subworkflows_generate_fda_metrics.cwl
APipe Tester edited this page Dec 12, 2022
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Calculate FDA-requested metrics on all aligned and unaligned sequence files
| 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? |
| 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 |
| Name | CWL Run |
|---|---|
| unaligned_normal_dna_fastqc | tools/fastqc.cwl |
| unaligned_normal_dna_metrics | tools/unaligned_seq_fda_stats.cwl |
| rename_unaligned_normal_dna_metrics | tools/rename_for_staging.cwl |
| unaligned_normal_dna_md5 | tools/md5sum.cwl |
| unaligned_normal_dna_table | tools/generate_fda_tables.cwl |
| unaligned_tumor_dna_fastqc | tools/fastqc.cwl |
| unaligned_tumor_dna_metrics | tools/unaligned_seq_fda_stats.cwl |
| rename_unaligned_tumor_dna_metrics | tools/rename_for_staging.cwl |
| unaligned_tumor_dna_md5 | tools/md5sum.cwl |
| unaligned_tumor_dna_table | tools/generate_fda_tables.cwl |
| unaligned_tumor_rna_fastqc | tools/fastqc.cwl |
| unaligned_tumor_rna_metrics | tools/unaligned_seq_fda_stats.cwl |
| rename_unaligned_tumor_rna_metrics | tools/rename_for_staging.cwl |
| unaligned_tumor_rna_md5 | tools/md5sum.cwl |
| unaligned_tumor_rna_table | tools/generate_fda_tables.cwl |
| aligned_normal_dna_cram_index | tools/index_cram.cwl |
| aligned_normal_dna_cram_to_bam | tools/cram_to_bam.cwl |
| aligned_normal_dna_fastqc | tools/fastqc.cwl |
| aligned_normal_dna_metrics | tools/aligned_seq_fda_stats.cwl |
| aligned_normal_dna_md5 | tools/md5sum.cwl |
| aligned_normal_dna_table | tools/generate_fda_tables.cwl |
| aligned_tumor_dna_cram_index | tools/index_cram.cwl |
| aligned_tumor_dna_cram_to_bam | tools/cram_to_bam.cwl |
| aligned_tumor_dna_fastqc | tools/fastqc.cwl |
| aligned_tumor_dna_metrics | tools/aligned_seq_fda_stats.cwl |
| aligned_tumor_dna_md5 | tools/md5sum.cwl |
| aligned_tumor_dna_table | tools/generate_fda_tables.cwl |
| aligned_tumor_rna_fastqc | tools/fastqc.cwl |
| aligned_tumor_rna_metrics | tools/aligned_seq_fda_stats.cwl |
| aligned_tumor_rna_md5 | tools/md5sum.cwl |
| aligned_tumor_rna_table | tools/generate_fda_tables.cwl |