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xenbase-rnaseq-pe.cwl
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xenbase-rnaseq-pe.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
expressionLib:
- var default_output_name = function(named_input, ext, segment) {
ext = ext || "";
segment = segment || 1;
if (Array.isArray(named_input) && named_input.length > 0){
return named_input[0].location.split('/').slice(-1)[0].split('.').slice(0,segment).join('.')+ext;
} else {
return named_input.location.split('/').slice(-1)[0].split('.').slice(0,segment).join('.')+ext;
}
};
inputs:
fastq_file_upstream:
type: File
label: "FASTQ upstream input file"
format: "http://edamontology.org/format_1930"
doc: "Upstream reads data in a FASTQ format, received after paired end sequencing"
fastq_file_downstream:
type: File
label: "FASTQ downstream input file"
format: "http://edamontology.org/format_1930"
doc: "Downstream reads data in a FASTQ format, received after paired end sequencing"
fasta_file_adapters:
type: File
label: "Adapters FASTA file"
format: "http://edamontology.org/format_1929"
doc: "Adapters FASTA file to be used by Trimmomatic"
rsem_indices_folder:
type: Directory
label: "RSEM indices folder"
doc: "Path to RSEM indices generated with BowTie2"
bowtie_indices_folder:
type: Directory
label: "BowTie Ribosomal Indices"
doc: "Path to Bowtie generated indices for ribosomal FASTA"
threads:
type: int?
default: 2
label: "Number of threads"
doc: "Number of threads for those steps that support multithreading"
outputs:
rsem_isoforms_file:
type: File
format: "http://edamontology.org/format_3475"
label: "RSEM isoforms expression file"
doc: "RSEM isoforms expression file"
outputSource: rename_rsem_isoforms_file/target_file
biowardrobe_isoforms_file:
type: File
format: "http://edamontology.org/format_3752"
label: "Biowardrobe compatible isoforms expression file"
doc: "Biowardrobe compatible isoforms expression file"
outputSource: make_biowardrobe_isoforms/biowardrobe_isoforms_file
rsem_genes_file:
type: File
format: "http://edamontology.org/format_3475"
label: "RSEM genes expression file"
doc: "RSEM genes expression file"
outputSource: rename_rsem_genes_file/target_file
bambai_pair:
type: File
format: "http://edamontology.org/format_2572"
label: "Coordinate sorted BAM alignment file (+index BAI)"
doc: "Coordinate sorted BAM file and BAI index file"
outputSource: rename_rsem_bambai_pair/target_file
bigwig_file:
type: File
format: "http://edamontology.org/format_3006"
label: "BigWig file"
doc: "Generated BigWig file"
outputSource: bam_to_bigwig/bigwig_file
fastx_statistics_upstream:
type: File
format: "http://edamontology.org/format_2330"
label: "FASTQ upstream statistics"
doc: "fastx_quality_stats generated upstream FASTQ quality statistics file"
outputSource: fastx_quality_stats_upstream/statistics_file
fastx_statistics_downstream:
type: File
format: "http://edamontology.org/format_2330"
label: "FASTQ downstream statistics"
doc: "fastx_quality_stats generated downstream FASTQ quality statistics file"
outputSource: fastx_quality_stats_downstream/statistics_file
get_stat_log:
type: File
label: "RSEM & Bowtie combined log"
format: "http://edamontology.org/format_2330"
doc: "Mapping statistics from RSEM & Bowtie logs"
outputSource: get_stat/output_file
rsem_stat_folder:
type: Directory
label: "RSEM alignment statistics"
doc: "RSEM generated statistics folder. Mostly for debug purposes"
outputSource: rsem_calculate_expression/stat_folder
bowtie_log:
type: File
format: "http://edamontology.org/format_2330"
label: "Ribo Bowtie alignment log"
doc: "Ribo Bowtie alignment log file. Mostly for debug purposes"
outputSource: ribo_bowtie_aligner/log_file
steps:
extract_fastq_upstream:
run: ../tools/extract-fastq.cwl
in:
compressed_file: fastq_file_upstream
out: [fastq_file]
extract_fastq_downstream:
run: ../tools/extract-fastq.cwl
in:
compressed_file: fastq_file_downstream
out: [fastq_file]
fastx_quality_stats_upstream:
run: ../tools/fastx-quality-stats.cwl
in:
input_file: extract_fastq_upstream/fastq_file
out: [statistics_file]
fastx_quality_stats_downstream:
run: ../tools/fastx-quality-stats.cwl
in:
input_file: extract_fastq_downstream/fastq_file
out: [statistics_file]
fastqc_stats_upstream:
run: ../tools/fastqc.cwl
in:
fastq_file: extract_fastq_upstream/fastq_file
out: [summary_file]
fastqc_stats_downstream:
run: ../tools/fastqc.cwl
in:
fastq_file: extract_fastq_downstream/fastq_file
out: [summary_file]
fastqc_results_trigger_upstream:
run: ../expressiontools/fastqc-results-trigger.cwl
in:
summary_file: fastqc_stats_upstream/summary_file
out: [trigger]
fastqc_results_trigger_downstream:
run: ../expressiontools/fastqc-results-trigger.cwl
in:
summary_file: fastqc_stats_downstream/summary_file
out: [trigger]
trim_adapters:
run: ../tools/trimmomatic.cwl
in:
fastq_file_upstream: extract_fastq_upstream/fastq_file
fastq_file_downstream: extract_fastq_downstream/fastq_file
adapters_file: fasta_file_adapters
trigger:
source: [fastqc_results_trigger_upstream/trigger, fastqc_results_trigger_downstream/trigger]
valueFrom: |
${
return self[0] && self[1];
}
lib_type:
default: "PE"
illuminaclip_step_param:
default: '2:30:15'
threads: threads
out:
- upstream_trimmed_file
- downstream_trimmed_file
rsem_calculate_expression:
run: ../tools/rsem-calculate-expression.cwl
in:
upstream_read_file: trim_adapters/upstream_trimmed_file
downstream_read_file: trim_adapters/downstream_trimmed_file
indices_folder: rsem_indices_folder
bowtie2:
default: true
sort_bam_by_coordinate:
default: true
output_genome_bam:
default: true
threads: threads
out:
- isoform_results_file
- gene_results_file
- genome_sorted_bam_bai_pair
- stat_folder
- total_reads_number
- mapped_reads_number
- multimapped_reads_number
rename_rsem_bambai_pair:
run: ../tools/rename.cwl
in:
source_file: rsem_calculate_expression/genome_sorted_bam_bai_pair
target_filename:
source: fastq_file_upstream
valueFrom: $(default_output_name(self, ".bam"))
out: [target_file]
rename_rsem_isoforms_file:
run: ../tools/rename.cwl
in:
source_file: rsem_calculate_expression/isoform_results_file
target_filename:
source: fastq_file_upstream
valueFrom: $(default_output_name(self, ".isoforms.tsv"))
out: [target_file]
rename_rsem_genes_file:
run: ../tools/rename.cwl
in:
source_file: rsem_calculate_expression/gene_results_file
target_filename:
source: fastq_file_upstream
valueFrom: $(default_output_name(self, ".genes.tsv"))
out: [target_file]
get_chr_length_file:
run: ../expressiontools/get-file-by-name.cwl
in:
input_files: rsem_indices_folder
basename_regex:
default: "chrlist$"
out: [selected_file]
bam_to_bigwig:
run: ../subworkflows/bam-bedgraph-bigwig.cwl
in:
bam_file: rename_rsem_bambai_pair/target_file
chrom_length_file: get_chr_length_file/selected_file
mapped_reads_number:
source: rsem_calculate_expression/mapped_reads_number
valueFrom: $(self*2)
out: [bigwig_file]
ribo_bowtie_aligner:
run: ../tools/bowtie-alignreads.cwl
in:
upstream_filelist: trim_adapters/upstream_trimmed_file
downstream_filelist: trim_adapters/downstream_trimmed_file
indices_folder: bowtie_indices_folder
output_filename:
source: fastq_file_upstream
valueFrom: $(default_output_name(self, ".txt"))
v:
default: 3
threads: threads
out:
- mapped_reads_number
- log_file
get_stat:
run: ../tools/custom-bash.cwl
in:
input_file: rsem_calculate_expression/isoform_results_file
script:
default: "echo -n $1 $2 $3 $4 `cat $0 | cut -f 5 | grep -v expected_count | awk '{sum+=$1} END {print int(sum)}'` > $5"
param:
source:
- rsem_calculate_expression/total_reads_number
- rsem_calculate_expression/mapped_reads_number
- ribo_bowtie_aligner/mapped_reads_number
- rsem_calculate_expression/multimapped_reads_number
- fastq_file_upstream
valueFrom: |
${
self[4] = default_output_name(self[4], ".stat");
return self.map(String);
}
out: [output_file]
get_annotation_file:
run: ../expressiontools/get-file-by-name.cwl
in:
input_files: rsem_indices_folder
basename_regex:
default: "ti$"
out: [selected_file]
make_biowardrobe_isoforms:
run: ../tools/python-make-biowardrobe-isoforms.cwl
in:
rsem_isoforms_file: rename_rsem_isoforms_file/target_file
rsem_annotation_file: get_annotation_file/selected_file
out: [biowardrobe_isoforms_file]
$namespaces:
s: http://schema.org/
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
s:name: "xenbase-rnaseq-pe"
s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/workflows/xenbase-rnaseq-pe.cwl
s:codeRepository: https://github.com/Barski-lab/workflows
s:license: http://www.apache.org/licenses/LICENSE-2.0
s:isPartOf:
class: s:CreativeWork
s:name: Common Workflow Language
s:url: http://commonwl.org/
s:creator:
- class: s:Organization
s:legalName: "Cincinnati Children's Hospital Medical Center"
s:location:
- class: s:PostalAddress
s:addressCountry: "USA"
s:addressLocality: "Cincinnati"
s:addressRegion: "OH"
s:postalCode: "45229"
s:streetAddress: "3333 Burnet Ave"
s:telephone: "+1(513)636-4200"
s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
s:department:
- class: s:Organization
s:legalName: "Allergy and Immunology"
s:department:
- class: s:Organization
s:legalName: "Barski Research Lab"
s:member:
- class: s:Person
s:name: Michael Kotliar
s:email: mailto:misha.kotliar@gmail.com
s:sameAs:
- id: http://orcid.org/0000-0002-6486-3898
doc: |
XenBase workflow for analysing RNA-Seq paired-end data
s:about: |
1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump)
2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files)
3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files:
"Per base sequence quality",
"Per sequence quality scores",
"Overrepresented sequences",
"Adapter Content",
- trim adapters (run trimmomatic)
4. Align original or trimmed FASTQ files to reference genome, calculate genes and isoforms expression (run RSEM)
5. Count mapped reads number in sorted BAM file (run bamtools stats)
6. Generate genome coverage BED file (run bedtools genomecov)
7. Sort genearted BED file (run sort)
8. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)