Commit 6d73d6b3 authored by aknecht2's avatar aknecht2
Browse files

Updated yaml files. Added bowtie2 yaml files.

parent d2b21636
......@@ -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
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
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
......@@ -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
......
......@@ -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
......
- 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"
class WorkflowModule(Workflow):
def __init__(self):
return
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