Read summary
Sample Metadata
| Key | Value |
|---|---|
| sample | porec_test |
| type | test_sample |
| barcode | None |
Software versions
| Name | Version |
|---|---|
| fastcat | 0.15.1 |
| mosdepth | 0.3.6 |
| pairtools | 1.0.2 |
| whatshap | 2.1 |
| pore-c-py | 2.0.6 |
| samtools | 1.17 |
Workflow parameters
| Key | Value |
|---|---|
| help | False |
| version | False |
| bam | wf-pore-c/data/wf-pore-c-demo/porec_test.concatemers.bam |
| fastq | None |
| ref | wf-pore-c/data/wf-pore-c-demo/porec_test.fasta |
| cutter | NlaIII |
| out_dir | wf-pore-c |
| chunk_size | 100 |
| sample | None |
| vcf | wf-pore-c/data/wf-pore-c-demo/porec_test.phased_variants.vcf.gz |
| pairs | False |
| mcool | True |
| mcool_resolutions | 1000,2000,5000N |
| coverage | False |
| minimap2_settings | -x map-ont |
| threads | 4 |
| aws_image_prefix | None |
| aws_queue | None |
| disable_ping | False |
| analyse_unclassified | False |
| monochrome_logs | False |
| validate_params | True |
| show_hidden_params | False |
| schema_ignore_params | show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf |
| chromunity | False |
| chromunity_merge_distance | -1 |
| cool_bin_size | 1000 |
| paired_end | True |
| summary_json | True |
| filter_pairs | False |
| paired_end_minimum_distance | 100 |
| paired_end_maximum_distance | 200 |
| sample_sheet | None |
| hi_c | True |
| bed | False |
| pairtools_chunksize | 100000 |
| max_monomers | 250 |
| wf | {'name': 'wf-pore-c', 'example_cmd': ['--bam wf-pore-c-demo/porec_test.concatemers.bam', '--chunk_size 100', '--cutter NlaIII', '--hi_c', '--mcool', '--paired_end', '--paired_end_maximum_distance 200', '--paired_end_minimum_distance 100', '--phased_vcf wf-pore-c-demo/porec_test.phased_variants.vcf.gz', '--ref wf-pore-c-demo/porec_test.fasta', '--vcf wf-pore-c-demo/porec_test.phased_variants.vcf.gz'], 'common_sha': 'shad399cf22079b5b153920ac39ee40095a677933f1', 'container_sha': 'sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0', 'pore_c_py_sha': 'sha50378db56ddafe19f5e1d313ddb52dc70bbcc2bd', 'agent': 'cw-ci'} |
| store_dir | wf-pore-c/store_dir |