}")
-__bedtools_bamtofastq_pairs_output = "{dir}/{{sample}}".format(dir=__bedtools_bamtofastq_pairs_output_dir, sample="{sample}")
+__bedtools_bamtofastq_pairs_output_forward_name = "{dir}/{{sample}}_1".format(
+    dir=__bedtools_bamtofastq_pairs_output_dir, sample="{sample}"
+)
+__bedtools_bamtofastq_pairs_output_reverse_name = "{dir}/{{sample}}_2".format(
+    dir=__bedtools_bamtofastq_pairs_output_dir, sample="{sample}"
+)
 include: __bedtools_bamtofastq_pairs_rules
 
 rule all:
-    input: expand("{dir}/{{sample}}_unmapped.bam".format(dir=__bedtools_bamtofastq_pairs_output_dir), sample=SAMPLES)
+    input:
+        forward = expand(f"{__bedtools_bamtofastq_pairs_output_forward_name}.fq.gz", sample=SAMPLES),
+        reverse = expand(f"{__bedtools_bamtofastq_pairs_output_reverse_name}.fq.gz", sample=SAMPLES)