Commit 7dd31d1c authored by aknecht2's avatar aknecht2
Browse files

Updated module & param code to handle argument params.

parent caba5015
......@@ -3,78 +3,131 @@ align:
- single[read_end]:
- bwa_align_single:
inputs:
- ref_genome
- download_1.fastq
- ref_genome:
type: file
- download_1.fastq:
type: file
additional_inputs:
- ref_genome.amb
- ref_genome.ann
- ref_genome.bwt
- ref_genome.pac
- ref_genome.sa
- ref_genome.amb:
type: file
- ref_genome.ann:
type: file
- ref_genome.bwt:
type: file
- ref_genome.pac:
type: file
- ref_genome.sa:
type: file
outputs:
- bwa.sai
- bwa.sai:
type: file
- bwa_sai_to_sam:
inputs:
- ref_genome
- bwa.sai
- download_1.fastq
- ref_genome:
type: file
- bwa.sai:
type: file
- download_1.fastq:
type: file
additional_inputs:
- ref_genome.amb
- ref_genome.ann
- ref_genome.bwt
- ref_genome.pac
- ref_genome.sa
- ref_genome.amb:
type: file
- ref_genome.ann:
type: file
- ref_genome.bwt:
type: file
- ref_genome.pac:
type: file
- ref_genome.sa:
type: file
outputs:
- align.sam
- align.sam:
type: file
paired[read_end]:
- bwa_align_paired:
inputs:
- ref_genome
- download_1.fastq
- download_2.fastq
- ref_genome:
type: file
- download_1.fastq:
type: file
- download_2.fastq:
type: file
additional_inputs:
- ref_genome.amb
- ref_genome.ann
- ref_genome.bwt
- ref_genome.pac
- ref_genome.sa
- ref_genome.amb:
type: file
- ref_genome.ann:
type: file
- ref_genome.bwt:
type: file
- ref_genome.pac:
type: file
- ref_genome.sa:
type: file
outputs:
- align.sam
- align.sam:
type: file
bowtie2[tool]:
- single[read_end]:
- bowtie2_align_single:
inputs:
- ref_genome
- download_1.fastq
- ref_genome_prefix:
type: argument
- download_1.fastq:
type: file
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
- ref_genome:
type: file
- ref_genome.1.bt2:
type: file
- ref_genome.2.bt2:
type: file
- ref_genome.3.bt2:
type: file
- ref_genome.4.bt2:
type: file
- ref_genome.rev.1.bt2:
type: file
- ref_genome.rev.2.bt2:
type: file
outputs:
- align.sam
- align.quality
- align.sam:
type: file
- align.quality:
type: file
paired[read_end]:
- bowtie2_align_paired:
inputs:
- ref_genome
- download_1.fastq
- download_2.fastq
- ref_genome_prefix:
type: argument
- download_1.fastq:
type: file
- download_2.fastq:
type: file
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
- ref_genome:
type: file
- ref_genome.1.bt2:
type: file
- ref_genome.2.bt2:
type: file
- ref_genome.3.bt2:
type: file
- ref_genome.4.bt2:
type: file
- ref_genome.rev.1.bt2:
type: file
- ref_genome.rev.2.bt2:
type: file
outputs:
- align.sam
- align.quality
- align.sam:
type: file
- align.quality:
type: file
- samtools_sam_to_bam:
inputs:
- align.sam
- align.sam:
type: file
additional_inputs: null
outputs:
- align.bam
- align.bam:
type: file
......@@ -2,32 +2,46 @@ peak_call:
- spp[tool]:
- r_spp_nodups:
inputs:
- exp.bam
- control.bam
- exp.bam:
type: file
- control.bam:
type: file
- dir:
type: argument
additional_inputs: null
outputs:
- dir(HMMMMM)
- results.narrowPeak
- results.pdf
- results.ccscore
- results.narrowPeak:
type: file
- results.pdf:
type: file
- results.ccscore:
type: file
- zcat_awk_sort_peaks:
inputs:
- results.narrowPeak
- results.narrowPeak:
type: file
additional_inputs: null
outputs:
- results_sorted.narrowPeak
- results_sorted.narrowPeak:
type: file
- macs2[tool]:
- macs2_callpeak:
inputs:
- exp.bam
- control.bam
- prefix(HMMM)
- exp.bam:
type: file
- control.bam:
type: file
- prefix:
type: argument
additional_inputs: null
outputs:
- results.narrowPeak
- results.narrowPeak:
type: file
- sort_awk_sort_peaks:
inputs:
- results.narrowPeak
- results.narrowPeak:
type: file
additional_inputs: null
outputs:
- results_sorted.narrowPeak
- results_sorted.narrowPeak:
type: file
remove_duplicates:
- samtools_filter_bam:
inputs:
- align.bam
- align.bam:
type: file
additional_inputs: null
outputs:
- filtered.bam
- filtered.bam:
type: file
- picard_sort_sam:
inputs:
- filtered.bam
- filtered.bam:
type: file
additional_input: null
outputs:
- sorted.bam
- sorted.bam:
type: file
- picard_mark_duplicates:
inputs:
- sorted.bam
- sorted.bam:
type: file
additional_inputs: null
outputs:
- no_dups.bam
- quality.qc
- no_dups.bam:
type: file
- quality.qc:
type: file
bedtools_bam_to_bed:
inputs:
- bam
- bam:
type: file
outputs:
- bed
- bed:
type: file
command: bedtools
arguments:
- "bamtobed":
......
bowtie2_align_paired:
inputs:
- genome_index
- fastq
- fastq
- genome_prefix:
type: argument
- fastq:
type: file
- fastq:
type: file
additional_inputs:
- bowtie2_genome
- bowtie2_genome
- bowtie2_genome
- bowtie2_genome
- bowtie2_genome
- bowtie2_genome
- genome_index:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
outputs:
- sam
- quality
- sam:
type: file
- quality:
type: file
command: bowtie2
arguments:
- "-x":
......
bowtie2_align_single:
inputs:
- genome_index
- fastq
- genome_prefix:
type: argument
- fastq:
type: file
additional_inputs:
- bowtie2_genome
- bowtie2_genome
- bowtie2_genome
- bowtie2_genome
- bowtie2_genome
- bowtie2_genome
- genome_index:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
- bowtie2_genome:
type: file
outputs:
- sam
- quality
- sam:
type: file
- quality:
type: file
command: bowtie2
arguments:
- "-x":
......
bwa_align_paired:
inputs:
- genome_index
- fastq
- fastq
- genome_index:
type: file
- fastq:
type: file
- fastq:
type: file
additional_inputs:
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
outputs:
- sam
command: bwa
......
bwa_align_single:
inputs:
- genome_index
- fastq
- genome_index:
type: file
- fastq:
type: file
additional_inputs:
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
outputs:
- sai
- sai:
type: file
command: bwa
arguments:
- aln:
......
bwa_sai_to_sam:
inputs:
- genome_index
- sai
- fastq
- genome_index:
type: file
- sai:
type: file
- fastq:
type: file
additional_inputs:
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
- bwa_genome:
type: file
outputs:
- sam
command: bwa
......
macs2_callpeak:
inputs:
- bam
- bam
- prefix
- bam:
type: file
- bam:
type: file
- prefix:
type: argument
outputs:
- bed
- bed:
type: file
command: macs2
arguments:
- callpeak:
......
picard_mark_duplicates:
inputs:
- bam
- bam:
type: file
additional_inputs: null
outputs:
- bam
- qc
- bam:
type: file
- qc:
type: file
command: picard
arguments:
- MarkDuplicates:
......@@ -39,6 +42,6 @@ picard_mark_duplicates:
changeable: false
required: false
has_value: true
default: false
default: true
walltime: 2000
memory: 8000
picard_sort_sam:
inputs:
- bam
- bam:
type: file
outputs:
- bam
- bam:
type: file
command: picard
arguments:
- SortSam:
......
r_spp_nodups:
inputs:
- bam
- bam
- bam:
type: file
- bam:
type: file
- dir:
type: argument
outputs:
- dir
- bed
- pdf
- ccscore
- bed:
type: file
- pdf:
type: file
- ccscore:
type: file
command: r
arguments:
- "-c":
......@@ -28,7 +34,7 @@ r_spp_nodups:
changeable: false
required: true
has_value: true
default: $outputs.0
default: $inputs.2
- "-speak":
changeable: true
required: false
......
samtools_filter_bam:
inputs:
- bam
- bam:
type: file
outputs:
- bam
- bam:
type: file
command: samtools
arguments:
- view:
......
samtools_remove_duplicates:
inputs:
- bam
- bam:
type: file
outputs:
- bam
- bam:
type: file
command: samtools
arguments:
- view:
......
samtools_sam_to_bam:
inputs:
- sam
- sam:
type: file
additional_inputs: null
outputs:
- bam
- bam:
type: file
command: samtools
arguments:
- view:
......
sort_awk_sort_peaks:
inputs:
- bed
- bed:
type: file
outputs:
- bed
- bed:
type: file
command: sort
arguments:
- "$inputs.0":
......