Commit 3c5242b4 authored by aknecht2's avatar aknecht2
Browse files

Merge new_modules with master.

parents fce80a48 f4bf8215
......@@ -20,7 +20,10 @@ file_extensions = {
"bed": ["bed", "narrowPeak", "broadPeak"],
"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"]
"quality": ["quality"],
"qc": ["qc"],
"pdf": ["pdf"],
"ccscore": ["ccscore"]
}
# list of resources that can be specified per job (step) in
......@@ -33,9 +36,23 @@ resources = {
"memory": {
"namespace": "condor",
"key": "request_memory"
},
"cores": {
"namespace": "pegasus",
"key": "cores"
}
}
# Defines the types of input / output arguments
# argument -> Any non file argument
# file -> Any file argument that isn't redirected
# stdout -> Any file argument that is redirected from stdout
# stderr -> Any file argument that is redirected from stderr
argument_types = {
"argument": ["argument"],
"file": ["file", "stdout", "stderr"]
}
# param keys
param_keys = {
"required": ["arguments"],
......
......@@ -65,7 +65,7 @@ align:
type: file
outputs:
- align.sam:
type: file
type: stdout
bowtie2[tool]:
- single[read_end]:
- bowtie2_align_single:
......@@ -93,7 +93,7 @@ align:
- align.sam:
type: file
- align.quality:
type: file
type: stderr
paired[read_end]:
- bowtie2_align_paired:
inputs:
......@@ -122,7 +122,7 @@ align:
- align.sam:
type: file
- align.quality:
type: file
type: stderr
- samtools_sam_to_bam:
inputs:
- align.sam:
......
......@@ -2,12 +2,10 @@ peak_call:
- spp[tool]:
- r_spp_nodups:
inputs:
- exp.bam:
- exp.bed:
type: file
- control.bam:
- control.bed:
type: file
- dir:
type: argument
additional_inputs: null
outputs:
- results.narrowPeak:
......@@ -27,9 +25,9 @@ peak_call:
- macs2[tool]:
- macs2_callpeak:
inputs:
- exp.bam:
- exp.bed:
type: file
- control.bam:
- control.bed:
type: file
- prefix:
type: argument
......
......@@ -11,7 +11,7 @@ remove_duplicates:
inputs:
- filtered.bam:
type: file
additional_input: null
additional_inputs: null
outputs:
- sorted.bam:
type: file
......@@ -25,3 +25,11 @@ remove_duplicates:
type: file
- quality.qc:
type: file
- bedtools_bam_to_bed:
inputs:
- no_dups.bam:
type: file
additional_inputs: null
outputs:
- no_dups.bed:
type: stdout
......@@ -2,9 +2,10 @@ bedtools_bam_to_bed:
inputs:
- bam:
type: file
additional_inputs: null
outputs:
- bed:
type: file
type: stdout
command: bedtools
arguments:
- "bamtobed":
......@@ -16,9 +17,6 @@ bedtools_bam_to_bed:
required: true
has_value: true
default: $inputs.0
- "$outputs.0":
changeable: false
required: true
has_value: false
walltime: 2000
memory: 2000
cores: 1
......@@ -25,7 +25,7 @@ bowtie2_align_paired:
- sam:
type: file
- quality:
type: file
type: stderr
command: bowtie2
arguments:
- "-x":
......@@ -48,10 +48,11 @@ bowtie2_align_paired:
required: true
has_value: true
default: $outputs.0
- "2>":
changeable: false
required: true
- "-p":
changeable: true
required: false
has_value: true
default: $outputs.1
default: 8
walltime: 2000
memory: 2000
cores: 8
......@@ -23,7 +23,7 @@ bowtie2_align_single:
- sam:
type: file
- quality:
type: file
type: stderr
command: bowtie2
arguments:
- "-x":
......@@ -41,10 +41,11 @@ bowtie2_align_single:
required: true
has_value: true
default: $outputs.0
- "2>":
changeable: false
required: true
- "-p":
changeable: true
required: false
has_value: true
default: $outputs.1
default: 8
walltime: 2000
memory: 2000
cores: 8
......@@ -19,7 +19,7 @@ bwa_align_paired:
type: file
outputs:
- sam:
type: file
type: stderr
command: bwa
arguments:
- "mem":
......@@ -34,7 +34,7 @@ bwa_align_paired:
changeable: true
required: false
has_value: true
default: 1
default: 8
- "$inputs.0":
changeable: false
required: true
......@@ -47,10 +47,6 @@ bwa_align_paired:
changeable: false
required: true
has_value: false
- "2>":
changeable: false
required: true
has_value: true
default: $outputs.0
walltime: 2000
memory: 2000
cores: 8
......@@ -43,7 +43,7 @@ bwa_align_single:
changeable: true
required: false
has_value: true
default: 1
default: 8
- "-f":
changeable: false
required: true
......@@ -59,3 +59,4 @@ bwa_align_single:
has_value: false
walltime: 2000
memory: 2000
cores: 8
......@@ -45,3 +45,4 @@ bwa_sai_to_sam:
has_value: false
walltime: 2000
memory: 2000
cores: 1
macs2_callpeak:
inputs:
- bam:
- bed:
type: file
- bam:
- bed:
type: file
- prefix:
type: argument
additional_inputs: null
outputs:
- bed:
type: file
......@@ -69,3 +70,4 @@ macs2_callpeak:
has_value: false
walltime: 2000
memory: 8000
cores: 1
......@@ -27,7 +27,8 @@ picard_mark_duplicates:
- "METRICS_FILE=":
changeable: false
required: true
has_value: $outputs.1
has_value: true
default: $outputs.1
- "VALIDATION_STRINGENCY=":
changeable: true
required: false
......@@ -45,3 +46,4 @@ picard_mark_duplicates:
default: true
walltime: 2000
memory: 8000
cores: 1
......@@ -2,6 +2,7 @@ picard_sort_sam:
inputs:
- bam:
type: file
additional_inputs: null
outputs:
- bam:
type: file
......@@ -28,3 +29,4 @@ picard_sort_sam:
default: "coordinate"
walltime: 2000
memory: 8000
cores: 1
r_spp_nodups:
inputs:
- bam:
- bed:
type: file
- bam:
- bed:
type: file
- dir:
type: argument
additional_inputs: null
outputs:
- bed:
type: file
......@@ -34,7 +33,7 @@ r_spp_nodups:
changeable: false
required: true
has_value: true
default: $inputs.2
default: .
- "-speak":
changeable: true
required: false
......@@ -44,22 +43,22 @@ r_spp_nodups:
changeable: false
required: true
has_value: true
default: $outputs.1
default: $outputs.0
- "-savp":
changeable: false
required: true
has_value: true
default: $outputs.2
default: $outputs.1
- "-out":
changeable: false
required: true
has_value: true
default: $outputs.3
default: $outputs.2
- "-fdr":
changeable: true
required: false
has_value: true
default: 0.01
walltime: 2000
memory: 8000
cores: 1
......@@ -2,6 +2,7 @@ samtools_filter_bam:
inputs:
- bam:
type: file
additional_inputs: null
outputs:
- bam:
type: file
......@@ -21,6 +22,10 @@ samtools_filter_bam:
required: false
has_value: true
default: 30
- "-b":
changeable: false
required: true
has_value: false
- "-o":
changeable: false
required: true
......@@ -32,3 +37,4 @@ samtools_filter_bam:
has_value: false
walltime: 2000
memory: 2000
cores: 1
......@@ -2,6 +2,7 @@ samtools_remove_duplicates:
inputs:
- bam:
type: file
additional_inputs: null
outputs:
- bam:
type: file
......@@ -31,3 +32,4 @@ samtools_remove_duplicates:
has_value: false
walltime: 2000
memory: 2000
cores: 1
......@@ -27,3 +27,4 @@ samtools_sam_to_bam:
has_value: false
walltime: 2000
memory: 2000
cores: 1
......@@ -2,6 +2,7 @@ sort_awk_sort_peaks:
inputs:
- bed:
type: file
additional_inputs: null
outputs:
- bed:
type: file
......@@ -17,3 +18,4 @@ sort_awk_sort_peaks:
has_value: false
walltime: 2000
memory: 2000
cores: 1
......@@ -2,6 +2,7 @@ zcat_awk_sort_peaks:
inputs:
- bed:
type: file
additional_inputs: null
outputs:
- bed:
type: file
......@@ -17,3 +18,4 @@ zcat_awk_sort_peaks:
has_value: false
walltime: 2000
memory: 2000
cores: 1
import chipathlon.db
import argparse
parser = argparse.ArgumentParser(description="Download target file.")
parser.add_argument("-u", "--url", dest="url", required=True, help="Target url.")
parser.add_argument("-p", "--path", dest="path", required=True, help="Local path to file.")
parser.add_argument("-t", "--url_type", dest="url_type", default="ftp://", help="Type of url to access.")
parser.add_argument("-r", "--retries", dest="retries", default=3, type=int, help="Number of retries.")
parser.add_argument("-n", "--overwrite", dest="overwrite", default=True, action="store_false", help="Dont' overwrite local file if exists.")
parser.add_argument("-m", "--md5", dest="md5", help="Check md5 value against passed value.")
args = parser.parse_args()
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