- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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