Diff bind reorg

bin/prep_diffbind.py

@@ -5,7 +5,7 @@
 from os.path import join
 
 
-def main(condition, peaktool, peakext, peakcaller, csvfile, wp, bam_dir):
+def main(contrast, peaktool, peakext, peakcaller, csvfile, wp, bam_dir):
     config = json.load(open(join(wp, "config.json")))
     chip2input = config['project']['peaks']['inputs']
     groupdata = config['project']['groups']
@@ -21,7 +21,7 @@ def main(condition, peaktool, peakext, peakcaller, csvfile, wp, bam_dir):
 
     samplesheet = []
     # {group1}_vs_{group2} == condition
-    g1, g2 = condition.split('_')[0], condition.split('_')[2]
+    g1, g2 = contrast.split('_')[0], contrast.split('_')[2]
     for group in [g1, g2]:
         for chip in groupdata[group]:
             replicate = str([ i + 1 for i in range(len(groupdata[group])) if groupdata[group][i]== chip ][0])

config/cluster.json

@@ -99,21 +99,29 @@
     },
     "diffbindQC": {
         "threads": "16",
-        "mem": "120g"
+        "mem": "150g"
     },
-    "diffbind": {
+    "diffbind_deseq": {
         "threads": "16",
-        "mem": "120g"
+        "mem": "150g"
     },
-    "diffbind_blocking": {
+    "diffbind_edger": {
         "threads": "16",
-        "mem": "120g"
+        "mem": "150g"
+    },
+    "diffbind_edger_blocking": {
+        "threads": "16",
+        "mem": "150g"
+    },
+    "diffbind_deseq_blocking": {
+        "threads": "16",
+        "mem": "150g"
     },
     "diffbind_count": {
         "threads": "16",
         "mem": "120g"
     },
-    "UROPA_macsN": {
+    "UROPA_macsNarrow": {
         "threads": "16",
         "mem": "32g",
         "time": "1-00:00:00"
@@ -129,10 +137,11 @@
         "time": "1-00:00:00"
     },
     "MEME": {
-        "threads": "2",
+        "threads": "28",
         "mem": "32g",   
         "time": "3-00:00:00",
-        "ntasks": "28",
-        "ntasks_per_core": "1"
+        "ntasks": "--ntasks=28",
+        "ntasks_per_core": "--ntasks-per-core=1",
+        "exclusive": "--exclusive"
     }
 }

config/containers.json

@@ -3,7 +3,6 @@
         "cfchip": "docker://skchronicles/cfchip_toolkit:v0.5.0",
         "uropa": "docker://rroutsong/uropa:4.0.3",
         "python": "docker://asyakhleborodova/chrom_seek_python:v0.1.0",
-        "ppqt": "docker://asyakhleborodova/ppqt:v0.2.0",
-        "dedup": "docker://rroutsong/chrom_seek_dedup:0.0.1"
+        "ppqt": "docker://asyakhleborodova/ppqt:v0.2.0"
     }
 }

workflow/rules/uropa.smk

@@ -182,7 +182,7 @@ rule UROPA_prep_in_macsN:
         """)
 
 
-rule UROPA_macsN:
+rule UROPA_macsNarrow:
     input: join(uropa_dir, "macsNarrow", "{name}.macsNarrow.{_type}.json")
     params: 
         rname                           = "UROPA_macsN",