Updated conf to include tagalign files. Renamed script files from wrappers. ...

Updated conf to include tagalign files.  Renamed script files from wrappers.  Added cat_spp for ungzipped results.  Updated peak_call.yaml to rename .bed files to .tagAlign for spp.

chipathlon/conf.py

@@ -17,7 +17,7 @@ file_extensions = {
     "sai": ["sai"],
     "sam": ["sam"],
     "bam": ["bam"],
-    "bed": ["bed", "narrowPeak", "broadPeak"],
+    "bed": ["bed", "narrowPeak", "broadPeak", "tagAlign"],
     "bwa_genome": ["amb", "ann", "bwt", "pac", "sa"],
     "bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"],
     "quality": ["quality"],

chipathlon/jobs/modules/peak_call.yaml

 peak_call:
   - spp[tool]:
-    - r_spp_nodups:
+    - mv_bed_tagalign:
         inputs:
           - exp.bed:
               type: file
+        additional_inputs: null
+        outputs:
+          - exp.tagAlign:
+              type: file
+    - mv_bed_tagalign:
+        inputs:
           - control.bed:
               type: file
         additional_inputs: null
+        outputs:
+          - control.tagAlign:
+              type: file
+    - r_spp_nodups:
+        inputs:
+          - exp.tagAlign:
+              type: file
+          - control.tagAlign:
+              type: file
+        additional_inputs: null
         outputs:
           - results.narrowPeak:
               type: file
@@ -14,7 +30,7 @@ peak_call:
               type: file
           - results.ccscore:
               type: file
-    - zcat_awk_sort_peaks:
+    - cat_awk_sort_peaks:
         inputs:
           - results.narrowPeak:
               type: file

chipathlon/jobs/params/cat_awk_sort_peaks.yaml

+cat_awk_sort_peaks:
+  inputs:
+    - bed:
+        type: file
+  additional_inputs: null
+  outputs:
+    - bed:
+        type: file
+  command: cat_spp
+  arguments:
+    - "$inputs.0":
+        changeable: false
+        required: true
+        has_value: false
+    - "$outputs.0":
+        changeable: false
+        required: true
+        has_value: false
+  walltime: 2000
+  memory: 2000
+  cores: 1

chipathlon/jobs/params/mv_bed_tagalign.yaml

+zcat_awk_sort_peaks:
+  inputs:
+    - bed:
+        type: file
+  additional_inputs: null
+  outputs:
+    - bed:
+        type: file
+  command: mv_bed_tagalign
+  arguments:
+    - "$inputs.0":
+        changeable: false
+        required: true
+        has_value: false
+    - "$outputs.0":
+        changeable: false
+        required: true
+        has_value: false
+  walltime: 2000
+  memory: 2000
+  cores: 1

chipathlon/jobs/params/sort_awk_sort_peaks.yaml

@@ -6,7 +6,7 @@ sort_awk_sort_peaks:
   outputs:
     - bed:
         type: file
-  command: sort
+  command: sort_macs2
   arguments:
     - "$inputs.0":
         changeable: false

chipathlon/jobs/params/zcat_awk_sort_peaks.yaml

@@ -6,7 +6,7 @@ zcat_awk_sort_peaks:
   outputs:
     - bed:
         type: file
-  command: zcat
+  command: zcat_spp
   arguments:
     - "$inputs.0":
         changeable: false

chipathlon/jobs/scripts/cat_spp.sh

+#!/bin/bash
+
+/bin/cat "$1" | awk 'BEGIN{OFS="\t"}{print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' > "$2"

chipathlon/jobs/scripts/mv_bed_tagalign.sh

+#!/bin/bash
+
+/bin/mv "$1" "$2"