Commit 3eb1cb64 authored by aknecht2's avatar aknecht2
Browse files

Updated all yaml files to support type argument. Heavily updated workflow_job...

Updated all yaml files to support type argument.  Heavily updated workflow_job parsing and verbosity.
parent a37d5184
peak_call:
- gem[tool]:
- gem_callpeak:
inputs:
- chrom.sizes:
type: file
- exp.bed:
type: file
- control.bed:
type: file
- genome_dir:
type: file
- prefix:
type: file
additional_inputs: null
outputs: gem.narrowPeak
- spp[tool]:
- cp_bed_tagalign:
inputs:
......
......@@ -33,7 +33,7 @@ remove_duplicates:
outputs:
- no_dups.bed:
type: stdout
- chr_locus_convert.yaml:
- chr_locus_convert:
inputs:
- no_dups.bed:
type: file
......
......@@ -9,10 +9,12 @@ bedtools_bam_to_bed:
command: bedtools
arguments:
- "bamtobed":
type: string
changeable: false
required: true
has_value: false
- "-i":
type: file
changeable: false
required: true
has_value: true
......
bowtie2_align_paired:
inputs:
- genome_prefix:
type: argument
type: string
- fastq:
type: file
- fastq:
......@@ -29,26 +29,31 @@ bowtie2_align_paired:
command: bowtie2
arguments:
- "-x":
type: string
changeable: false
required: true
has_value: true
default: $inputs.0
- "-1":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
- "-2":
type: file
changeable: false
required: true
has_value: true
default: $inputs.2
- "-S":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
- "-p":
type: numeric
changeable: true
required: false
has_value: true
......
bowtie2_align_single:
inputs:
- genome_prefix:
type: argument
type: string
- fastq:
type: file
additional_inputs:
......@@ -27,21 +27,25 @@ bowtie2_align_single:
command: bowtie2
arguments:
- "-x":
type: string
changeable: false
required: true
has_value: true
default: $inputs.0
- "-U":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
- "-S":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
- "-p":
type: numeric
changeable: true
required: false
has_value: true
......
......@@ -23,27 +23,33 @@ bwa_align_paired:
command: bwa
arguments:
- "mem":
type: string
changeable: false
required: true
has_value: false
- "-M":
type: string
changeable: false
required: true
has_value: false
- "-t":
type: numeric
changeable: true
required: false
has_value: true
default: 8
- "$inputs.0":
type: file
changeable: false
required: true
has_value: false
- "$inputs.1":
type: file
changeable: false
required: true
has_value: false
- "$inputs.2":
type: file
changeable: false
required: true
has_value: false
......
......@@ -21,39 +21,47 @@ bwa_align_single:
command: bwa
arguments:
- aln:
type: string
changeable: false
required: true
has_value: false
- "-q":
type: numeric
changeable: true
required: false
has_value: true
default: 5
- "-l":
type: numeric
changeable: true
required: false
has_value: true
default: 32
- "-k":
type: numeric
changeable: true
required: false
has_value: true
default: 2
- "-t":
type: numeric
changeable: true
required: false
has_value: true
default: 8
- "-f":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
- "$inputs.0":
type: file
changeable: false
required: true
has_value: false
- "$inputs.1":
type: file
changeable: false
required: true
has_value: false
......
......@@ -23,23 +23,28 @@ bwa_sai_to_sam:
command: bwa
arguments:
- samse:
type: string
changeable: false
required: true
has_value: false
- "-f":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
- "$inputs.0":
type: file
changeable: false
required: true
has_value: false
- "$inputs.1":
type: file
changeable: false
required: true
has_value: false
- "$inputs.2":
type: file
changeable: false
required: true
has_value: false
......
......@@ -9,10 +9,12 @@ cat_awk_sort_peaks:
command: cat_spp.sh
arguments:
- "$inputs.0":
type: file
changeable: false
required: true
has_value: false
- "$outputs.0":
type: file
changeable: false
required: true
has_value: false
......
db_save_result:
chr_locus_convert:
inputs:
- bed:
type: file
......@@ -6,14 +6,16 @@ db_save_result:
outputs:
- bed:
type: file
command: db_save_result.py
command: chr_locus_convert.py
arguments:
- "-b":
type: file
changeable: false
required: true
has_value: true
default: $inputs.0
- "-o":
type: file
changeable: false
required: true
has_value: true
......
......@@ -9,10 +9,12 @@ cp_bed_tagalign:
command: cp
arguments:
- "$inputs.0":
type: file
changeable: false
required: true
has_value: false
- "$outputs.0":
type: file
changeable: false
required: true
has_value: false
......
......@@ -15,26 +15,31 @@ db_save_result:
command: db_save_result.py
arguments:
- "-u":
type: string
changeable: false
required: true
has_value: true
default: $inputs.0
- "-p":
type: string
changeable: false
required: true
has_value: true
default: $inputs.1
- "-d":
type: string
changeable: false
required: true
has_value: true
default: $inputs.2
- "-f":
type: file
changeable: false
required: true
has_value: true
default: $inputs.3
- "-m":
type: file
changeable: false
required: true
has_value: true
......
gem_callpeak:
inputs:
- txt:
type: rawfile
- chrom_sizes:
type: file
- bed:
......@@ -19,11 +17,10 @@ gem_callpeak:
command: gem
arguments:
- "--d":
type: file
type: rawfile
changeable: true
required: true
has_value: true
default: $inputs.0
- "--g":
type: file
changeable: false
......@@ -41,7 +38,7 @@ gem_callpeak:
changeable: false
required: true
has_value: true
defualt: $inputs.3
default: $inputs.3
- "--genome":
type: file
changeable: false
......@@ -79,9 +76,9 @@ gem_callpeak:
has_value: true
default: 2
- "--outNP":
type: boolean
type: string
changeable: false
required: false
required: true
has_value: false
walltime: 720
memory: 16000
......
......@@ -17,60 +17,72 @@ macs2_callpeak:
command: macs2
arguments:
- callpeak:
type: string
changeable: false
required: true
has_value: false
- "-t":
type: file
changeable: false
required: true
has_value: true
default: $inputs.0
- "-c":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
- "-f":
type: string
changeable: false
required: true
has_value: true
default: "BED"
- "-n":
type: string
changeable: false
required: true
has_value: true
default: $inputs.2
- "-g":
type: string
changeable: true
required: false
has_value: true
default: "hs"
- "-p":
type: numeric
changeable: true
required: false
has_value: true
default: 0.01
- "--nomodel":
changeable: true
required: false
type: string
changeable: false
required: true
has_value: false
- "--shift":
type: numeric
changeable: true
required: false
has_value: true
default: 0
- "--extsize":
type: numeric
changeable: true
required: false
has_value: true
default: 110
- "-B":
changeable: true
required: false
type: string
changeable: false
required: true
has_value: false
- "--SPMR":
changeable: true
required: false
type: string
changeable: false
required: true
has_value: false
walltime: 2000
memory: 8000
......
......@@ -11,37 +11,44 @@ picard_mark_duplicates:
command: picard
arguments:
- MarkDuplicates:
type: string
changeable: false
required: true
has_value: false
- "INPUT=":
type: file
changeable: false
required: true
has_value: true
default: $inputs.0
- "OUTPUT=":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
- "METRICS_FILE=":
type: file
changeable: false
required: true
has_value: true
default: $outputs.1
- "VALIDATION_STRINGENCY=":
type: string
changeable: true
required: false
has_value: true
default: "LENIENT"
- "ASSUME_SORTED=":
type: string
changeable: true
required: false
has_value: true
default: true
- "REMOVE_DUPLICATES=":
type: string
changeable: false
required: false
required: true
has_value: true
default: true
walltime: 2000
......
......@@ -9,20 +9,24 @@ picard_sort_sam:
command: picard
arguments:
- SortSam:
type: string
changeable: false
required: true
has_value: false
- "INPUT=":
type: file
changeable: false
required: true
has_value: true
default: $inputs.0
- "OUTPUT=":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
- "SORT_ORDER=":
type: string
changeable: true
required: true
has_value: true
......
......@@ -15,56 +15,67 @@ r_spp_nodups:
command: r
arguments:
- "-c=":
type: file
changeable: false
required: true
has_value: true
default: $inputs.0
- "-i=":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
- "-npeak=":
type: numeric
changeable: true
required: false
has_value: true
default: 300000
- "-odir=":
type: string
changeable: false
required: true
has_value: true
default: .
- "-speak=":
type: numeric
changeable: true
required: false
has_value: true
default: 110
- "-savn=":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
- "-savp=":
type: file
changeable: false
required: true
has_value: true
default: $outputs.1
- "-out=":
type: file
changeable: false
required: true
has_value: true
default: $outputs.2
- "-fdr=":
type: numeric
changeable: true
required: false
has_value: true
default: 0.01
- "-p=":
type: numeric
changeable: true
required: false
has_value: true
default: 8
- "-rf":
type: string
changeable: false
required: true
has_value: false
......
......@@ -9,29 +9,35 @@ samtools_filter_bam:
command: samtools
arguments:
- view:
type: string
changeable: false
required: true
has_value: false
- "-F":
type: numeric
changeable: true
required: false
default: 1804
has_value: true
- "-q":
type: numeric
changeable: true
required: false
has_value: true
default: 30
- "-b":
type: string
changeable: false
required: true
has_value: false
- "-o":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
- "$inputs.0":
type: file
changeable: false
required: true
has_value: false
......
......@@ -9,24 +9,29 @@ samtools_remove_duplicates: