Commit 3f707dfc authored by aknecht2's avatar aknecht2
Browse files

Added cores profile to jobs. Updated alignment request & default cores to 8.

parent 0db7bf1f
......@@ -36,6 +36,10 @@ resources = {
"memory": {
"namespace": "condor",
"key": "request_memory"
},
"cores": {
"namepsace": "pegasus",
"key": "cores"
}
}
......
......@@ -22,3 +22,4 @@ bedtools_bam_to_bed:
has_value: false
walltime: 2000
memory: 2000
cores: 1
......@@ -48,6 +48,11 @@ bowtie2_align_paired:
required: true
has_value: true
default: $outputs.0
- "-p":
changeable: true
required: false
has_value: true
default: 8
- "2>":
changeable: false
required: true
......@@ -55,3 +60,4 @@ bowtie2_align_paired:
default: $outputs.1
walltime: 2000
memory: 2000
cores: 8
......@@ -41,6 +41,11 @@ bowtie2_align_single:
required: true
has_value: true
default: $outputs.0
- "-p":
changeable: true
required: false
has_value: true
default: 8
- "2>":
changeable: false
required: true
......@@ -48,3 +53,4 @@ bowtie2_align_single:
default: $outputs.1
walltime: 2000
memory: 2000
cores: 8
......@@ -34,7 +34,7 @@ bwa_align_paired:
changeable: true
required: false
has_value: true
default: 1
default: 8
- "$inputs.0":
changeable: false
required: true
......@@ -54,3 +54,4 @@ bwa_align_paired:
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
......@@ -70,3 +70,4 @@ macs2_callpeak:
has_value: false
walltime: 2000
memory: 8000
cores: 1
......@@ -46,3 +46,4 @@ picard_mark_duplicates:
default: true
walltime: 2000
memory: 8000
cores: 1
......@@ -29,3 +29,4 @@ picard_sort_sam:
default: "coordinate"
walltime: 2000
memory: 8000
cores: 1
......@@ -59,6 +59,6 @@ r_spp_nodups:
required: false
has_value: true
default: 0.01
walltime: 2000
memory: 8000
cores: 1
......@@ -33,3 +33,4 @@ samtools_filter_bam:
has_value: false
walltime: 2000
memory: 2000
cores: 1
......@@ -32,3 +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
......@@ -18,3 +18,4 @@ sort_awk_sort_peaks:
has_value: false
walltime: 2000
memory: 2000
cores: 1
......@@ -18,3 +18,4 @@ zcat_awk_sort_peaks:
has_value: false
walltime: 2000
memory: 2000
cores: 1
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