working for PE data

Author: niekwit

workflow/rules/damid.smk

@@ -66,6 +66,7 @@ if config["plasmid_fasta"] == "none":
                 idx=f"resources/bowtie2_index/{resources.genome}_{resources.build}_{maskedgenes}.masked/index",
                 binsize=config["damidseq_pipeline"]["binsize"],
                 normalization_method=config["damidseq_pipeline"]["normalization"],
+                extension=".sorted.bam",
                 extra=config["damidseq_pipeline"]["extra"],
             conda:
                 "../envs/damid.yaml"
@@ -196,6 +197,7 @@ if config["plasmid_fasta"] == "none":
                 idx=f"resources/bowtie2_index/{resources.genome}_{resources.build}_{maskedgenes}.masked/index",
                 binsize=config["damidseq_pipeline"]["binsize"],
                 normalization_method=config["damidseq_pipeline"]["normalization"],
+                extension=".extended.bam",
                 extra=config["damidseq_pipeline"]["extra"],
             conda:
                 "../envs/damid.yaml"

workflow/scripts/damidseq_pipeline.py

@@ -33,12 +33,13 @@ def move_files(extension):
 
 # Load Snakemake variables
 bams = snakemake.input["bam"]
-bams = [os.path.join(cwd,x) for x in bams]
+bams = [os.path.join(cwd, x) for x in bams]
 gatc = os.path.join(cwd, snakemake.input["gatc"])
 threads = snakemake.threads
 bins = snakemake.params["binsize"]
 normalization_method = snakemake.params["normalization_method"]
 idx = os.path.join(cwd,snakemake.params["idx"])
+extension = snakemake.params["extension"]
 extra = snakemake.params["extra"]
 log = os.path.join(cwd, snakemake.log[0])
 
@@ -57,8 +58,8 @@ def move_files(extension):
 damidseq_pipeline = os.path.join(cwd,"resources/damidseq_pipeline/damidseq_pipeline")
 
 # Get dam bam
-dam_bam = [x for x in bams if re.search("dam.extended.bam$", x.lower())]
-assert len(dam_bam) == 1
+dam_bam = [x for x in bams if x.lower().endswith(f"dam{extension}")]
+assert len(dam_bam) == 1, "No Dam only bam file found..."
 # TO DO: allow for multiple Dam only bam files (i.e. multiple conditions)
 
 # Get non-Dam bam files