Merge pull request #63 from maxplanck-ie/develop

fix: hardcode snakemake version to 3.12 in all wrappers to avoid missing

shared/common_functions.py

@@ -103,7 +103,7 @@ def get_sample_names(infiles, ext, reads):
         x = os.path.basename(x).replace(ext, "")
         try:
             x = x.replace(reads[0], "").replace(reads[1], "")
-        except:
+        except IndexError:
             pass
         s.append(x)
     return sorted(list(set(s)))
@@ -145,7 +145,7 @@ def get_fragment_length(infile):
                 try:
                     median = next(f).split()[0]
                     return int(median)
-                except:
+                except TypeError:
                     print("ERROR: File", infile, "is NOT a proper Picard CollectInsertSizeMetrics metrics file.\n")
                     exit(1)
     # no match in infile

shared/tools/sample_qc_report_PE.py

@@ -19,7 +19,7 @@
 try:
     infile_MACS2_xls = sys.argv[4]              # sample_name.filtered.BAM_peaks.xls (optional)
     infile_MACS2_qc_txt = sys.argv[5]           # ample_name.filtered.BAM_peaks.qc.txt (optional)
-except:
+except IndexError:
     pass
 
 
@@ -49,7 +49,7 @@
     fmapped_pairs = 1.0 * mapped_pairs / read_pairs
     fmapped_singletons = 1.0 * (mapped_reads - mapped_reads_in_pairs) / total_reads
 
-except:
+except OSError:
     exit("ERROR! Unable to read: {}".format(infile_AlignmentSummaryMetrics))
 
 
@@ -63,7 +63,7 @@
     fdup_mapped_pairs = 1.0 * dup_mapped_pairs / mapped_pairs
     dupfree_mapped_pairs = mapped_pairs - dup_mapped_pairs
     fdupfree_mapped_pairs = 1.0 * dupfree_mapped_pairs / read_pairs
-except:
+except OSError:
     exit("ERROR! Unable to read: {}".format(infile_MarkDuplicates))
 
 
@@ -83,7 +83,7 @@
         fragment_size = int(columns.split(" = ")[1])
     else:
         fragment_size = "NA"
-except:
+except OSError:
     fragment_size = "NA"
 
 
@@ -94,7 +94,7 @@
         peak_count = int(columns[0])
         frip = round(float(columns[1]), 3)
         peak_genome_coverage = round(columns[2], 3)
-except:
+except OSError:
     peak_count = "NA"
     frip = "NA"
     peak_genome_coverage = "NA"

shared/tools/sample_qc_report_SE.py

@@ -16,7 +16,7 @@
 try:
     infile_MACS2_xls = sys.argv[3]              # sample_name.filtered.BAM_peaks.xls (optional)
     infile_MACS2_qc_txt = sys.argv[4]           # ample_name.filtered.BAM_peaks.qc.txt (optional)
-except:
+except IndexError:
     pass
 
 
@@ -37,7 +37,7 @@
 
     # fraction of high-quality mapped reads (MAPQ >=20)
     fhq_mapped_reads = 1.0 * int(columns[8]) / total_reads
-except:
+except OSError:
     exit("ERROR! Unable to read: {}\n".format(infile_AlignmentSummaryMetrics))
 
 
@@ -58,7 +58,7 @@
 
     # fraction of duplication free mapped reads
     fdupfree_mapped_reads = 1.0 * dupfree_mapped_reads / total_reads
-except:
+except OSError:
     exit("ERROR! Unable to read: {}".format(infile_MarkDuplicates))
 
 
@@ -68,7 +68,7 @@
         lines = f.readlines()
     columns = filter(lambda x: x.startswith("# d"), lines)[0].strip()
     fragment_size = int(columns.split(" = ")[1])
-except:
+except OSError:
     fragment_size = "NA"
 
 
@@ -79,7 +79,7 @@
         peak_count = int(columns[0])
         frip = round(float(columns[1]), 3)
         peak_genome_coverage = round(columns[2], 3)
-except:
+except OSError:
     peak_count = "NA"
     frip = "NA"
     peak_genome_coverage = "NA"

workflows/ATAC-seq/ATAC-seq

@@ -130,7 +130,7 @@ def main():
     with open(os.path.join(args.outdir,'config.yaml'), 'w') as f:
         yaml.dump(config, f, default_flow_style=True)
 
-    snakemake_module_load = "module load snakemake slurm &&".split()
+    snakemake_module_load = "module load snakemake/3.12.0 slurm &&".split()
     snakemake_cmd = """
                     snakemake {snakemake_options} --latency-wait 300 --snakefile {snakefile} --jobs {max_jobs} --directory {outdir} --configfile {configfile}
                     """.format( snakefile = os.path.join(args.this_script_dir, "Snakefile"),

workflows/ChIP-seq/ChIP-seq

@@ -188,7 +188,7 @@ def main():
     ## save to configs.yaml in outdir
     cf.write_configfile(os.path.join(args.outdir,'ChIP-seq.config.yaml'),config)
 
-    snakemake_module_load = "module load snakemake slurm &&".split()
+    snakemake_module_load = "module load snakemake/3.12.0 slurm &&".split()
     snakemake_cmd = """
                     snakemake {snakemake_options} --latency-wait 300 --snakefile {snakefile} --jobs {max_jobs} --directory {workingdir} --configfile {configfile}
                     """.format( snakefile = os.path.join(this_script_dir, "Snakefile"),

workflows/scRNAseq/scRNAseq-mapcount

@@ -134,7 +134,7 @@ def main():
     ## save to configs.yaml in outdir
     cf.write_configfile(os.path.join(args.outdir,'config.yaml'),config)
 
-    snakemake_module_load = "module load snakemake slurm &&".split()
+    snakemake_module_load = "module load snakemake/3.12.0 slurm &&".split()
     snakemake_cmd = """
                     snakemake {snakemake_options} --latency-wait 300 --snakefile {snakefile} --jobs {max_jobs} --directory {outdir} --configfile {configfile}
                     """.format( snakefile = os.path.join(this_script_dir, "Snakefile"),