Commit 23ad9c33 authored by aknecht2's avatar aknecht2
Browse files

Added module workflow files. Updated run.yaml

parent 4ea8345f
align:
bwa:
- single:
- bwa_align_single
- bwa_sai_to_sam
paired:
- bwa_align_paired
- samtools_sam_to_bam
bowtie2:
- single: bowtie2_align_single
paired: bowtie2_align_paired
- samtools_sam_to_bam
duplicates:
- samtools_filter
- picard_sort
- picard_remove_duplicates
- bedtools_bam_to_bed
peak:
macs2:
- run_macs2
- sort_macs2
spp:
- run_spp
- unzip_spp
......@@ -6,6 +6,10 @@ bwa_align_paired:
outputs:
- sam
arguments:
- "mem":
changeable: false
required: true
value: false
- "-M":
changeable: false
required: true
......
- SRR1.fastq.gz:
filetype: fastq
organism: human
genome: hg19
celltype: k562
transcription_factor: ctcf
control: false
- SRR2.fastq.gz:
filetype: fastq
organism: human
genome: hg19
celltype: k562
control: true
bwa_sai_to_sam:
arguments: none
arguments: None
walltime: 2000
memory: 2000
bwa_align_single:
......@@ -16,6 +16,6 @@ bwa_align_paired:
walltime: 2000
memory: 2000
samtools_sam_to_bam:
arguments: none
arguments: None
walltime: 2000
memory: 2000
- run1:
experiment: "expeirment name"
align: bwa
peak: spp
- run2:
experiment: "experiment name"
align: bowtie2
peak: spp
......@@ -229,6 +229,6 @@ class Workflow(object):
def write(self):
with open(self.basepath + "/input/encode.dax", "w") as wh:
with open(self.basepath + "/input/chipathlon.dax", "w") as wh:
self.dax.writeXML(wh)
return
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