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fastq_single.cwl
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fastq_single.cwl
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class: Workflow
cwlVersion: v1.0
id: main_single
label: main_single
$namespaces:
sbg: 'https://www.sevenbridges.com'
inputs:
- id: cwl_wf_url
type: string
- id: cwl_args_url
type: string
- id: index_synapseid
type: string
- id: synapse_config
type: File
'sbg:x': -522.0704956054688
'sbg:y': -348.93670654296875
- id: synapseid
type: 'string[]'
'sbg:x': -405
'sbg:y': -412
- id: nthreads
type: int
'sbg:x': -422
'sbg:y': -411
- id: genstr
type: string?
- id: output_metrics_filename
type: string?
- id: synapse_parentid
type: string
- id: strand_specificity
type: string?
- id: column_number
type: int?
- id: alignEndsType
type: string?
- id: outFilterMismatchNmax
type: int?
- id: outFilterMultimapScoreRange
type: int?
- id: outFilterMultimapNmax
type: int?
- id: outFilterScoreMinOverLread
type: int?
- id: outFilterMatchNminOverLread
type: int?
- id: outFilterMatchNmin
type: int?
- id: alignSJDBoverhangMin
type: int?
- id: alignIntronMax
type: int?
outputs:
- id: clean_counts
outputSource:
- clean_tables/clean_counts
type: File
- id: clean_log
outputSource:
- clean_tables/clean_log
type: File
- id: clean_metrics
outputSource:
- clean_tables/clean_metrics
type: File
steps:
- id: input_provenance
in:
- id: argurl
source: cwl_args_url
- id: synapseconfig
source: synapse_config
out:
- id: provenance_csv
run: tools/provenance.cwl
label: gather sample provenance
doc: capture the version numbers of input files on Synapse
- id: wf_getindexes
in:
- id: synapseid
source: index_synapseid
- id: synapse_config
source: synapse_config
out:
- id: files
- id: genome_fasta
- id: genemodel_gtf
run: subworkflows/wf-getindexes.cwl
label: Get index files
doc: download the indexed reference genome
- id: wf_alignment
in:
- id: genome_dir
source: wf_getindexes/files
- id: genstr
source: genstr
- id: nthreads
source: nthreads
- id: synapse_config
source: synapse_config
- id: synapseid
source: synapseid
- id: alignEndsType
source: alignEndsType
- id: outFilterMismatchNmax
source: outFilterMismatchNmax
- id: outFilterMultimapScoreRange
source: outFilterMultimapScoreRange
- id: outFilterMultimapNmax
source: outFilterMultimapNmax
- id: outFilterScoreMinOverLread
source: outFilterScoreMinOverLread
- id: outFilterMatchNminOverLread
source: outFilterMatchNminOverLread
- id: outFilterMatchNmin
source: outFilterMatchNmin
- id: alignSJDBoverhangMin
source: alignSJDBoverhangMin
- id: alignIntronMax
source: alignIntronMax
out:
- id: splice_junctions
- id: reads_per_gene
- id: logs
- id: realigned_reads_sam
run: subworkflows/wf-alignment-single-fastq.cwl
label: Alignment sub-workflow
doc: run the alignment sub-workflow
scatter:
- synapseid
'sbg:x': -310.91680908203125
'sbg:y': -200.39964294433594
- id: wf_buildrefs
in:
- id: genemodel_gtf
source: wf_getindexes/genemodel_gtf
- id: aligned_reads_sam
source: wf_alignment/realigned_reads_sam
valueFrom: $(self[0])
out:
- id: picard_riboints
- id: picard_refflat
run: subworkflows/wf-buildrefs.cwl
label: Reference building sub-workflow
doc: run the subworkflow that builds reference files for picard tools
'sbg:x': -516
'sbg:y': 12
- id: wf_metrics
in:
- id: genome_fasta
source: wf_getindexes/genome_fasta
- id: aligned_reads_sam
source: wf_alignment/realigned_reads_sam
- id: picard_refflat
source: wf_buildrefs/picard_refflat
- id: picard_riboints
source: wf_buildrefs/picard_riboints
- id: basef
source: synapseid
- id: output_metrics_filename
source: output_metrics_filename
- id: strand_specificity
source: strand_specificity
out:
- id: combined_metrics_csv
run: subworkflows/wf-metrics.cwl
label: Metrics sub-workflow
doc: run the metrics subworkflow
scatter:
- aligned_reads_sam
- basef
scatterMethod: dotproduct
'sbg:x': 128
'sbg:y': -185
- id: combine_counts
in:
- id: read_counts
source:
- wf_alignment/reads_per_gene
- id: column_number
source: column_number
out:
- id: combined_counts
run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-tool-star/v1.0.0/cwl/combine_counts_study.cwl
label: Combine read counts across samples
doc: combine read counts across all samples
'sbg:x': -63.8984375
'sbg:y': 31.5
- id: combine_metrics
in:
- id: picard_metrics
source:
- wf_metrics/combined_metrics_csv
out:
- id: combined_metrics
run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-tool-picardtools/v1.0.1/cwl/combine_metrics_study.cwl
label: Combine Picard metrics across samples
doc: combine picard metrics across all samples
'sbg:x': 343.8936767578125
'sbg:y': -158.5
- id: merge_starlog
in:
- id: logs
source:
- wf_alignment/logs
out:
- id: starlog_merged
run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-tool-rnaseq-utils/v1.0.0/cwl/merge_starlog.cwl
label: merge_starlog
doc: merge STAR log files into a single table
'sbg:x': -132.7860107421875
'sbg:y': 294.5
- id: synapse_upload
in:
- id: infiles
source:
- merge_starlog/starlog_merged
- input_provenance/provenance_csv
- combine_counts/combined_counts
- combine_metrics/combined_metrics
- id: synapse_parentid
source: synapse_parentid
- id: synapseconfig
source: synapse_config
- id: argurl
source: cwl_args_url
- id: wfurl
source: cwl_wf_url
out: []
run: tools/upload_synapse.cwl
doc: upload output files to Synapse
- id: clean_tables
in:
- id: count_table
source: combine_counts/combined_counts
- id: star_table
source: merge_starlog/starlog_merged
- id: metric_table
source: combine_metrics/combined_metrics
- id: provenance_csv
source: input_provenance/provenance_csv
out:
- id: clean_counts
- id: clean_log
- id: clean_metrics
run: https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/dockstore-tool-rnaseq-utils/v1.0.0/cwl/clean_tables.cwl
doc: clean output tables and convert Synapse ID's to specimen ID's
- id: clean_upload
in:
- id: infiles
source:
- clean_tables/clean_counts
- clean_tables/clean_log
- clean_tables/clean_metrics
- id: synapse_parentid
source: synapse_parentid
- id: synapseconfig
source: synapse_config
- id: argurl
source: cwl_args_url
- id: wfurl
source: cwl_wf_url
out: []
run: tools/upload_synapse.cwl
doc: upload the cleaned tables to Synapse
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement