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Holland Computing Center
chipathlon
Commits
6d73d6b3
Commit
6d73d6b3
authored
Mar 03, 2016
by
aknecht2
Browse files
Updated yaml files. Added bowtie2 yaml files.
parent
d2b21636
Changes
7
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Inline
Side-by-side
chipathlon/jobs/modules/align.yaml
View file @
6d73d6b3
...
...
@@ -24,7 +24,7 @@ align:
paired
:
-
bwa_align_paired
:
inputs
:
-
ref_genome
.fa
-
ref_genome
-
download_1.fastq
-
download_2.fastq
additional_inputs
:
...
...
@@ -43,7 +43,37 @@ align:
-
align.bam
bowtie2
:
-
single
:
-
bowtie2_align_single
-
bowtie2_align_single
:
inputs
:
-
ref_genome
-
download_1.fastq
additional_inputs
:
-
ref_genome.1.bt2
-
ref_genome.2.bt2
-
ref_genome.3.bt2
-
ref_genome.4.bt2
-
ref_genome.rev.1.bt2
-
ref_genome.rev.2.bt2
outputs
:
-
align.sam
paired
:
-
bowtie2_align_paired
-
samtools_sam_to_bam
-
bowtie2_align_paired
:
inputs
:
-
ref_genome
-
download_1.fastq
-
download_2.fastq
additional_inputs
:
-
ref_genome.1.bt2
-
ref_genome.2.bt2
-
ref_genome.3.bt2
-
ref_genome.4.bt2
-
ref_genome.rev.1.bt2
-
ref_genome.rev.2.bt2
outputs
:
-
align.sam
-
samtools_sam_to_bam
:
inputs
:
-
align.sam
additional_inputs
:
null
outputs
:
-
align.bam
chipathlon/jobs/params/bowtie2_align_paired.yaml
0 → 100644
View file @
6d73d6b3
bwa_align_paired
:
inputs
:
-
-
fna
-
fa
-
fastq
-
fastq
additional_inputs
:
-
.1.bt2
-
.2.bt2
-
.3.bt2
-
.4.bt2
-
.rev.1.bt2
-
.rev.2.bt2
outputs
:
-
sam
command
:
bowtie2
arguments
:
-
"
-x"
:
changeable
:
false
required
:
true
value
:
$inputs.0
-
"
-1"
:
changeable
:
false
required
:
true
value
:
$inputs.1
-
"
-2"
:
changeable
:
false
required
:
true
value
:
$inputs.2
-
"
-S"
:
changeable
:
false
required
:
true
value
:
$outputs.0
walltime
:
2000
memory
:
2000
chipathlon/jobs/params/bowtie2_align_single.yaml
0 → 100644
View file @
6d73d6b3
bwa_align_single
:
inputs
:
-
-
fna
-
fa
-
fastq
additional_inputs
:
-
.1.bt2
-
.2.bt2
-
.3.bt2
-
.4.bt2
-
.rev.1.bt2
-
.rev.2.bt2
outputs
:
-
sam
command
:
bowtie2
arguments
:
-
"
-x"
:
changeable
:
false
required
:
true
value
:
$inputs.0
-
"
-U"
:
changeable
:
false
required
:
true
value
:
$inputs.1
-
"
-S"
:
changeable
:
false
required
:
true
value
:
$outputs.0
walltime
:
2000
memory
:
2000
chipathlon/jobs/params/bwa_align_paired.yaml
View file @
6d73d6b3
...
...
@@ -6,11 +6,11 @@ bwa_align_paired:
-
fastq
-
fastq
additional_inputs
:
-
fa
.amb
-
fa
.ann
-
fa
.bwt
-
fa
.pac
-
fa
.sa
-
.amb
-
.ann
-
.bwt
-
.pac
-
.sa
outputs
:
-
sam
command
:
bwa
...
...
chipathlon/jobs/params/bwa_align_single.yaml
View file @
6d73d6b3
...
...
@@ -5,11 +5,11 @@ bwa_align_single:
-
fa
-
fastq
additional_inputs
:
-
fa
.amb
-
fa
.ann
-
fa
.bwt
-
fa
.pac
-
fa
.sa
-
.amb
-
.ann
-
.bwt
-
.pac
-
.sa
outputs
:
-
sai
command
:
bwa
...
...
chipathlon/test/run/run.yaml
View file @
6d73d6b3
-
experiment
:
"
ENCSR000BSE"
align
:
bwa
peak
:
spp
-
experiment
:
"
ENCSR000BSE"
align
:
bowtie2
peak
:
spp
runs
:
-
experiment
:
"
ENCSR000BSE"
align
:
bwa
peak
:
spp
-
experiment
:
"
ENCSR000BSE"
align
:
bowtie2
peak
:
spp
genomes
:
bwa
:
hg19
:
"
/path/to/genome/base"
mm9
:
"
/path/to/genome/base"
bowtie2
:
hg19
:
"
/path/to/genome/base"
mm9
:
"
/path/to/genome/base"
chipathlon/workflow_module.py
0 → 100644
View file @
6d73d6b3
class
WorkflowModule
(
Workflow
):
def
__init__
(
self
):
return
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