Workflow: Calculate FDA-requested metrics on all aligned and unaligned sequence files
Fetched 2024-08-08 23:39:54 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reference | File | ||
| rna_metrics | File | ||
| rna_RIN_score | String (Optional) | ||
| rna_total_RNA | String (Optional) | ||
| tumor_flagstat | File | ||
| normal_flagstat | File | ||
| rna_sample_name | String (Optional) | ||
| reference_genome | String (Optional) | ||
| tumor_hs_metrics | File | ||
| aligned_tumor_dna | File | ||
| aligned_tumor_rna | File | ||
| normal_hs_metrics | File | ||
| aligned_normal_dna | File | ||
| dna_sequencing_kit | String (Optional) | ||
| rna_sequencing_kit | String (Optional) | ||
| dna_sequencing_type | String (Optional) | ||
| rna_annotation_file | String (Optional) | ||
| rna_sequencing_type | String (Optional) | ||
| tumor_dna_total_DNA | String (Optional) | ||
| unaligned_tumor_dna | https://w3id.org/cwl/view/git/5fda2d9eb52a363bd51011b3851c2afb86318c0c/definitions/types/sequence_data.yml#sequence_data[] | ||
| unaligned_tumor_rna | https://w3id.org/cwl/view/git/5fda2d9eb52a363bd51011b3851c2afb86318c0c/definitions/types/sequence_data.yml#sequence_data[] | ||
| normal_dna_total_DNA | String (Optional) | ||
| unaligned_normal_dna | https://w3id.org/cwl/view/git/5fda2d9eb52a363bd51011b3851c2afb86318c0c/definitions/types/sequence_data.yml#sequence_data[] | ||
| tumor_dna_sample_name | String (Optional) | ||
| normal_dna_sample_name | String (Optional) | ||
| dna_sequencing_platform | String (Optional) | ||
| rna_sequencing_platform | String (Optional) | ||
| rna_spike_in_error_rate | String (Optional) | ||
| dna_single_or_paired_end | String (Optional) | ||
| rna_single_or_paired_end | String (Optional) | ||
| dna_sequencing_instrument | String (Optional) | ||
| rna_sequencing_instrument | String (Optional) | ||
| tumor_duplication_metrics | File | ||
| tumor_insert_size_metrics | File | ||
| normal_duplication_metrics | File | ||
| normal_insert_size_metrics | File | ||
| rna_freq_normalization_method | String (Optional) | ||
| tumor_dna_spike_in_error_rate | String (Optional) | ||
| normal_dna_spike_in_error_rate | String (Optional) | ||
| tumor_alignment_summary_metrics | File | ||
| normal_alignment_summary_metrics | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| aligned_tumor_dna_md5 |
../tools/md5sum.cwl
(CommandLineTool)
|
||
| aligned_tumor_rna_md5 |
../tools/md5sum.cwl
(CommandLineTool)
|
||
| aligned_normal_dna_md5 |
../tools/md5sum.cwl
(CommandLineTool)
|
||
| aligned_tumor_dna_table |
../tools/generate_fda_tables.cwl
(CommandLineTool)
|
Script to create FDA-requested summary tables | |
| aligned_tumor_rna_table |
../tools/generate_fda_tables.cwl
(CommandLineTool)
|
Script to create FDA-requested summary tables | |
| unaligned_tumor_dna_md5 |
../tools/md5sum.cwl
(CommandLineTool)
|
||
| unaligned_tumor_rna_md5 |
../tools/md5sum.cwl
(CommandLineTool)
|
||
| aligned_normal_dna_table |
../tools/generate_fda_tables.cwl
(CommandLineTool)
|
Script to create FDA-requested summary tables | |
| aligned_tumor_dna_fastqc |
../tools/fastqc.cwl
(CommandLineTool)
|
Report metrics on bam or fastq files using fastqc | |
| aligned_tumor_rna_fastqc |
../tools/fastqc.cwl
(CommandLineTool)
|
Report metrics on bam or fastq files using fastqc | |
| unaligned_normal_dna_md5 |
../tools/md5sum.cwl
(CommandLineTool)
|
||
| aligned_normal_dna_fastqc |
../tools/fastqc.cwl
(CommandLineTool)
|
Report metrics on bam or fastq files using fastqc | |
| aligned_tumor_dna_metrics |
../tools/aligned_seq_fda_stats.cwl
(CommandLineTool)
|
||
| aligned_tumor_rna_metrics |
../tools/aligned_seq_fda_stats.cwl
(CommandLineTool)
|
||
| unaligned_tumor_dna_table |
../tools/generate_fda_tables.cwl
(CommandLineTool)
|
Script to create FDA-requested summary tables | |
| unaligned_tumor_rna_table |
../tools/generate_fda_tables.cwl
(CommandLineTool)
|
Script to create FDA-requested summary tables | |
| aligned_normal_dna_metrics |
../tools/aligned_seq_fda_stats.cwl
(CommandLineTool)
|
||
| unaligned_normal_dna_table |
../tools/generate_fda_tables.cwl
(CommandLineTool)
|
Script to create FDA-requested summary tables | |
| unaligned_tumor_dna_fastqc |
../tools/fastqc.cwl
(CommandLineTool)
|
Report metrics on bam or fastq files using fastqc | |
| unaligned_tumor_rna_fastqc |
../tools/fastqc.cwl
(CommandLineTool)
|
Report metrics on bam or fastq files using fastqc | |
| unaligned_normal_dna_fastqc |
../tools/fastqc.cwl
(CommandLineTool)
|
Report metrics on bam or fastq files using fastqc | |
| unaligned_tumor_dna_metrics |
../tools/unaligned_seq_fda_stats.cwl
(CommandLineTool)
|
||
| unaligned_tumor_rna_metrics |
../tools/unaligned_seq_fda_stats.cwl
(CommandLineTool)
|
||
| aligned_tumor_dna_cram_index |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| unaligned_normal_dna_metrics |
../tools/unaligned_seq_fda_stats.cwl
(CommandLineTool)
|
||
| aligned_normal_dna_cram_index |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| aligned_tumor_dna_cram_to_bam |
../tools/cram_to_bam.cwl
(CommandLineTool)
|
samtools view cram to bam | |
| aligned_normal_dna_cram_to_bam |
../tools/cram_to_bam.cwl
(CommandLineTool)
|
samtools view cram to bam | |
| rename_unaligned_tumor_dna_metrics |
../tools/rename_for_staging.cwl
(CommandLineTool)
|
Rename file paths with identical basenames so that output staging works | |
| rename_unaligned_tumor_rna_metrics |
../tools/rename_for_staging.cwl
(CommandLineTool)
|
Rename file paths with identical basenames so that output staging works | |
| rename_unaligned_normal_dna_metrics |
../tools/rename_for_staging.cwl
(CommandLineTool)
|
Rename file paths with identical basenames so that output staging works |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| aligned_tumor_dna_table2 | File | ||
| aligned_tumor_rna_table3 | File | ||
| aligned_normal_dna_table2 | File | ||
| aligned_tumor_dna_md5sums | File | ||
| aligned_tumor_rna_md5sums | File | ||
| aligned_normal_dna_md5sums | File | ||
| unaligned_tumor_dna_table1 | File | ||
| unaligned_tumor_rna_table1 | File | ||
| unaligned_normal_dna_table1 | File | ||
| unaligned_tumor_dna_md5sums | File | ||
| unaligned_tumor_rna_md5sums | File | ||
| unaligned_normal_dna_md5sums | File | ||
| aligned_tumor_dna_fastqc_data | File[] | ||
| aligned_tumor_rna_fastqc_data | File[] | ||
| aligned_normal_dna_fastqc_data | File[] | ||
| aligned_tumor_dna_table_metrics | File | ||
| aligned_tumor_rna_table_metrics | File | ||
| unaligned_tumor_dna_fastqc_data | File[] | ||
| unaligned_tumor_rna_fastqc_data | File[] | ||
| aligned_normal_dna_table_metrics | File | ||
| unaligned_normal_dna_fastqc_data | File[] | ||
| unaligned_tumor_dna_table_metrics | File[] | ||
| unaligned_tumor_rna_table_metrics | File[] | ||
| unaligned_normal_dna_table_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/5fda2d9eb52a363bd51011b3851c2afb86318c0c/definitions/subworkflows/generate_fda_metrics.cwl
