Workflow: transform.cwl

Fetched 2018-12-15 10:54:05 GMT
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Inputs

ID Type Title Doc
reference_fasta_path File
bam_path File
thread_count Integer
db_snp_path File
uuid String

Steps

ID Runs Label Doc
fastqc_se_basicstats_json
../../tools/fastqc_basicstatistics_json.cwl (CommandLineTool)
sort_scattered_fastq_s
../../tools/sort_scatter_expression.cwl (ExpressionTool)
merge_readgroup_json_db
../../tools/merge_sqlite.cwl (CommandLineTool)
picard_validatesamfile_markduplicates
../../tools/picard_validatesamfile.cwl (CommandLineTool)
fastqc_o2_basicstats_json
../../tools/fastqc_basicstatistics_json.cwl (CommandLineTool)
fastqc_db_s
../../tools/fastqc_db.cwl (CommandLineTool)
remove_duplicate_fastq2
../../tools/fastq_remove_duplicate_qname.cwl (CommandLineTool)
decider_bwa_pe
../../tools/decider_bwa_expression.cwl (ExpressionTool)
integrity
integrity.cwl (Workflow)
picard_mergesamfiles_o1
../../tools/picard_mergesamfiles.cwl (CommandLineTool)
remove_duplicate_fastq1
../../tools/fastq_remove_duplicate_qname.cwl (CommandLineTool)
bam_readgroup_to_json
../../tools/bam_readgroup_to_json.cwl (CommandLineTool)
picard_mergesamfiles_o2
../../tools/picard_mergesamfiles.cwl (CommandLineTool)
picard_mergesamfiles
../../tools/picard_mergesamfiles.cwl (CommandLineTool)
merge_metrics_pe
../../tools/merge_sqlite.cwl (CommandLineTool)
bwa_pe
../../tools/bwa_pe.cwl (CommandLineTool)
picard_mergesamfiles_se
../../tools/picard_mergesamfiles.cwl (CommandLineTool)
fastqc_s
../../tools/fastqc.cwl (CommandLineTool)
merge_fastqc_db_o1_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
sort_scattered_fastq_o1
../../tools/sort_scatter_expression.cwl (ExpressionTool)
bwa_se
../../tools/bwa_se.cwl (CommandLineTool)
sort_scattered_fastq_o2
../../tools/sort_scatter_expression.cwl (ExpressionTool)
bam_reheader
../../tools/bam_reheader.cwl (CommandLineTool)
picard_validatesamfile_original_to_sqlite
../../tools/picard_validatesamfile_to_sqlite.cwl (CommandLineTool)
picard_validatesamfile_original
../../tools/picard_validatesamfile.cwl (CommandLineTool)
decider_bwa_se
../../tools/decider_bwa_expression.cwl (ExpressionTool)
merge_fastqc_db2_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
merge_all_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
picard_sortsam_o1
../../tools/picard_sortsam.cwl (CommandLineTool)
picard_sortsam_o2
../../tools/picard_sortsam.cwl (CommandLineTool)
fastqc_db1
../../tools/fastqc_db.cwl (CommandLineTool)
fastqc_db2
../../tools/fastqc_db.cwl (CommandLineTool)
sort_scattered_fastq1
../../tools/sort_scatter_expression.cwl (ExpressionTool)
decider_bwa_o2
../../tools/decider_bwa_expression.cwl (ExpressionTool)
picard_markduplicates_to_sqlite
../../tools/picard_markduplicates_to_sqlite.cwl (CommandLineTool)
decider_bwa_o1
../../tools/decider_bwa_expression.cwl (ExpressionTool)
picard_sortsam_pe
../../tools/picard_sortsam.cwl (CommandLineTool)
fastqc2
../../tools/fastqc.cwl (CommandLineTool)
fastqc_o1
../../tools/fastqc.cwl (CommandLineTool)
picard_mergesamfiles_pe
../../tools/picard_mergesamfiles.cwl (CommandLineTool)
fastqc1
../../tools/fastqc.cwl (CommandLineTool)
fastqc_o2
../../tools/fastqc.cwl (CommandLineTool)
remove_duplicate_fastq_o1
../../tools/fastq_remove_duplicate_qname.cwl (CommandLineTool)
remove_duplicate_fastq_s
../../tools/fastq_remove_duplicate_qname.cwl (CommandLineTool)
biobambam_bamtofastq
../../tools/biobambam2_bamtofastq.cwl (CommandLineTool)
samtools_bamtobam
../../tools/samtools_bamtobam.cwl (CommandLineTool)
remove_duplicate_fastq_o2
../../tools/fastq_remove_duplicate_qname.cwl (CommandLineTool)
metrics_pe
metrics.cwl (Workflow)
fastqc_pe_basicstats_json
../../tools/fastqc_basicstatistics_json.cwl (CommandLineTool)
fastqc_db_o2
../../tools/fastqc_db.cwl (CommandLineTool)
fastqc_db_o1
../../tools/fastqc_db.cwl (CommandLineTool)
bwa_o1
../../tools/bwa_se.cwl (CommandLineTool)
merge_fastqc_db_s_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
bwa_o2
../../tools/bwa_se.cwl (CommandLineTool)
metrics_se
metrics.cwl (Workflow)
picard_sortsam_se
../../tools/picard_sortsam.cwl (CommandLineTool)
picard_validatesamfile_markdupl_to_sqlite
../../tools/picard_validatesamfile_to_sqlite.cwl (CommandLineTool)
merge_fastqc_db_o2_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
merge_metrics_se
../../tools/merge_sqlite.cwl (CommandLineTool)
merge_fastqc_db1_sqlite
../../tools/merge_sqlite.cwl (CommandLineTool)
metrics_markduplicates
picard_markduplicates
../../tools/picard_markduplicates.cwl (CommandLineTool)
readgroup_json_db
../../tools/readgroup_json_db.cwl (CommandLineTool)
fastqc_o1_basicstats_json
../../tools/fastqc_basicstatistics_json.cwl (CommandLineTool)
sort_scattered_fastq2
../../tools/sort_scatter_expression.cwl (ExpressionTool)

Outputs

ID Type Label Doc
picard_markduplicates_output File
merge_all_sqlite_destination_sqlite File
Permalink: https://w3id.org/cwl/view/git/3279c271cbb771674ef4339e775120627a0ddc46/workflows/dnaseq/transform.cwl