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preprocess-ont.cwl
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preprocess-ont.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
ScatterFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
MultipleInputFeatureRequirement: {}
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}
inputs:
illumina_accession: string
ref_human_genome: File
steps:
fetch_fastqs:
in:
sra_accession: illumina_accession
out:
- fastq_file_1
- fastq_files
run: ../bio-cwl-tools/sratoolkit/prefetch_fastq.cwl
nanoplot:
in:
fastq_files:
source: fetch_fastqs/fastq_files
loglength:
valueFrom: $(true)
format:
valueFrom: "png"
out:
- dynamic_histogram_read_length
- histogram_read_length
- length_v_qual_scatter_plot_dot
- length_v_qual_scatter_plot_kde
- log_transformed_histogram_read_length
- report
- logfile
- nanostats
- weighted_histogram_read_length
- weighted_log_transform_histogram_read_length
- yield_by_length_img
run: ../bio-cwl-tools/nanoplot/nanoplot.cwl
fastqc:
in:
reads_file: fetch_fastqs/fastq_file_1
nogroup:
valueFrom: $(true)
kmers:
valueFrom: $(7)
out:
- zipped_file
- summary_file
- html_file
run: ../bio-cwl-tools/fastqc/fastqc_2.cwl
multiqc:
in:
qc_files_array: fastqc/zipped_file
out:
- multiqc_zip
- multiqc_html
run: ../bio-cwl-tools/multiqc/multiqc.cwl
minimap2:
in:
indexFile: ref_human_genome
fastqFiles: fetch_fastqs/fastq_file_1
samOutput:
valueFrom: $(true)
out:
- samfile
run: ../bio-cwl-tools/minimap2/minimap2.cwl
sam2bam:
in:
sam: minimap2/samfile
out:
- bam
run: ../bio-cwl-tools/samtools/samtools_view_sam2bam.cwl
samtools_fastq:
in:
bam_sorted: sam2bam/bam
out:
- fastq
run: ../bio-cwl-tools/samtools/samtools_fastq.cwl
rename_multiqc_html:
in:
srcfile: multiqc/multiqc_html
newname:
source: illumina_accession
valueFrom: $(self)_multiqc.html
out:
- outfile
run: ../bio-cwl-tools/util/rename.cwl
rename_multiqc_zip:
in:
srcfile: multiqc/multiqc_zip
newname:
source: illumina_accession
valueFrom: $(self)_multiqc.zip
out:
- outfile
run: ../bio-cwl-tools/util/rename.cwl
rename_fastqc_summary:
in:
srcfile: fastqc/summary_file
newname:
source: illumina_accession
valueFrom: $(self)_fastqc.html
out:
- outfile
run: ../bio-cwl-tools/util/rename.cwl
rename_fastqc_zip:
in:
srcfile: fastqc/zipped_file
newname:
source: illumina_accession
valueFrom: $(self)_fastqc.zip
out:
- outfile
run: ../bio-cwl-tools/util/rename.cwl
rename_fastq:
in:
srcfile: samtools_fastq/fastq
newname:
source: illumina_accession
valueFrom: $(self).fastq
out:
- outfile
run: ../bio-cwl-tools/util/rename.cwl
rename_bam:
in:
srcfile: sam2bam/bam
newname:
source: illumina_accession
valueFrom: $(self).bam
out:
- outfile
run: ../bio-cwl-tools/util/rename.cwl
outputs:
original_fastq1:
type: File
outputSource: rename_fastq/outfile
fastqc_summary:
type: File
outputSource: rename_fastqc_summary/outfile
fastqc_zip:
type: File
outputSource: rename_fastqc_zip/outfile
multiqc_html:
type: File
outputSource: rename_multiqc_html/outfile
multiqc_zip:
type: File
outputSource: rename_multiqc_zip/outfile
bam:
type: File
outputSource: rename_bam/outfile