Use python drop-in replacement in case FASTQ_COUNT conig value is not supplied

README.md

@@ -55,8 +55,9 @@ is not yet in conda, it must be compiled on the user's system before
 running the pipeline. When compiled, the path to the executable can be
 supplied via `--config FASTQ_COUNT=/path/to/fastq-count`.
 
-TODO: Implement drop-in replacement in python for users not wanting to
-compile fastq-count.
+A drop-in replacement implemented in python exists in this repository.
+Not specifing the `FASTQ_COUNT` config value will use the python replacement.
+Do note that this python replacement is an order of magnitude slower.
 
 ## Operating system
 

Snakefile

@@ -29,6 +29,11 @@ colpy = join(join(_this_dir, "src"), "collect_stats.py")
 vs_py = join(join(_this_dir, "src"), "vcfstats.py")
 mpy = join(join(_this_dir, "src"), "merge_stats.py")
 
+if FASTQ_COUNT is None:
+    fqc = "python {0}".format(join(join(_this_dir, "src"), "fastq-count.py"))
+else:
+    fqc = FASTQ_COUNT
+
 with open(config.get("SAMPLE_CONFIG")) as handle:
     SAMPLE_CONFIG = json.load(handle)
 SAMPLES = SAMPLE_CONFIG['samples'].keys()
@@ -396,7 +401,7 @@ rule fqcount_preqc:
         r1=out_path("{sample}/pre_process/{sample}.merged_R1.fastq.gz"),
         r2=out_path("{sample}/pre_process/{sample}.merged_R2.fastq.gz")
     params:
-        fastqcount=FASTQ_COUNT
+        fastqcount=fqc
     output:
         out_path("{sample}/pre_process/{sample}.preqc_count.json")
     shell: "{params.fastqcount} {input.r1} {input.r2} > {output}"
@@ -407,7 +412,7 @@ rule fqcount_postqc:
         r1=out_path("{sample}/pre_process/{sample}.cutadapt_R1.fastq"),
         r2=out_path("{sample}/pre_process/{sample}.cutadapt_R2.fastq")
     params:
-        fastqcount=FASTQ_COUNT
+        fastqcount=fqc
     output:
         out_path("{sample}/pre_process/{sample}.postqc_count.json")
     shell: "{params.fastqcount} {input.r1} {input.r2} > {output}"