mv log purging to launch script

harpy/snakefiles/align_bwa.smk

@@ -256,13 +256,6 @@ rule workflow_summary:
         unmapped = "" if keep_unmapped else "-F 4",
         extra   = extra
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         with open(outdir + "/workflow/align.bwa.summary", "w") as f:
             _ = f.write("The harpy align bwa workflow ran using these parameters:\n\n")
             _ = f.write(f"The provided genome: {genomefile}\n")

harpy/snakefiles/align_ema.smk

@@ -337,13 +337,6 @@ rule workflow_summary:
         beadtech = "-p" if platform == "haplotag" else f"-w {barcode_list}",
         unmapped = "" if keep_unmapped else "-F 4"
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         with open(outdir + "/workflow/align.ema.summary", "w") as f:
             _ = f.write("The harpy align ema workflow ran using these parameters:\n\n")
             _ = f.write(f"The provided genome: {bn}\n")

harpy/snakefiles/align_strobealign.smk

@@ -250,13 +250,6 @@ rule workflow_summary:
         unmapped = "" if keep_unmapped else "-F 4",
         extra   = extra
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         with open(outdir + "/workflow/align.strobealign.summary", "w") as f:
             _ = f.write("The harpy align strobealign workflow ran using these parameters:\n\n")
             _ = f.write(f"The provided genome: {bn}\n")

harpy/snakefiles/impute.smk

@@ -222,13 +222,6 @@ rule workflow_summary:
         agg_report = collect(outdir + "/{stitchparams}/reports/variants.imputed.html", stitchparams=paramspace.instance_patterns) if not skipreports else [],
         contig_report = collect(outdir + "/{stitchparams}/reports/{part}.stitch.html", stitchparams=paramspace.instance_patterns, part = contigs) if not skipreports else [],
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         with open(outdir + "/workflow/impute.summary", "w") as f:
             _ = f.write("The harpy impute workflow ran using these parameters:\n\n")
             _ = f.write(f"The provided variant file: {variantfile}\n")

harpy/snakefiles/phase.smk

@@ -278,13 +278,6 @@ rule workflow_summary:
         prune = f"--threshold {pruning}" if pruning > 0 else "--no_prune 1",
         extra = extra
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         with open(outdir + "/workflow/phase.summary", "w") as f:
             _ = f.write("The harpy phase workflow ran using these parameters:\n\n")
             _ = f.write(f"The provided variant file: {variantfile}\n")

harpy/snakefiles/preflight_fastq.smk

@@ -21,12 +21,6 @@ envdir      = os.getcwd() + "/.harpy_envs"
 bn_r = r"([_\.][12]|[_\.][FR]|[_\.]R[12](?:\_00[0-9])*)?\.((fastq|fq)(\.gz)?)$"
 samplenames = {re.sub(bn_r, "", os.path.basename(i), flags = re.IGNORECASE) for i in fqlist}
 
-onstart:
-    logger.logger.addHandler(logging.FileHandler(config["snakemake_log"]))
-onsuccess:
-    os.remove(logger.logfile)
-onerror:
-    os.remove(logger.logfile)
 def get_fq1(wildcards):
     # returns a list of fastq files for read 1 based on *wildcards.sample* e.g.
     #samples_FR = [i for i in fqlist if wildcards.sample in i]

harpy/snakefiles/qc.smk

@@ -182,13 +182,6 @@ rule workflow_summary:
         dedup = "-D" if dedup else "",
         extra = extra
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         with open(outdir + "/workflow/qc.summary", "w") as f:
             _ = f.write("The harpy qc workflow ran using these parameters:\n\n")
             _ = f.write("fastp trimming ran using:\n")

harpy/snakefiles/sv_leviathan.smk

@@ -211,13 +211,6 @@ rule workflow_summary:
         iters  = f"-B {iterations}",
         extra = extra
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         with open(outdir + "/workflow/sv.leviathan.summary", "w") as f:
             _ = f.write("The harpy sv leviathan workflow ran using these parameters:\n\n")
             _ = f.write(f"The provided genome: {bn}\n")

harpy/snakefiles/sv_leviathan_pop.smk

@@ -273,13 +273,6 @@ rule workflow_summary:
         iters  = f"-B {iterations}",
         extra = extra
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         with open(outdir + "/workflow/sv.leviathan.summary", "w") as f:
             _ = f.write("The harpy sv leviathan workflow ran using these parameters:\n\n")
             _ = f.write(f"The provided genome: {bn}\n")

harpy/snakefiles/sv_naibr.smk

@@ -216,13 +216,6 @@ rule workflow_summary:
         bedpe_agg = collect(outdir + "/{sv}.bedpe", sv = ["inversions", "deletions","duplications"]),
         reports =  collect(outdir + "/reports/{sample}.naibr.html", sample = samplenames) if not skipreports else []
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         os.system(f"rm -rf {outdir}/naibrlog")
         argdict = process_args(extra)
         with open(outdir + "/workflow/sv.naibr.summary", "w") as f:

harpy/snakefiles/sv_naibr_phase.smk

@@ -274,13 +274,6 @@ rule workflow_summary:
         phaselog = outdir + "/logs/whatshap-haplotag.log",
         reports =  collect(outdir + "/reports/{sample}.naibr.html", sample = samplenames) if not skipreports else []
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         os.system(f"rm -rf {outdir}/naibrlog")
         argdict = process_args(extra)
         with open(outdir + "/workflow/sv.naibr.summary", "w") as f:

harpy/snakefiles/sv_naibr_pop.smk

@@ -263,13 +263,6 @@ rule workflow_summary:
         reports = collect(outdir + "/reports/{pop}.naibr.html", pop = populations) if not skipreports else [],
         agg_report = outdir + "/reports/naibr.pop.summary.html" if not skipreports else []
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         os.system(f"rm -rf {outdir}/naibrlog")
         argdict = process_args(extra)
         with open(outdir + "/workflow/sv.naibr.summary", "w") as f:

harpy/snakefiles/sv_naibr_pop_phase.smk

@@ -346,13 +346,6 @@ rule workflow_summary:
         reports = collect(outdir + "/reports/{pop}.naibr.html", pop = populations) if not skipreports else [],
         agg_report = outdir + "/reports/naibr.pop.summary.html" if not skipreports else []
     run:
-        import glob
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isfile(logfile) and os.path.getsize(logfile) == 0:
-                os.remove(logfile)
-        for logfile in glob.glob(f"{outdir}/logs/**/*", recursive = True):
-            if os.path.isdir(logfile) and not os.listdir(logfile):
-                os.rmdir(logfile)
         os.system(f"rm -rf {outdir}/naibrlog")
         argdict = process_args(extra)
         with open(outdir + "/workflow/sv.naibr.summary", "w") as f: