subworkflows_generate_fda_metrics.cwl - genome/analysis-workflows GitHub Wiki
Documentation for generate_fda_metrics.cwl
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Overview
Calculate FDA-requested metrics on all aligned and unaligned sequence files
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference |
|
|
['string', 'File'] |
|
| unaligned_normal_dna |
|
|
../types/sequence_data.yml#sequence_data[] |
|
| unaligned_tumor_dna |
|
|
../types/sequence_data.yml#sequence_data[] |
|
| unaligned_tumor_rna |
|
|
../types/sequence_data.yml#sequence_data[] |
|
| aligned_normal_dna |
|
|
File |
|
| aligned_tumor_dna |
|
|
File |
|
| aligned_tumor_rna |
|
|
File |
|
| normal_alignment_summary_metrics |
|
|
File |
|
| normal_duplication_metrics |
|
|
File |
|
| normal_insert_size_metrics |
|
|
File |
|
| normal_hs_metrics |
|
|
File |
|
| normal_flagstat |
|
|
File |
|
| tumor_alignment_summary_metrics |
|
|
File |
|
| tumor_duplication_metrics |
|
|
File |
|
| tumor_insert_size_metrics |
|
|
File |
|
| tumor_hs_metrics |
|
|
File |
|
| tumor_flagstat |
|
|
File |
|
| rna_metrics |
|
|
File |
|
| reference_genome |
|
|
string? |
|
| dna_sequencing_platform |
|
|
string? |
|
| dna_sequencing_instrument |
|
|
string? |
|
| dna_sequencing_kit |
|
|
string? |
|
| dna_sequencing_type |
|
|
string? |
|
| dna_single_or_paired_end |
|
|
string? |
|
| normal_dna_spike_in_error_rate |
|
|
string? |
|
| tumor_dna_spike_in_error_rate |
|
|
string? |
|
| normal_dna_total_DNA |
|
|
string? |
|
| tumor_dna_total_DNA |
|
|
string? |
|
| normal_dna_sample_name |
|
|
string? |
|
| tumor_dna_sample_name |
|
|
string? |
|
| rna_sequencing_platform |
|
|
string? |
|
| rna_sequencing_instrument |
|
|
string? |
|
| rna_sequencing_kit |
|
|
string? |
|
| rna_sequencing_type |
|
|
string? |
|
| rna_single_or_paired_end |
|
|
string? |
|
| rna_spike_in_error_rate |
|
|
string? |
|
| rna_total_RNA |
|
|
string? |
|
| rna_RIN_score |
|
|
string? |
|
| rna_freq_normalization_method |
|
|
string? |
|
| rna_annotation_file |
|
|
string? |
|
| rna_sample_name |
|
|
string? |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| unaligned_normal_dna_fastqc_data |
|
|
File[] |
|
| unaligned_normal_dna_table_metrics |
|
|
File[] |
|
| unaligned_normal_dna_md5sums |
|
|
File |
|
| unaligned_normal_dna_table1 |
|
|
File |
|
| unaligned_tumor_dna_fastqc_data |
|
|
File[] |
|
| unaligned_tumor_dna_table_metrics |
|
|
File[] |
|
| unaligned_tumor_dna_md5sums |
|
|
File |
|
| unaligned_tumor_dna_table1 |
|
|
File |
|
| unaligned_tumor_rna_fastqc_data |
|
|
File[] |
|
| unaligned_tumor_rna_table_metrics |
|
|
File[] |
|
| unaligned_tumor_rna_md5sums |
|
|
File |
|
| unaligned_tumor_rna_table1 |
|
|
File |
|
| aligned_normal_dna_fastqc_data |
|
|
File[] |
|
| aligned_normal_dna_table_metrics |
|
|
File |
|
| aligned_normal_dna_md5sums |
|
|
File |
|
| aligned_normal_dna_table2 |
|
|
File |
|
| aligned_tumor_dna_fastqc_data |
|
|
File[] |
|
| aligned_tumor_dna_table_metrics |
|
|
File |
|
| aligned_tumor_dna_md5sums |
|
|
File |
|
| aligned_tumor_dna_table2 |
|
|
File |
|
| aligned_tumor_rna_fastqc_data |
|
|
File[] |
|
| aligned_tumor_rna_table_metrics |
|
|
File |
|
| aligned_tumor_rna_md5sums |
|
|
File |
|
| aligned_tumor_rna_table3 |
|
|
File |
|
Steps