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Commit 999824e6 authored by aknecht2's avatar aknecht2
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Updated all alignment job yaml files to conform to new standard.

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with 77 additions and 116 deletions
chipathlon/jobs/params/bowtie2_align_paired.yaml
+ 21
− 31
View file @ 999824e6
bowtie2_align_paired:
inputs:
- name: genome_prefix
genome_prefix:
type: string
- name: fastq1
fastq1:
type: file
file_type: fastq
- name: fastq2
fastq2:
type: file
file_type: fastq
additional_inputs:
- name: base_genome_file
base_genome_file:
type: file
file_type: genome_index
- name: genome.1.bt2
genome.1.bt2:
type: file
file_type: bowtie2_genome
- name: genome.2.bt2
file_type: bwa_genome
genome.2.bt2:
type: file
file_type: bowtie2_genome
- name: genome.3.bt2
file_type: bwa_genome
genome.3.bt2:
type: file
file_type: bowtie2_genome
- name: genome.4.bt2
file_type: bwa_genome
genome.4.bt2:
type: file
file_type: bowtie2_genome
- name: genome.rev.1.bt2
file_type: bwa_genome
genome.rev.1.bt2:
type: file
file_type: bowtie2_genome
- name: genome.rev.2.bt2
file_type: bwa_genome
genome.rev.2.bt2:
type: file
file_type: bowtie2_genome
outputs:
- name: output_sam
output_sam:
type: file
file_type: sam
- name: fastq_quality
fastq_quality:
type: stderr
file_type: quality
command: bowtie2
......@@ -53,25 +43,25 @@ bowtie2_align_paired:
changeable: false
required: true
has_value: true
default: $inputs.0
default: $genome_prefix
- "-1":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
default: $fastq1
- "-2":
type: file
changeable: false
required: true
has_value: true
default: $inputs.2
default: $fastq2
- "-S":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
default: $output_sam
- "-p":
type: numeric
changeable: true
......
chipathlon/jobs/params/bowtie2_align_single.yaml
+ 19
− 28
View file @ 999824e6
bowtie2_align_single:
inputs:
- name: genome_prefix
genome_prefix:
type: string
- name: fastq1
fastq1:
type: file
file_type: fastq
additional_inputs:
- name: base_genome_file
base_genome_file:
type: file
file_type: genome_index
- name: genome.1.bt2
genome.1.bt2:
type: file
file_type: bowtie2_genome
- name: genome.2.bt2
file_type: bwa_genome
genome.2.bt2:
type: file
file_type: bowtie2_genome
- name: genome.3.bt2
file_type: bwa_genome
genome.3.bt2:
type: file
file_type: bowtie2_genome
- name: genome.4.bt2
file_type: bwa_genome
genome.4.bt2:
type: file
file_type: bowtie2_genome
- name: genome.rev.1.bt2
file_type: bwa_genome
genome.rev.1.bt2:
type: file
file_type: bowtie2_genome
- name: genome.rev.2.bt2
file_type: bwa_genome
genome.rev.2.bt2:
type: file
file_type: bowtie2_genome
outputs:
- name: output_sam
output_sam:
type: file
file_type: sam
- name: fastq_quality
fastq_quality:
type: stderr
file_type: quality
command: bowtie2
......@@ -49,19 +40,19 @@ bowtie2_align_single:
changeable: false
required: true
has_value: true
default: $inputs.0
default: $genome_prefix
- "-U":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
default: $fastq1
- "-S":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
default: $output_sam
- "-p":
type: numeric
changeable: true
......
chipathlon/jobs/params/bwa_align_paired.yaml
+ 13
− 20
View file @ 999824e6
bwa_align_paired:
inputs:
- name: base_genome_file
base_genome_file:
type: file
file_type: genome_index
- name: fastq1
fastq1:
type: file
file_type: fastq
- name: fastq2
fastq2:
type: file
file_type: fastq
additional_inputs:
- name: genome.fna.amb
genome.fna.amb:
type: file
file_type: bwa_genome
- name: genome.fna.ann
genome.fna.ann:
type: file
file_type: bwa_genome
- name: genome.fna.bwt
genome.fna.bwt:
type: file
file_type: bwa_genome
- name: genome.fna.pac
genome.fna.pac:
type: file
file_type: bwa_genome
- name: genome.fna.sa
genome.fna.sa:
type: file
file_type: bwa_genome
outputs:
- name: output_sam
type: file
output_sam:
type: stdout
file_type: sam
command: bwa
arguments:
......@@ -53,17 +46,17 @@ bwa_align_paired:
required: false
has_value: true
default: 8
- "$inputs.0":
- "$base_genome_file":
type: file
changeable: false
required: true
has_value: false
- "$inputs.1":
- "$fastq1":
type: file
changeable: false
required: true
has_value: false
- "$inputs.2":
- "$fastq2":
type: file
changeable: false
required: true
......
chipathlon/jobs/params/bwa_align_single.yaml
+ 11
− 17
View file @ 999824e6
bwa_align_single:
inputs:
- name: base_genome_file
base_genome_file:
type: file
file_type: genome_index
- name: fastq1
fastq1:
type: file
file_type: fastq
additional_inputs:
- name: genome.fna.amb
genome.fna.amb:
type: file
file_type: bwa_genome
- name: genome.fna.ann
genome.fna.ann:
type: file
file_type: bwa_genome
- name: genome.fna.bwt
genome.fna.bwt:
type: file
file_type: bwa_genome
- name: genome.fna.pac
genome.fna.pac:
type: file
file_type: bwa_genome
- name: genome.fna.sa
genome.fna.sa:
type: file
file_type: bwa_genome
outputs:
- name: output_sai
output_sai:
type: file
file_type: sai
command: bwa
......@@ -67,13 +61,13 @@ bwa_align_single:
changeable: false
required: true
has_value: true
default: $outputs.0
- "$inputs.0":
default: $output_sai
- "$base_genome_file":
type: file
changeable: false
required: true
has_value: false
- "$inputs.1":
- "$fastq1":
type: file
changeable: false
required: true
......
chipathlon/jobs/params/bwa_sai_to_sam.yaml
+ 9
− 15
View file @ 999824e6
bwa_sai_to_sam:
inputs:
- name: base_genome_file
base_genome_file:
type: file
file_type: genome_index
- name: input_sai
input_sai:
type: file
file_type: sai
- name: base_fastq
base_fastq:
type: file
file_type: fastq
additional_inputs:
- name: genome.fna.amb
genome.fna.amb:
type: file
file_type: bwa_genome
- name: genome.fna.ann
genome.fna.ann:
type: file
file_type: bwa_genome
- name: genome.fna.bwt
genome.fna.bwt:
type: file
file_type: bwa_genome
- name: genome.fna.pac
genome.fna.pac:
type: file
file_type: bwa_genome
- name: genome.fna.sa
genome.fna.sa:
type: file
file_type: bwa_genome
outputs:
- name: output_sam
output_sam:
type: file
file_type: sam
command: bwa
......
chipathlon/jobs/params/samtools_sam_to_bam.yaml
+ 4
− 5
View file @ 999824e6
samtools_sam_to_bam:
inputs:
- name: align_sam
align_sam:
type: file
file_type: sam
additional_inputs: null
outputs:
- name: align_bam
align_bam:
type: file
file_type: bam
command: samtools
......@@ -25,8 +24,8 @@ samtools_sam_to_bam:
changeable: false
required: true
has_value: true
default: $outputs.0
- "$inputs.0":
default: $align_bam
- "$align_sam":
type: file
changeable: false
required: true
......
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