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.

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.
3eb1cb64 · aknecht2 · a37d5184 · 3eb1cb64 · 3eb1cb64 · 3eb1cb64
Commit 3eb1cb64 authored Apr 18, 2016 by aknecht2
--- a/chipathlon/jobs/modules/peak_call.yaml
+++ b/chipathlon/jobs/modules/peak_call.yaml
 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:

--- a/chipathlon/jobs/modules/remove_duplicates.yaml
+++ b/chipathlon/jobs/modules/remove_duplicates.yaml
@@ -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

--- a/chipathlon/jobs/params/bedtools_bam_to_bed.yaml
+++ b/chipathlon/jobs/params/bedtools_bam_to_bed.yaml
@@ -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

--- a/chipathlon/jobs/params/bowtie2_align_paired.yaml
+++ b/chipathlon/jobs/params/bowtie2_align_paired.yaml
 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

--- a/chipathlon/jobs/params/bowtie2_align_single.yaml
+++ b/chipathlon/jobs/params/bowtie2_align_single.yaml
 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

--- a/chipathlon/jobs/params/bwa_align_paired.yaml
+++ b/chipathlon/jobs/params/bwa_align_paired.yaml
@@ -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

--- a/chipathlon/jobs/params/bwa_align_single.yaml
+++ b/chipathlon/jobs/params/bwa_align_single.yaml
@@ -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

--- a/chipathlon/jobs/params/bwa_sai_to_sam.yaml
+++ b/chipathlon/jobs/params/bwa_sai_to_sam.yaml
@@ -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

--- a/chipathlon/jobs/params/cat_awk_sort_peaks.yaml
+++ b/chipathlon/jobs/params/cat_awk_sort_peaks.yaml
@@ -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

--- a/chipathlon/jobs/params/chr_locus_convert.yaml
+++ b/chipathlon/jobs/params/chr_locus_convert.yaml
-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

--- a/chipathlon/jobs/params/cp_bed_tagalign.yaml
+++ b/chipathlon/jobs/params/cp_bed_tagalign.yaml
@@ -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

--- a/chipathlon/jobs/params/db_save_result.yaml
+++ b/chipathlon/jobs/params/db_save_result.yaml
@@ -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

--- a/chipathlon/jobs/params/gem_callpeak.yaml
+++ b/chipathlon/jobs/params/gem_callpeak.yaml
 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

--- a/chipathlon/jobs/params/macs2_callpeak.yaml
+++ b/chipathlon/jobs/params/macs2_callpeak.yaml
@@ -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

--- a/chipathlon/jobs/params/picard_mark_duplicates.yaml
+++ b/chipathlon/jobs/params/picard_mark_duplicates.yaml
@@ -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

--- a/chipathlon/jobs/params/picard_sort_sam.yaml
+++ b/chipathlon/jobs/params/picard_sort_sam.yaml
@@ -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

--- a/chipathlon/jobs/params/r_spp_nodups.yaml
+++ b/chipathlon/jobs/params/r_spp_nodups.yaml
@@ -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

--- a/chipathlon/jobs/params/samtools_filter_bam.yaml
+++ b/chipathlon/jobs/params/samtools_filter_bam.yaml
@@ -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

--- a/chipathlon/jobs/params/samtools_remove_duplicates.yaml
+++ b/chipathlon/jobs/params/samtools_remove_duplicates.yaml
@@ -9,24 +9,29 @@ samtools_remove_duplicates: