Workflow: alignment for nonhuman with qc

Fetched 2023-01-09 22:54:24 GMT
children parents
workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs picard_metric_accumulation_level picard_metric_accumulation_level qc WGS QC workflow nonhuman picard_metric_accumulation_level->qc picard_metric_accumulation_level minimum_mapping_quality minimum_mapping_quality minimum_mapping_quality->qc minimum_mapping_quality per_target_intervals per_target_intervals per_target_intervals->qc per_target_intervals minimum_base_quality minimum_base_quality minimum_base_quality->qc minimum_base_quality sequence sequence: sequencing data and readgroup information alignment Alignment without BQSR sequence->alignment unaligned reference reference reference->qc reference reference->alignment reference summary_intervals summary_intervals summary_intervals->qc summary_intervals final_name final_name final_name->alignment final_name per_base_intervals per_base_intervals per_base_intervals->qc per_base_intervals trimming trimming trimming->alignment trimming gc_bias_metrics_chart gc_bias_metrics_chart per_base_hs_metrics per_base_hs_metrics summary_hs_metrics summary_hs_metrics gc_bias_metrics_summary gc_bias_metrics_summary per_target_hs_metrics per_target_hs_metrics insert_size_metrics insert_size_metrics per_target_coverage_metrics per_target_coverage_metrics alignment_summary_metrics alignment_summary_metrics bam bam flagstats flagstats gc_bias_metrics gc_bias_metrics per_base_coverage_metrics per_base_coverage_metrics insert_size_histogram insert_size_histogram mark_duplicates_metrics mark_duplicates_metrics wgs_metrics wgs_metrics bamcoverage_bigwig bamcoverage_bigwig qc->gc_bias_metrics_chart qc->per_base_hs_metrics qc->summary_hs_metrics qc->gc_bias_metrics_summary qc->per_target_hs_metrics qc->insert_size_metrics qc->per_target_coverage_metrics qc->alignment_summary_metrics qc->flagstats qc->gc_bias_metrics qc->per_base_coverage_metrics qc->insert_size_histogram qc->wgs_metrics qc->bamcoverage_bigwig alignment->bam alignment->mark_duplicates_metrics alignment->qc bam
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
sequence https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/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/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/trimming_options.yml#trimming_options (Optional)
reference File
final_name String (Optional)
summary_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/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[]
Permalink: https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/pipelines/alignment_wgs_nonhuman.cwl