Workflow: transform.cwl
Fetched 2023-01-12 05:47:25 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
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- Default Values
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| sqlite_file | File | ||
| exp_count_readgroups | Integer | ||
| sql_count_readgroups | String | ||
| exp_count_fastq_files | Integer | ||
| sql_count_fastq_files | String | ||
| exp_count_files_output | Integer | ||
| sql_count_files_output | String | ||
| exp_seqs_samtools_stats | Integer | ||
| sql_seqs_samtools_stats | String | ||
| exp_reads_dup_samtools_stats | Integer | ||
| exp_reads_mq0_samtools_stats | Integer | ||
| sql_reads_dup_samtools_stats | String | ||
| sql_reads_mq0_samtools_stats | String | ||
| exp_reads_paired_samtool_stats | Integer | ||
| sql_reads_paired_samtool_stats | String | ||
| exp_bases_mapped_samtools_stats | Integer | ||
| exp_reads_mapped_samtools_stats | Integer | ||
| exp_total_length_samtools_stats | Integer | ||
| sql_bases_mapped_samtools_stats | String | ||
| sql_reads_mapped_samtools_stats | String | ||
| sql_total_length_samtools_stats | String | ||
| exp_raw_total_seq_samtools_stats | Integer | ||
| exp_read_unmapped_samtools_stats | Integer | ||
| sql_raw_total_seq_samtools_stats | String | ||
| sql_read_unmapped_samtools_stats | String | ||
| exp_pairs_diff_chr_samtools_stats | Integer | ||
| sql_pairs_diff_chr_samtools_stats | String | ||
| exp_average_quality_samtools_stats | Double | ||
| sql_average_quality_samtools_stats | String | ||
| exp_bases_duplicated_samtools_stats | Integer | ||
| sql_bases_duplicated_samtools_stats | String | ||
| exp_read_pairs_picard_markduplicates | Integer | ||
| exp_reads_prop_paired_samtools_stats | Integer | ||
| sql_read_pairs_picard_markduplicates | String | ||
| sql_reads_prop_paired_samtools_stats | String | ||
| exp_pairs_other_orient_samtools_stats | Integer | ||
| sql_pairs_other_orient_samtools_stats | String | ||
| exp_read_pair_dups_picard_markduplicates | Integer | ||
| sql_read_pair_dups_picard_markduplicates | String | ||
| exp_reads_mapped_and_paired_samtools_stats | Integer | ||
| sql_reads_mapped_and_paired_samtools_stats | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| test_count_readgroups |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/test_int.cwl
(CommandLineTool)
|
||
| test_count_fastq_files |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/test_int.cwl
(CommandLineTool)
|
||
| sqlite_count_readgroups |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/get_int_sqlite.cwl
(CommandLineTool)
|
||
| test_count_files_output |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/test_int.cwl
(CommandLineTool)
|
||
| sqlite_count_fastq_files |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/get_int_sqlite.cwl
(CommandLineTool)
|
||
| sqlite_count_files_output |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/get_int_sqlite.cwl
(CommandLineTool)
|
||
| tests_logical_conjunction |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/logical_conjunction_expression.cwl
(ExpressionTool)
|
||
| test_bases_mapped_samtools_stats |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/test_int.cwl
(CommandLineTool)
|
||
| test_reads_mapped_samtools_stats |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/test_int.cwl
(CommandLineTool)
|
||
| sqlite_bases_mapped_samtools_stats |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/get_int_sqlite.cwl
(CommandLineTool)
|
||
| sqlite_reads_mapped_samtools_stats |
/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/tools/get_int_sqlite.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| tests_logical_conjunction_result | Boolean |
Permalink:
https://w3id.org/cwl/view/git/b110a23e2efaaadfd4feca4f9e130946d1c5418d/workflows/dnaseq/validate/transform.cwl
