remove now-deprecated onstarts/onerrors

pdimens · Aug 12, 2024 · c0117e6 · c0117e6
1 parent a500729
commit c0117e6
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Showing 20 changed files with 44 additions and 769 deletions.
diff --git a/harpy/snakefiles/align_bwa.smk b/harpy/snakefiles/align_bwa.smk
@@ -3,11 +3,7 @@ containerized: "docker://pdimens/harpy:latest"
 import os
 import re
 import sys
-import glob
 import logging as pylogging
-from datetime import datetime
-from rich.panel import Panel
-from rich import print as rprint
 
 outdir      = config["output_directory"]
 envdir      = os.getcwd() + "/.harpy_envs"
@@ -21,46 +17,15 @@ genome_zip  = True if bn.lower().endswith(".gz") else False
 bn_idx      = f"{bn}.gzi" if genome_zip else f"{bn}.fai"
 skipreports = config["skip_reports"]
 windowsize  = config["depth_windowsize"]
-## the log file ##
-attempts = glob.glob(f"{outdir}/logs/snakemake/*.snakelog")
-if not attempts:
-    logfile = f"{outdir}/logs/snakemake/align_bwa.run1." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
-else:
-    increment = sorted([int(i.split(".")[1].replace("run","")) for i in attempts])[-1] + 1
-    logfile = f"{outdir}/logs/snakemake/align_bwa.run{increment}." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
+snakemake_log = config["snakemake_log"]
 
 wildcard_constraints:
     sample = "[a-zA-Z0-9._-]+"
 
 onstart:
-    os.makedirs(f"{outdir}/logs/snakemake", exist_ok = True)
-    extra_logfile_handler = pylogging.FileHandler(logfile)
+    extra_logfile_handler = pylogging.FileHandler(snakemake_log)
     logger.logger.addHandler(extra_logfile_handler)
 
-onerror:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{logfile}[/bold]",
-            title = "[bold]harpy align bwa",
-            title_align = "left",
-            border_style = "red"
-            ),
-        file = sys.stderr
-    )
-
-onsuccess:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has finished successfully! Find the results in [bold]{outdir}[/bold]",
-            title = "[bold]harpy align bwa",
-            title_align = "left",
-            border_style = "green"
-            ),
-        file = sys.stderr
-    )
-
 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}
 d = dict(zip(samplenames, samplenames))

diff --git a/harpy/snakefiles/align_ema.smk b/harpy/snakefiles/align_ema.smk
@@ -2,13 +2,9 @@ containerized: "docker://pdimens/harpy:latest"
 
 import os
 import re
-import glob
 import shutil
 import logging as pylogging
-from datetime import datetime
 from pathlib import Path
-from rich.panel import Panel
-from rich import print as rprint
 
 outdir      = config["output_directory"]
 nbins 		= config["EMA_bins"]
@@ -25,48 +21,15 @@ envdir      = os.getcwd() + "/.harpy_envs"
 windowsize  = config["depth_windowsize"]
 keep_unmapped = config["keep_unmapped"]
 skipreports = config["skip_reports"]
-
-## the log file ##
-attempts = glob.glob(f"{outdir}/logs/snakemake/*.snakelog")
-if not attempts:
-    logfile = f"{outdir}/logs/snakemake/align_ema.run1." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
-else:
-    increment = sorted([int(i.split(".")[1].replace("run","")) for i in attempts])[-1] + 1
-    logfile = f"{outdir}/logs/snakemake/align_ema.run{increment}." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
+snakemake_log = config["snakemake_log"]
 
 wildcard_constraints:
     sample = "[a-zA-Z0-9._-]+"
 
 onstart:
-    os.makedirs(f"{outdir}/logs/snakemake", exist_ok = True)
-    extra_logfile_handler = pylogging.FileHandler(logfile)
+    extra_logfile_handler = pylogging.FileHandler(snakemake_log)
     logger.logger.addHandler(extra_logfile_handler)
 
-onerror:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{logfile}[/bold]",
-            title = "[bold]harpy align ema",
-            title_align = "left",
-            border_style = "red"
-            ),
-        file = sys.stderr
-    )
-
-onsuccess:
-    print("")
-    shutil.rmtree(f'{outdir}/bxcount', ignore_errors=True)
-    rprint(
-        Panel(
-            f"The workflow has finished successfully! Find the results in [bold]{outdir}[/bold]",
-            title = "[bold]harpy align ema",
-            title_align = "left",
-            border_style = "green"
-            ),
-        file = sys.stderr
-    )
-
 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}
 d = dict(zip(samplenames, samplenames))

diff --git a/harpy/snakefiles/align_strobealign.smk b/harpy/snakefiles/align_strobealign.smk
@@ -3,11 +3,7 @@ containerized: "docker://pdimens/harpy:latest"
 import os
 import re
 import sys
-import glob
 import logging as pylogging
-from datetime import datetime
-from rich.panel import Panel
-from rich import print as rprint
 
 outdir      = config["output_directory"]
 envdir      = os.getcwd() + "/.harpy_envs"
@@ -23,47 +19,15 @@ molecule_distance = config["molecule_distance"]
 keep_unmapped = config["keep_unmapped"]
 readlen = config["average_read_length"]
 autolen = isinstance(readlen, str)
-
-## the log file ##
-attempts = glob.glob(f"{outdir}/logs/snakemake/*.snakelog")
-if not attempts:
-    logfile = f"{outdir}/logs/snakemake/align_strobe.run1." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
-else:
-    increment = sorted([int(i.split(".")[1].replace("run","")) for i in attempts])[-1] + 1
-    logfile = f"{outdir}/logs/snakemake/align_strobe.run{increment}." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
+snakemake_log = config["snakemake_log"]
 
 wildcard_constraints:
     sample = "[a-zA-Z0-9._-]+"
 
 onstart:
-    os.makedirs(f"{outdir}/logs/snakemake", exist_ok = True)
-    extra_logfile_handler = pylogging.FileHandler(logfile)
+    extra_logfile_handler = pylogging.FileHandler(snakemake_log)
     logger.logger.addHandler(extra_logfile_handler)
 
-onerror:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{logfile}[/bold]",
-            title = "[bold]harpy align strobealign",
-            title_align = "left",
-            border_style = "red"
-            ),
-        file = sys.stderr
-    )
-
-onsuccess:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has finished successfully! Find the results in [bold]{outdir}[/bold]",
-            title = "[bold]harpy align strobealign",
-            title_align = "left",
-            border_style = "green"
-            ),
-        file = sys.stderr
-    )
-
 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}
 d = dict(zip(samplenames, samplenames))

diff --git a/harpy/snakefiles/deconvolve.smk b/harpy/snakefiles/deconvolve.smk
@@ -3,11 +3,7 @@ containerized: "docker://pdimens/harpy:latest"
 import os
 import re
 import sys
-import glob
 import logging as pylogging
-from datetime import datetime
-from rich.panel import Panel
-from rich import print as rprint
 
 envdir      = os.getcwd() + "/.harpy_envs"
 fqlist      = config["inputs"]
@@ -16,14 +12,7 @@ kmer_length = config["kmer_length"]
 window_size = config["window_size"]
 density 	= config["density"] 
 dropout     = config["dropout"]
-
-## the log file ##
-attempts = glob.glob(f"{outdir}/logs/snakemake/*.snakelog")
-if not attempts:
-    logfile = f"{outdir}/logs/snakemake/deconvolve.run1." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
-else:
-    increment = sorted([int(i.split(".")[1].replace("run","")) for i in attempts])[-1] + 1
-    logfile = f"{outdir}/logs/snakemake/deconvolve.run{increment}." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
+snakemake_log = config["snakemake_log"]
 
 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}
@@ -32,34 +21,9 @@ wildcard_constraints:
     sample = "[a-zA-Z0-9._-]+"
 
 onstart:
-    os.makedirs(f"{outdir}/logs/snakemake", exist_ok = True)
-    extra_logfile_handler = pylogging.FileHandler(logfile)
+    extra_logfile_handler = pylogging.FileHandler(snakemake_log)
     logger.logger.addHandler(extra_logfile_handler)
 
-onsuccess:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has finished successfully! Find the results in [bold]{outdir}/[/bold]",
-            title = "[bold]harpy deconvolve",
-            title_align = "left",
-            border_style = "green"
-            ),
-        file = sys.stderr
-    )
-
-onerror:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{logfile}[/bold]",
-            title = "[bold]harpy deconvolve",
-            title_align = "left",
-            border_style = "red"
-            ),
-        file = sys.stderr
-    )
-
 def get_fq1(wildcards):
     # returns a list of fastq files for read 1 based on *wildcards.sample* e.g.
     r = re.compile(fr"(.*/{re.escape(wildcards.sample)})([_\.]1|[_\.]F|[_\.]R1(?:\_00[0-9])*)?\.((fastq|fq)(\.gz)?)$", flags = re.IGNORECASE)

diff --git a/harpy/snakefiles/demultiplex_gen1.smk b/harpy/snakefiles/demultiplex_gen1.smk
@@ -3,11 +3,7 @@ containerized: "docker://pdimens/harpy:latest"
 import os
 import re
 import sys
-import glob
 import logging as pylogging
-from datetime import datetime
-from rich.panel import Panel
-from rich import print as rprint
 
 R1 = config["inputs"]["R1"]
 R2 = config["inputs"]["R2"]
@@ -17,15 +13,9 @@ samplefile = config["inputs"]["demultiplex_schema"]
 skipreports = config["skip_reports"]
 outdir = config["output_directory"]
 envdir = os.getcwd() + "/.harpy_envs"
+snakemake_log = config["snakemake_log"]
 
 ## the log file ##
-attempts = glob.glob(f"{outdir}/logs/snakemake/*.snakelog")
-if not attempts:
-    logfile = f"{outdir}/logs/snakemake/demultiplex_gen1.run1." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
-else:
-    increment = sorted([int(i.split(".")[1].replace("run","")) for i in attempts])[-1] + 1
-    logfile = f"{outdir}/logs/snakemake/demultiplex_gen1.run{increment}." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
-
 def barcodedict(smpl):
     d = {}
     with open(smpl, "r") as f:
@@ -42,34 +32,9 @@ samples = barcodedict(samplefile)
 samplenames = [i for i in samples.keys()]
 
 onstart:
-    os.makedirs(f"{outdir}/logs/snakemake", exist_ok = True)
-    extra_logfile_handler = pylogging.FileHandler(logfile)
+    extra_logfile_handler = pylogging.FileHandler(snakemake_log)
     logger.logger.addHandler(extra_logfile_handler)
 
-onerror:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{logfile}[/bold]",
-            title = "[bold]harpy demultiplex",
-            title_align = "left",
-            border_style = "red"
-            ),
-        file = sys.stderr
-    )
-
-onsuccess:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has finished successfully! Find the results in [bold]{outdir}[/bold]",
-            title = "[bold]harpy demultiplex",
-            title_align = "left",
-            border_style = "green"
-            ),
-        file = sys.stderr
-    )
-
 rule link_R1:
     input:
         R1

diff --git a/harpy/snakefiles/impute.smk b/harpy/snakefiles/impute.smk
@@ -3,36 +3,24 @@ containerized: "docker://pdimens/harpy:latest"
 import os
 import re
 import sys
-import glob
 import subprocess
 import pandas as pd
 import multiprocessing
 import logging as pylogging
-from datetime import datetime
-from rich.panel import Panel
-from rich import print as rprint
 from snakemake.utils import Paramspace
 
 bamlist     = config["inputs"]["alignments"]
 variantfile = config["inputs"]["variantfile"]
 paramfile   = config["inputs"]["paramfile"]
 biallelic   = config["inputs"]["biallelic_contigs"]
-skipreports = config["skip_reports"]
 outdir      = config["output_directory"]
 envdir      = os.getcwd() + "/.harpy_envs"
+skipreports = config["skip_reports"]
+snakemake_log = config["snakemake_log"]
 paramspace  = Paramspace(pd.read_csv(paramfile, sep=r"\s+", skip_blank_lines=True).rename(columns=str.lower), param_sep = "", filename_params = ["k", "s", "ngen", "bxlimit"])
 with open(biallelic, "r") as f_open:
     contigs = [i.rstrip() for i in f_open.readlines()]
 
-
-## the log file ##
-attempts = glob.glob(f"{outdir}/logs/snakemake/*.snakelog")
-if not attempts:
-    logfile = f"{outdir}/logs/snakemake/impute.run1." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
-else:
-    increment = sorted([int(i.split(".")[1].replace("run","")) for i in attempts])[-1] + 1
-    logfile = f"{outdir}/logs/snakemake/impute.run{increment}." + datetime.now().strftime("%d_%m_%Y") + ".snakelog"
-
 wildcard_constraints:
     sample = "[a-zA-Z0-9._-]+"
 
@@ -42,34 +30,9 @@ def sam_index(infile):
         subprocess.run(f"samtools index {infile} {infile}.bai".split())
 
 onstart:
-    os.makedirs(f"{outdir}/logs/snakemake", exist_ok = True)
-    extra_logfile_handler = pylogging.FileHandler(logfile)
+    extra_logfile_handler = pylogging.FileHandler(snakemake_log)
     logger.logger.addHandler(extra_logfile_handler)
 
-onerror:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{logfile}[/bold]",
-            title = "[bold]harpy impute",
-            title_align = "left",
-            border_style = "red"
-            ),
-        file = sys.stderr
-    )
-
-onsuccess:
-    print("")
-    rprint(
-        Panel(
-            f"The workflow has finished successfully! Find the results in [bold]{outdir}/[/bold]",
-            title = "[bold]harpy impute",
-            title_align = "left",
-            border_style = "green"
-            ),
-        file = sys.stderr
-    )
-
 rule sort_bcf:
     input:
         variantfile