Workflow: mixed_library_metrics.cwl

Fetched 2023-01-04 03:47:48 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs job_uuid job_uuid picard_collectoxogmetrics_to_sqlite picard_collectoxogmetrics_to_sqlite job_uuid->picard_collectoxogmetrics_to_sqlite job_uuid samtools_stats_to_sqlite samtools_stats_to_sqlite job_uuid->samtools_stats_to_sqlite job_uuid picard_collectmultiplemetrics_to_sqlite picard_collectmultiplemetrics_to_sqlite job_uuid->picard_collectmultiplemetrics_to_sqlite job_uuid samtools_flagstat_to_sqlite samtools_flagstat_to_sqlite job_uuid->samtools_flagstat_to_sqlite job_uuid picard_collectwgsmetrics_to_sqlite picard_collectwgsmetrics_to_sqlite job_uuid->picard_collectwgsmetrics_to_sqlite job_uuid merge_sqlite merge_sqlite job_uuid->merge_sqlite job_uuid samtools_idxstats_to_sqlite samtools_idxstats_to_sqlite job_uuid->samtools_idxstats_to_sqlite job_uuid bam bam picard_collectoxogmetrics picard_collectoxogmetrics bam->picard_collectoxogmetrics INPUT samtools_flagstat samtools_flagstat bam->samtools_flagstat INPUT picard_collectmultiplemetrics picard_collectmultiplemetrics bam->picard_collectmultiplemetrics INPUT bam->picard_collectoxogmetrics_to_sqlite bam bam->samtools_stats_to_sqlite bam bam->picard_collectmultiplemetrics_to_sqlite bam samtools_idxstats samtools_idxstats bam->samtools_idxstats INPUT bam->samtools_flagstat_to_sqlite bam picard_collectwgsmetrics picard_collectwgsmetrics bam->picard_collectwgsmetrics INPUT bam->picard_collectwgsmetrics_to_sqlite bam samtools_stats samtools_stats bam->samtools_stats INPUT bam->samtools_idxstats_to_sqlite bam fasta fasta fasta->picard_collectoxogmetrics REFERENCE_SEQUENCE fasta->picard_collectmultiplemetrics REFERENCE_SEQUENCE fasta->picard_collectoxogmetrics_to_sqlite fasta fasta->picard_collectmultiplemetrics_to_sqlite fasta fasta->picard_collectwgsmetrics REFERENCE_SEQUENCE fasta->picard_collectwgsmetrics_to_sqlite fasta input_state input_state input_state->picard_collectoxogmetrics_to_sqlite input_state input_state->samtools_stats_to_sqlite input_state input_state->picard_collectmultiplemetrics_to_sqlite input_state input_state->samtools_flagstat_to_sqlite input_state input_state->picard_collectwgsmetrics_to_sqlite input_state input_state->samtools_idxstats_to_sqlite input_state known_snp known_snp known_snp->picard_collectoxogmetrics DB_SNP known_snp->picard_collectmultiplemetrics DB_SNP known_snp->picard_collectoxogmetrics_to_sqlite vcf known_snp->picard_collectmultiplemetrics_to_sqlite vcf thread_count thread_count merge_sqlite_destination_sqlite merge_sqlite_destination_sqlite picard_collectoxogmetrics->picard_collectoxogmetrics_to_sqlite metric_path samtools_flagstat->samtools_flagstat_to_sqlite metric_path picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite quality_yield_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite pre_adapter_detail_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite insert_size_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite bait_bias_summary_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite quality_by_cycle_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite quality_distribution_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite alignment_summary_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite gc_bias_detail_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite base_distribution_by_cycle_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite gc_bias_summary_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite bait_bias_detail_metrics picard_collectmultiplemetrics->picard_collectmultiplemetrics_to_sqlite pre_adapter_summary_metrics picard_collectoxogmetrics_to_sqlite->merge_sqlite source_sqlite samtools_stats_to_sqlite->merge_sqlite source_sqlite picard_collectmultiplemetrics_to_sqlite->merge_sqlite source_sqlite samtools_idxstats->samtools_idxstats_to_sqlite metric_path samtools_flagstat_to_sqlite->merge_sqlite source_sqlite picard_collectwgsmetrics->picard_collectwgsmetrics_to_sqlite metric_path picard_collectwgsmetrics_to_sqlite->merge_sqlite source_sqlite samtools_stats->samtools_stats_to_sqlite metric_path merge_sqlite->merge_sqlite_destination_sqlite samtools_idxstats_to_sqlite->merge_sqlite source_sqlite
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Inputs

ID Type Title Doc
bam File
fasta File
job_uuid String
known_snp File
input_state String
thread_count Long

Steps

ID Runs Label Doc
merge_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
samtools_stats
../../tools/samtools_stats.cwl (CommandLineTool)
samtools_flagstat
../../tools/samtools_flagstat.cwl (CommandLineTool)
samtools_idxstats
../../tools/samtools_idxstats.cwl (CommandLineTool)
picard_collectwgsmetrics
../../tools/picard_collectwgsmetrics.cwl (CommandLineTool)
samtools_stats_to_sqlite
../../tools/samtools_stats_to_sqlite.cwl (CommandLineTool)
picard_collectoxogmetrics
../../tools/picard_collectoxogmetrics.cwl (CommandLineTool)
samtools_flagstat_to_sqlite
../../tools/samtools_flagstat_to_sqlite.cwl (CommandLineTool)
samtools_idxstats_to_sqlite
../../tools/samtools_idxstats_to_sqlite.cwl (CommandLineTool)
picard_collectmultiplemetrics
../../tools/picard_collectmultiplemetrics.cwl (CommandLineTool)
picard_collectwgsmetrics_to_sqlite
../../tools/picard_collectwgsmetrics_to_sqlite.cwl (CommandLineTool)
picard_collectoxogmetrics_to_sqlite
../../tools/picard_collectoxogmetrics_to_sqlite.cwl (CommandLineTool)
picard_collectmultiplemetrics_to_sqlite
../../tools/picard_collectmultiplemetrics_to_sqlite.cwl (CommandLineTool)

Outputs

ID Type Label Doc
merge_sqlite_destination_sqlite File
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/a57b8f0d8708078e87f13297e065d72db10e38a0/workflows/mirnaseq/mixed_library_metrics.cwl