Workflow: transform.cwl

Fetched 2018-12-31 01:44:26 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
reference_sequence File
job_uuid String
bam_name String
known_snp File
readgroup_fastq_se_file_list https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/readgroup.yml#readgroup_fastq_se_file[]
readgroups_bam_file_list https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/readgroup.yml#readgroups_bam_file[]
common_biallelic_vcf File
run_markduplicates Long[]
readgroup_fastq_pe_file_list https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/readgroup.yml#readgroup_fastq_pe_file[]
capture_kit_set_file_list https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/capture_kit.yml#capture_kit_set_file[]
amplicon_kit_set_file_list https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/tools/amplicon_kit.yml#amplicon_kit_set_file[]
run_bamindex Long[]
thread_count Long

Steps

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

Outputs

ID Type Label Doc
sqlite File
output_bam File
Permalink: https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/workflows/bamfastq_align/transform.cwl