Workflow: transform.cwl

Fetched 2023-01-12 03:25:07 GMT
children parents
workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs job_uuid job_uuid merge_all_sqlite merge_all_sqlite job_uuid->merge_all_sqlite job_uuid merge_sqlite_bwa_se merge_sqlite_bwa_se job_uuid->merge_sqlite_bwa_se job_uuid bwa_o1 bwa_o1 job_uuid->bwa_o1 job_uuid bwa_o2 bwa_o2 job_uuid->bwa_o2 job_uuid bwa_pe bwa_pe job_uuid->bwa_pe job_uuid conditional_markduplicates conditional_markduplicates job_uuid->conditional_markduplicates job_uuid integrity integrity job_uuid->integrity job_uuid picard_validatesamfile_bqsr_to_sqlite picard_validatesamfile_bqsr_to_sqlite job_uuid->picard_validatesamfile_bqsr_to_sqlite job_uuid merge_sqlite_bwa_pe merge_sqlite_bwa_pe job_uuid->merge_sqlite_bwa_pe job_uuid metrics metrics job_uuid->metrics job_uuid bwa_se bwa_se job_uuid->bwa_se job_uuid readgroup_fastq_se_file_list readgroup_fastq_se_file_list merge_se_fastq_records merge_se_fastq_records readgroup_fastq_se_file_list->merge_se_fastq_records input run_markduplicates run_markduplicates run_markduplicates->conditional_markduplicates run_markduplicates readgroups_bam_file_list readgroups_bam_file_list readgroups_bam_to_readgroups_fastq_lists readgroups_bam_to_readgroups_fastq_lists readgroups_bam_file_list->readgroups_bam_to_readgroups_fastq_lists readgroups_bam_file readgroup_fastq_pe_file_list readgroup_fastq_pe_file_list merge_pe_fastq_records merge_pe_fastq_records readgroup_fastq_pe_file_list->merge_pe_fastq_records input thread_count thread_count thread_count->bwa_o1 thread_count conditional_index conditional_index thread_count->conditional_index thread_count thread_count->bwa_o2 thread_count thread_count->bwa_pe thread_count thread_count->bwa_se thread_count known_snp known_snp gatk_baserecalibrator gatk_baserecalibrator known_snp->gatk_baserecalibrator known-sites known_snp->metrics known_snp reference_sequence reference_sequence reference_sequence->gatk_baserecalibrator reference reference_sequence->bwa_o1 reference_sequence reference_sequence->bwa_o2 reference_sequence reference_sequence->bwa_pe reference_sequence reference_sequence->metrics fasta reference_sequence->bwa_se reference_sequence amplicon_kit_set_file_list amplicon_kit_set_file_list amplicon_kit_set_file_list->metrics amplicon_kit_set_file_list capture_kit_set_file_list capture_kit_set_file_list capture_kit_set_file_list->metrics capture_kit_set_file_list run_bamindex run_bamindex run_bamindex->conditional_index run_bamindex bam_name bam_name picard_mergesamfiles picard_mergesamfiles bam_name->picard_mergesamfiles OUTPUT sqlite sqlite output_bam output_bam merge_all_sqlite->sqlite gatk_applybqsr gatk_applybqsr gatk_baserecalibrator->gatk_applybqsr bqsr-recal-file merge_sqlite_bwa_se->merge_all_sqlite source_sqlite merge_pe_fastq_records->bwa_pe readgroup_fastq_pe merge_bam_se_fastq_records merge_bam_se_fastq_records merge_bam_se_fastq_records->merge_se_fastq_records input bam_reheader bam_reheader picard_mergesamfiles->bam_reheader input merge_o1_fastq_records merge_o1_fastq_records merge_o1_fastq_records->bwa_o1 readgroup_fastq_se merge_o2_fastq_records merge_o2_fastq_records merge_o2_fastq_records->bwa_o2 readgroup_fastq_se bwa_o1->picard_mergesamfiles INPUT gatk_applybqsr->output_bam gatk_applybqsr->integrity bai gatk_applybqsr->integrity bam picard_validatesamfile_bqsr picard_validatesamfile_bqsr gatk_applybqsr->picard_validatesamfile_bqsr INPUT gatk_applybqsr->picard_validatesamfile_bqsr_to_sqlite bam gatk_applybqsr->metrics bam bam_reheader->conditional_index bam bam_reheader->conditional_markduplicates bam decide_markduplicates_index decide_markduplicates_index conditional_index->decide_markduplicates_index conditional_bam2 conditional_index->decide_markduplicates_index conditional_sqlite2 merge_se_fastq_records->bwa_se readgroup_fastq_se bwa_o2->picard_mergesamfiles INPUT bwa_pe->picard_mergesamfiles INPUT bwa_pe->merge_sqlite_bwa_pe source_sqlite conditional_markduplicates->decide_markduplicates_index conditional_sqlite1 conditional_markduplicates->decide_markduplicates_index conditional_bam1 integrity->merge_all_sqlite source_sqlite merge_bam_pe_fastq_records merge_bam_pe_fastq_records merge_bam_pe_fastq_records->merge_pe_fastq_records input readgroups_bam_to_readgroups_fastq_lists->merge_bam_se_fastq_records input readgroups_bam_to_readgroups_fastq_lists->merge_o1_fastq_records input readgroups_bam_to_readgroups_fastq_lists->merge_o2_fastq_records input readgroups_bam_to_readgroups_fastq_lists->merge_bam_pe_fastq_records input picard_validatesamfile_bqsr->picard_validatesamfile_bqsr_to_sqlite metric_path picard_validatesamfile_bqsr_to_sqlite->merge_all_sqlite source_sqlite merge_sqlite_bwa_pe->merge_all_sqlite source_sqlite metrics->merge_all_sqlite source_sqlite bwa_se->merge_sqlite_bwa_se source_sqlite bwa_se->picard_mergesamfiles INPUT decide_markduplicates_index->merge_all_sqlite source_sqlite decide_markduplicates_index->gatk_baserecalibrator input decide_markduplicates_index->gatk_applybqsr input
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
bam_name String
job_uuid String
known_snp File
run_bamindex Long[]
thread_count Long
reference_sequence File
run_markduplicates Long[]
readgroups_bam_file_list https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/readgroup.yml#readgroups_bam_file[]
capture_kit_set_file_list https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/capture_kit.yml#capture_kit_set_file[]
amplicon_kit_set_file_list https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/amplicon_kit.yml#amplicon_kit_set_file[]
readgroup_fastq_pe_file_list https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/readgroup.yml#readgroup_fastq_pe_file[]
readgroup_fastq_se_file_list https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/tools/readgroup.yml#readgroup_fastq_se_file[]

Steps

ID Runs Label Doc
bwa_o1
bwa_se.cwl (Workflow)
bwa_o2
bwa_se.cwl (Workflow)
bwa_pe
bwa_pe.cwl (Workflow)
bwa_se
bwa_se.cwl (Workflow)
metrics
metrics.cwl (Workflow)
integrity
integrity.cwl (Workflow)
bam_reheader
../../tools/bam_reheader.cwl (CommandLineTool)
gatk_applybqsr
../../tools/gatk4_applybqsr.cwl (CommandLineTool)
merge_all_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
conditional_index
merge_sqlite_bwa_pe
../../tools/merge_sqlite.cwl (CommandLineTool)
merge_sqlite_bwa_se
../../tools/merge_sqlite.cwl (CommandLineTool)
picard_mergesamfiles
../../tools/picard_mergesamfiles_aoa.cwl (CommandLineTool)
gatk_baserecalibrator
../../tools/gatk4_baserecalibrator.cwl (CommandLineTool)
merge_o1_fastq_records
../../tools/merge_se_fastq_records.cwl (ExpressionTool)
merge_o2_fastq_records
../../tools/merge_se_fastq_records.cwl (ExpressionTool)
merge_pe_fastq_records
../../tools/merge_pe_fastq_records.cwl (ExpressionTool)
merge_se_fastq_records
../../tools/merge_se_fastq_records.cwl (ExpressionTool)
conditional_markduplicates
merge_bam_pe_fastq_records
../../tools/merge_pe_fastq_records.cwl (ExpressionTool)
merge_bam_se_fastq_records
../../tools/merge_se_fastq_records.cwl (ExpressionTool)
decide_markduplicates_index
../../tools/decider_conditional_bams.cwl (ExpressionTool)
picard_validatesamfile_bqsr
../../tools/picard_validatesamfile.cwl (CommandLineTool)
picard_validatesamfile_bqsr_to_sqlite
../../tools/picard_validatesamfile_to_sqlite.cwl (CommandLineTool)
readgroups_bam_to_readgroups_fastq_lists

Outputs

ID Type Label Doc
sqlite File
output_bam File
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/f34d3963b33e0a379338cb3cb75b0016f012bf2c/workflows/bamfastq_align/transform.cwl