Commit 9f63e3db authored by LETORT Sebastien's avatar LETORT Sebastien

Test for a new format cwl.

parent 6c62a480
cwlVersion: v1.0
class: CommandLineTool
label: gatb-pipeline uses gatb tools to generate an assembly from short reads.
doc: |
gatb-pipeline uses gatb tools to generate an assembly from short reads.
It uses bloocoo, minia, and a non gatb-tool named BESST.
baseCommand: gatb
requirements:
SoftwareRequirement:
packages:
- package: python
- package: python-scipy
- package: pysam
version: 0.8.3
- package: mathstats
- package: bwa
- package: make
inputs:
#inputs:
single_reads_infile:
label: single reads
type: File?
format:
- http://edamontology.org/format_2182 # fastq-like (text)
- http://edamontology.org/format_2546 # fasta-like
inputBinding:
prefix: -s
single_reads_fof:
label: list of single reads, one file name per line
type: File?
format: http://edamontology.org/format_2330 # textual
inputBinding:
prefix: -l
interleaved_reads_infile:
label : interleaved paired reads,
type: File?
format:
- http://edamontology.org/format_2182 # fastq-like (text)
- http://edamontology.org/format_2546 # fasta-like
inputBinding:
prefix: --12
interleaved_mate_reads_infile:
label: interleaved mate paired reads
type: File?
format:
- http://edamontology.org/format_2182 # fastq-like (text)
- http://edamontology.org/format_2546 # fasta-like
inputBinding:
prefix: --mp-12
non_interleaved_paired_read:
label: non-interleaved paired reads
type: record
fields:
forward_reads_infile:
name: forward_reads_infile
label: non-interleaved paired reads (forward)
type: File?
format:
- http://edamontology.org/format_2182 # fastq-like (text)
- http://edamontology.org/format_2546 # fasta-like
inputBinding:
prefix: -1
reverse_reads_infile:
label: non-interleaved paired reads (reverse)
type: File?
format:
- http://edamontology.org/format_2182 # fastq-like (text)
- http://edamontology.org/format_2546 # fasta-like
inputBinding:
prefix: -2
non_interleaved_mate_paired_reads:
label: non-interleaved mate paired reads
type : record
fields:
forward_mate_reads_infile:
name: forward_mate_reads_infile
label: non-interleaved mate paired reads (forward mates)
type: File?
format:
- http://edamontology.org/format_2182 # fastq-like (text)
- http://edamontology.org/format_2546 # fasta-like
inputBinding:
prefix: --mp-1
reverse_mate_reads_infile:
name: reverse_mate_reads_infile
label: non-interleaved mate paired reads (reverse mates)
type: File?
format:
- http://edamontology.org/format_2182 # fastq-like (text)
- http://edamontology.org/format_2546 # fasta-like
inputBinding:
prefix: --mp-2
#paramaters:
out_prefix:
label: prefix of the output files.
default: assembly
type: string
inputBinding:
prefix: -o
step:
label: step size to control increments of k values.
default: 20
type: int
inputBinding:
prefix: --step
kmer-sizes:
label: comma-separated list of k-mer sizes.
doc: "default: 21, 21+step, 21+2*step, ..."
type: string
inputBinding:
prefix: --kmer-sizes
abundance-mins:
label: list of low abundance thresholds.
doc: "default: 2,2,2, ..."
type: string
inputBinding:
prefix: --abundance-mins
max-memory:
label: go faster by using more memory (in MB).
type: int
inputBinding:
prefix: --max-memory
restart-from:
label: value where to restart the multi-k process (useful for interrupted jobs)
type: int
inputBinding:
prefix: --restart-from
no-error-correction:
label: skips error correction.
type: null
inputBinding:
prefix: --no-error-correction
contig_filename:
label: filename of contigs, will only perform scaffolding+gapfilling.
type: string
inputBinding:
prefix: -c
continue-scaffolding:
label: continue an interrupted scaffolding.
doc:
- already mapped libraries are not remapped;
- should be used along with -c <assembly_kXXX.fa>
type: null
inputBinding:
prefix: --continue-scaffolding
besst_iter:
label: number of iteration during Besst scaffolding.
default: 10000
type: int
inputBinding:
prefix: --besst_iter
outputs:
corrected_reads:
label: all reads are corrected with Bloocoo program.
type: File
outputBinding:
glob: $(out_prefix +'.corrected_with_bloocoo_*')
corrected_reads_h5_file:
label: corrected reads are used to generate a kmer graph.
type: File
outputBinding:
glob: $(out_prefix +'.corrected_with_bloocoo.fa.h5')
contig_fasta_files:
label: a contig fasta file is produce after each step.
type: File
outputBinding:
glob: $(out_prefix +'_k*.contigs.fa')
contig_h5_files:
label: a contig kmer graph file is produce after each step.
type: File
outputBinding:
glob: $(out_prefix +'_k*.h5')
reads_alignment:
label: all reads are mapped onto the last contig assembly with bwa.
type: File
outputBinding:
glob: $(out_prefix +'.lib_0.bam*')
assembly_file:
label: final assembly, containing scaffolds and nodes.
type: File
outputBinding:
glob: $(out_prefix +'.fasta')
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