Workflow: alignment for nonhuman with qc

Fetched 2023-01-10 00:46:30 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs final_name final_name alignment Alignment without BQSR final_name->alignment final_name minimum_mapping_quality minimum_mapping_quality qc WGS QC workflow nonhuman minimum_mapping_quality->qc minimum_mapping_quality per_base_intervals per_base_intervals per_base_intervals->qc per_base_intervals reference reference reference->alignment reference reference->qc reference summary_intervals summary_intervals summary_intervals->qc summary_intervals trimming trimming trimming->alignment trimming sequence sequence: sequencing data and readgroup information sequence->alignment unaligned minimum_base_quality minimum_base_quality minimum_base_quality->qc minimum_base_quality picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->qc picard_metric_accumulation_level per_target_intervals per_target_intervals per_target_intervals->qc per_target_intervals bamcoverage_bigwig bamcoverage_bigwig gc_bias_metrics_summary gc_bias_metrics_summary mark_duplicates_metrics mark_duplicates_metrics gc_bias_metrics gc_bias_metrics per_base_hs_metrics per_base_hs_metrics insert_size_histogram insert_size_histogram alignment_summary_metrics alignment_summary_metrics flagstats flagstats per_target_hs_metrics per_target_hs_metrics summary_hs_metrics summary_hs_metrics per_base_coverage_metrics per_base_coverage_metrics per_target_coverage_metrics per_target_coverage_metrics insert_size_metrics insert_size_metrics gc_bias_metrics_chart gc_bias_metrics_chart bam bam wgs_metrics wgs_metrics alignment->mark_duplicates_metrics alignment->bam alignment->qc bam qc->bamcoverage_bigwig qc->gc_bias_metrics_summary qc->gc_bias_metrics qc->per_base_hs_metrics qc->insert_size_histogram qc->alignment_summary_metrics qc->flagstats qc->per_target_hs_metrics qc->summary_hs_metrics qc->per_base_coverage_metrics qc->per_target_coverage_metrics qc->insert_size_metrics qc->gc_bias_metrics_chart qc->wgs_metrics
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Inputs

ID Type Title Doc
sequence https://w3id.org/cwl/view/git/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/types/sequence_data.yml#sequence_data[] sequence: sequencing data and readgroup information

sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.

trimming https://w3id.org/cwl/view/git/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/types/trimming_options.yml#trimming_options (Optional)
reference File
final_name String (Optional)
summary_intervals https://w3id.org/cwl/view/git/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/types/labelled_file.yml#labelled_file[]
minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String

Steps

ID Runs Label Doc
qc WGS QC workflow nonhuman
alignment Alignment without BQSR

Outputs

ID Type Label Doc
bam File
flagstats File
wgs_metrics File
gc_bias_metrics File
bamcoverage_bigwig File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
gc_bias_metrics_chart File
insert_size_histogram File
per_target_hs_metrics File[]
gc_bias_metrics_summary File
mark_duplicates_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
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Permalink: https://w3id.org/cwl/view/git/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/pipelines/alignment_wgs_nonhuman.cwl