snk

repeats/Snakefile

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+import sys
+import logging
+from snakemake.io import glob_wildcards, expand
+import glob,os
+import pathlib
+import csv
+import pandas as pd
+import numpy as np
+
+
+#run with snakemake --profile slurm --use-conda
+
+
+#import multiqc
+
+DATADIR_SHORT="/beegfs/scratch/ric.cosr/ric.cosr/Menarini/ALL_BAM_sorted_markdup/start/"
+
+files = []
+
+for file_name in os.listdir(DATADIR_SHORT):
+    if file_name.endswith("_markdup.bam"):
+        files.append(file_name)
+
+SUFF = []
+SAMPLELIST = []
+for file in files:
+    A = file.split("_")[0]
+    B = file.split("_")[1]
+    E = A + '_' + B
+    SUFF.append(E)
+
+SUFF=set(SUFF)
+
+SUFFIX = ' '.join(map(str, SUFF))
+print("SUFFIX", SUFFIX)
+
+#SUFFIX = "URIN101220_D10_2linfocitiadesi"
+path = "logs_slurm"
+try:
+    os.mkdir(path)
+except OSError:
+    print ("Creation of the directory %s failed" % path)
+else:
+    print ("Successfully created the directory %s " % path)
+
+
+
+rule all:
+    input:
+        expand(["coverage/{pref}_coverage.txt"], pref=SUFFIX.split(' '))
+
+
+rule bTb:
+    input:
+        BAM = "/beegfs/scratch/ric.cosr/ric.cosr/Menarini/ALL_BAM_sorted_markdup/start/{pref}_markdup.bam",
+    output:
+        "coverage/{pref}_coverage.txt"
+    resources: time_min = 5000, mem_mb=2500, cpus = 1
+    shell:"""
+        mkdir -p bed
+        count=$(samtools view -F 4 -c {input.BAM})
+        echo -e "{wildcards.pref}\t$count" > {output}
+        """