Commit 7c797795 authored by aknecht2's avatar aknecht2
Browse files

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.
parent 1ad7c145
......@@ -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"],
......
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
......
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
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
......@@ -6,7 +6,7 @@ sort_awk_sort_peaks:
outputs:
- bed:
type: file
command: sort
command: sort_macs2
arguments:
- "$inputs.0":
changeable: false
......
......@@ -6,7 +6,7 @@ zcat_awk_sort_peaks:
outputs:
- bed:
type: file
command: zcat
command: zcat_spp
arguments:
- "$inputs.0":
changeable: false
......
#!/bin/bash
/bin/cat "$1" | awk 'BEGIN{OFS="\t"}{print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' > "$2"
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