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umccr / cwl-ica

A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guide
MIT License
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Reduce step names to 21 characters for ICAv2 compatibility #159

Closed alexiswl closed 1 year ago

alexiswl commented 1 year ago

See https://github.com/umccr-illumina/ica_v2/issues/116 for more information.

Will complete a full list of steps that exceed this length.

21 characters is the upper limit for steps that are subject to scatter. This includes steps that may not be a scatter step themselves but may be part of a subworkflow that is scattered. For steps that are scattered less than 10 times, this limit may be extended to 23 characters.

If a step is in no way scattered, its name may extend up to 25 characters.

Placed the issue here so I can run a full sweep of our existing workflows in this repository to see which workflows contain steps that violate this rule.

Will also create a PR to the cwl-ica-cli repo that warns users if a step name for a workflow contains more than 21 characters

alexiswl commented 1 year ago

workflows/bcl-conversion/3.7.5/bcl-conversion__3.7.5.cwl

2022-10-30 10:55:06,249 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 10:55:06,249 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'flatten_fastq_list_rows_array' is greater than 21 characters.
2022-10-30 10:55:06,249 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'samplesheet_split_by_settings_step' is greater than 21 characters.

workflows/bclconvert-scatter/4.0.3/bclconvert-scatter__4.0.3.cwl

2022-10-30 10:55:56,538 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'bcl_convert_samplesheet_check_scatter_step' is greater than 21 characters.
2022-10-30 10:55:56,538 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'bcl_convert_scatter_step' is greater than 21 characters.
2022-10-30 10:55:56,538 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'flatten_fastq_list_rows_array_step' is greater than 21 characters.
2022-10-30 10:55:56,538 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_bcl_convert_run_configuration_object_step' is greater than 21 characters.

workflows/bclconvert-with-qc-pipeline/4.0.3/bclconvert-with-qc-pipeline__4.0.3.cwl

2022-10-30 10:56:38,514 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.

workflows/dragen-alignment-pipeline/3.7.5/dragen-alignment-pipeline__3.7.5.cwl

2022-10-30 10:57:22,666 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 10:57:22,666 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_fastq_list_csv_step' is greater than 21 characters.
2022-10-30 10:57:22,666 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_alignment_step' is greater than 21 characters.

workflows/dragen-alignment-pipeline/3.9.3/dragen-alignment-pipeline__3.9.3.cwl

2022-10-30 10:57:49,906 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 10:57:49,906 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_alignment_step' is greater than 21 characters.

workflows/dragen-germline-pipeline/3.7.5/dragen-germline-pipeline__3.7.5.cwl

2022-10-30 10:58:11,457 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 10:58:11,458 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_fastq_list_csv_step' is greater than 21 characters.
2022-10-30 10:58:11,458 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_germline_step' is greater than 21 characters.

workflows/dragen-germline-pipeline/3.9.3/dragen-germline-pipeline__3.9.3.cwl

2022-10-30 10:58:32,012 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 10:58:32,012 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_germline_step' is greater than 21 characters.

workflows/dragen-pon-qc/3.9.3/dragen-pon-qc__3.9.3.cwl

2022-10-30 10:58:32,929 - WARNING  - cwl                       - check_id_conformance                     : LineNo. 355  - Found inputs 'GC_depth' uses chars 'C, G' that aren't recommended in names of inputs
2022-10-30 10:59:03,518 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_somatic_step' is greater than 21 characters.

workflows/dragen-qc-hla-pipeline/3.7.5--1.3.5/dragen-qc-hla-pipeline__3.7.5--1.3.5.cwl

2022-10-30 10:59:56,715 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 10:59:56,715 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_hla_regions_bed_step' is greater than 21 characters.

workflows/dragen-somatic-pipeline/3.7.5/dragen-somatic-pipeline__3.7.5.cwl

2022-10-30 11:00:23,305 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 11:00:23,305 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_fastq_list_csv_step' is greater than 21 characters.
2022-10-30 11:00:23,305 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_tumor_fastq_list_csv_step' is greater than 21 characters.
2022-10-30 11:00:23,305 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_somatic_step' is greater than 21 characters.

workflows/dragen-somatic-pipeline/3.9.3/dragen-somatic-pipeline__3.9.3.cwl

2022-10-30 11:00:47,817 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 11:00:47,817 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_somatic_step' is greater than 21 characters.

workflows/dragen-transcriptome-pipeline/3.7.5/dragen-transcriptome-pipeline__3.7.5.cwl

2022-10-30 11:01:11,807 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_arriba_output_directory' is greater than 21 characters.
2022-10-30 11:01:11,808 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 11:01:11,808 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_fastq_list_csv_step' is greater than 21 characters.
2022-10-30 11:01:11,808 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_transcriptome_step' is greater than 21 characters.

workflows/dragen-transcriptome-pipeline/3.8.4/dragen-transcriptome-pipeline__3.8.4.cwl

2022-10-30 11:01:56,314 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_arriba_output_directory' is greater than 21 characters.
2022-10-30 11:01:56,314 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 11:01:56,314 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_fastq_list_csv_step' is greater than 21 characters.
2022-10-30 11:01:56,314 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_transcriptome_step' is greater than 21 characters.

workflows/dragen-transcriptome-pipeline/3.9.3/dragen-transcriptome-pipeline__3.9.3.cwl

2022-10-30 11:02:23,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_arriba_output_directory' is greater than 21 characters.
2022-10-30 11:02:23,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 11:02:23,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_transcriptome_step' is greater than 21 characters.

workflows/dragen-wts-qc-pipeline/3.9.3/dragen-wts-qc-pipeline__3.9.3.cwl

2022-10-30 11:03:39,543 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_transcriptome_step' is greater than 21 characters.

workflows/get-hla-regions-bed/1.0.0/get-hla-regions-bed__1.0.0.cwl

2022-10-30 11:04:03,361 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_contig_obj_for_chr6_step' is greater than 21 characters.
2022-10-30 11:04:03,361 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_regions_bed_for_chr_6_hla_region_step' is greater than 21 characters.
2022-10-30 11:04:03,361 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_regions_bed_for_hla_contigs_step' is greater than 21 characters.

workflows/ghif-qc/1.0.0/ghif-qc__1.0.0.cwl

2022-10-30 11:04:04,786 - WARNING  - cwl                       - check_id_conformance                     : LineNo. 355  - Found inputs 'GC_depth' uses chars 'C, G' that aren't recommended in names of inputs

workflows/ghif-qc/1.0.1/ghif-qc__1.0.1.cwl

2022-10-30 11:04:29,768 - WARNING  - cwl                       - check_id_conformance                     : LineNo. 355  - Found inputs 'GC_depth' uses chars 'G, C' that aren't recommended in names of inputs
2022-10-30 11:04:57,369 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'calculate_coverage_step' is greater than 21 characters.

workflows/optitype-pipeline/1.3.5/optitype-pipeline__1.3.5.cwl

2022-10-30 11:05:17,648 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_bam_slice_from_bed_step' is greater than 21 characters.
2022-10-30 11:05:17,648 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_unmapped_file_from_sorted_bam_step' is greater than 21 characters.
2022-10-30 11:05:17,648 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'merge_hla_and_unmapped_bam_files_step' is greater than 21 characters.
2022-10-30 11:05:17,648 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'sort_merged_bam_by_name_step' is greater than 21 characters.
2022-10-30 11:05:17,648 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'unmapped_and_hla_bam_to_fastq_step' is greater than 21 characters.

workflows/tso500-ctdna/1.1.0--120/tso500-ctdna__1.1.0--120.cwl

2022-10-30 11:05:43,754 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'add_sample_type_and_pair_id_to_samplesheet_step' is greater than 21 characters.
2022-10-30 11:05:43,754 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'assert_all_samples_passing' is greater than 21 characters.
2022-10-30 11:05:43,754 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_cttso_outputs_by_sample' is greater than 21 characters.
2022-10-30 11:05:43,754 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_tso500_ctdna_analysis_workflow_step' is greater than 21 characters.
2022-10-30 11:05:43,754 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_tso500_ctdna_demultiplex_workflow_step' is greater than 21 characters.
2022-10-30 11:05:43,754 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_tso500_ctdna_reporting_workflow_step' is greater than 21 characters.

workflows/tso500-ctdna-post-processing-pipeline/1.0.0/tso500-ctdna-post-processing-pipeline__1.0.0.cwl

2022-10-30 11:06:32,480 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'compress_reporting_jsons_with_gzip_step' is greater than 21 characters.
2022-10-30 11:06:32,480 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'compress_vcf_files_step' is greater than 21 characters.
2022-10-30 11:06:32,480 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'convert_metric_csvs_into_json_gzip_step' is greater than 21 characters.
2022-10-30 11:06:32,480 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_custom_output_entry_list_array_step' is greater than 21 characters.
2022-10-30 11:06:32,480 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_file_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_output_directory' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'dragen_metrics_to_json_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'gather_compressed_metric_json_files_into_tar_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'gather_compressed_reporting_json_files_into_tar_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'gather_compressed_vcf_files_into_tar_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_align_collapse_fusion_caller_metrics_csv_files_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_fragment_length_hist_csv_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_fusion_csv_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_msi_json_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_one_val_for_skip_rows_parameter' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_raw_bam_file_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_sample_analysis_results_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tmb_json_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tmb_trace_tsv_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,481 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_vcf_files_intermediate_step' is greater than 21 characters.
2022-10-30 11:06:32,482 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_zero_val_for_skip_rows_parameter' is greater than 21 characters.
2022-10-30 11:06:32,482 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'make_exon_coverage_qc_step' is greater than 21 characters.
2022-10-30 11:06:32,482 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'make_per_coverage_threshold_qc_step' is greater than 21 characters.
2022-10-30 11:06:32,482 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_multiqc_on_align_collapse_fusion_caller_dir_step' is greater than 21 characters.

workflows/tso500-ctdna-with-post-processing-pipeline/1.1.0--1.0.0/tso500-ctdna-with-post-processing-pipeline__1.1.0--1.0.0.cwl

2022-10-30 11:07:31,209 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_final_output_directory' is greater than 21 characters.
2022-10-30 11:07:31,209 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_final_directory_output_for_tso500_pipeline' is greater than 21 characters.
2022-10-30 11:07:31,209 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_intermediate_samplesheet_from_validation_step' is greater than 21 characters.
2022-10-30 11:07:31,209 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_sample_ids_from_tso500_sample_object' is greater than 21 characters.
2022-10-30 11:07:31,209 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_sample_output_directory' is greater than 21 characters.
2022-10-30 11:07:31,209 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tso_manifest_bed_from_resources_dir' is greater than 21 characters.
2022-10-30 11:07:31,209 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_tso_ctdna_post_processing_workflow_step' is greater than 21 characters.
2022-10-30 11:07:31,210 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_tso_ctdna_workflow_step' is greater than 21 characters.

workflows/umccrise-pipeline/1.2.1--0/umccrise-pipeline__1.2.1--0.cwl

2022-10-30 11:07:48,256 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_mount_paths_and_umccrise_tsv_input_jsons_step' is greater than 21 characters.
2022-10-30 11:07:48,257 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_umccrise_tsv_step' is greater than 21 characters.

workflows/umccrise-pipeline/1.2.2--0/umccrise-pipeline__1.2.2--0.cwl

2022-10-30 11:08:06,092 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_mount_paths_and_umccrise_tsv_input_jsons_step' is greater than 21 characters.
2022-10-30 11:08:06,092 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_umccrise_tsv_step' is greater than 21 characters.

workflows/umccrise-with-dragen-germline-pipeline/2.0.0--3.9.3/umccrise-with-dragen-germline-pipeline__2.0.0--3.9.3.cwl

2022-10-30 11:08:28,044 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_bam_file_from_somatic_directory' is greater than 21 characters.
2022-10-30 11:08:28,044 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_name_from_bam_header' is greater than 21 characters.
2022-10-30 11:08:28,044 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_germline_pipeline_step' is greater than 21 characters.
2022-10-30 11:08:28,044 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_umccrise_pipeline_step' is greater than 21 characters.

workflows/umccrise-with-dragen-germline-pipeline/2.0.1--3.9.3/umccrise-with-dragen-germline-pipeline__2.0.1--3.9.3.cwl

2022-10-30 11:08:49,134 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_bam_file_from_somatic_directory' is greater than 21 characters.
2022-10-30 11:08:49,134 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_name_from_bam_header' is greater than 21 characters.
2022-10-30 11:08:49,134 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_germline_pipeline_step' is greater than 21 characters.
2022-10-30 11:08:49,134 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_umccrise_pipeline_step' is greater than 21 characters.

workflows/umccrise-with-dragen-germline-pipeline/2.0.2--3.9.3/umccrise-with-dragen-germline-pipeline__2.0.2--3.9.3.cwl

2022-10-30 11:09:11,271 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_bam_file_from_somatic_directory' is greater than 21 characters.
2022-10-30 11:09:11,271 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_name_from_bam_header' is greater than 21 characters.
2022-10-30 11:09:11,271 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_germline_pipeline_step' is greater than 21 characters.
2022-10-30 11:09:11,271 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_umccrise_pipeline_step' is greater than 21 characters.

workflows/umccrise-with-dragen-germline-pipeline/2.1.0--3.9.3/umccrise-with-dragen-germline-pipeline__2.1.0--3.9.3.cwl

2022-10-30 11:09:32,971 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_bam_file_from_somatic_directory' is greater than 21 characters.
2022-10-30 11:09:32,971 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_name_from_bam_header' is greater than 21 characters.
2022-10-30 11:09:32,971 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_germline_pipeline_step' is greater than 21 characters.
2022-10-30 11:09:32,971 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_umccrise_pipeline_step' is greater than 21 characters.

workflows/umccrise-with-dragen-germline-pipeline/2.1.1--3.9.3/umccrise-with-dragen-germline-pipeline__2.1.1--3.9.3.cwl

2022-10-30 11:09:54,242 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_bam_file_from_somatic_directory' is greater than 21 characters.
2022-10-30 11:09:54,242 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_tumor_name_from_bam_header' is greater than 21 characters.
2022-10-30 11:09:54,242 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_dragen_germline_pipeline_step' is greater than 21 characters.
2022-10-30 11:09:54,242 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'run_umccrise_pipeline_step' is greater than 21 characters.

workflows/validate-bclconvert-samplesheet/4.0.3/validate-bclconvert-samplesheet__4.0.3.cwl

2022-10-30 11:10:19,406 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'bcl_convert_samplesheet_check_step' is greater than 21 characters.
2022-10-30 11:10:19,406 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'create_dummy_directory_step' is greater than 21 characters.
2022-10-30 11:10:19,406 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_bcl_convert_run_configuration_object_step' is greater than 21 characters.
2022-10-30 11:10:19,406 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_run_info_file_from_directory_expression_step' is greater than 21 characters.
2022-10-30 11:10:19,407 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 103  - Step name 'get_samplesheet_file_from_directory_expression_step' is greater than 21 characters.
alexiswl commented 1 year ago

Increasing to 23 characters and only selecting steps that invoke a tool we get a slightly lower amount

workflows/bcl-conversion/3.7.5/bcl-conversion__3.7.5.cwl

2022-10-31 17:17:27,033 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'samplesheet_split_by_settings_step' is greater than 23 characters

workflows/dragen-alignment-pipeline/3.7.5/dragen-alignment-pipeline__3.7.5.cwl

2022-10-31 17:17:54,138 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_fastq_list_csv_step' is greater than 23 characters
2022-10-31 17:17:54,161 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_alignment_step' is greater than 23 characters

workflows/dragen-alignment-pipeline/3.9.3/dragen-alignment-pipeline__3.9.3.cwl

2022-10-31 17:19:03,805 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_alignment_step' is greater than 23 characters

workflows/dragen-germline-pipeline/3.7.5/dragen-germline-pipeline__3.7.5.cwl

2022-10-31 17:20:01,761 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_fastq_list_csv_step' is greater than 23 characters
2022-10-31 17:20:01,791 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters

workflows/dragen-germline-pipeline/3.9.3/dragen-germline-pipeline__3.9.3.cwl

2022-10-31 17:20:56,414 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters

workflows/dragen-pon-qc/3.9.3/dragen-pon-qc__3.9.3.cwl

workflows/dragen-qc-hla-pipeline/3.7.5--1.3.5/dragen-qc-hla-pipeline__3.7.5--1.3.5.cwl

2022-10-31 17:24:05,491 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_fastq_list_csv_step' is greater than 23 characters
2022-10-31 17:24:05,518 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters
2022-10-31 17:24:05,641 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_regions_bed_for_chr_6_hla_region_step' is greater than 23 characters
2022-10-31 17:24:05,656 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_regions_bed_for_hla_contigs_step' is greater than 23 characters
2022-10-31 17:24:05,724 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_bam_slice_from_bed_step' is greater than 23 characters
2022-10-31 17:24:05,741 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_unmapped_file_from_sorted_bam_step' is greater than 23 characters
2022-10-31 17:24:05,757 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'merge_hla_and_unmapped_bam_files_step' is greater than 23 characters
2022-10-31 17:24:05,790 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'sort_merged_bam_by_name_step' is greater than 23 characters
2022-10-31 17:24:05,822 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'unmapped_and_hla_bam_to_fastq_step' is greater than 23 characters

workflows/dragen-somatic-pipeline/3.7.5/dragen-somatic-pipeline__3.7.5.cwl

2022-10-31 17:24:52,379 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_fastq_list_csv_step' is greater than 23 characters
2022-10-31 17:24:52,400 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_tumor_fastq_list_csv_step' is greater than 23 characters

workflows/dragen-somatic-pipeline/3.9.3/dragen-somatic-pipeline__3.9.3.cwl

workflows/dragen-transcriptome-pipeline/3.7.5/dragen-transcriptome-pipeline__3.7.5.cwl

2022-10-31 17:27:36,311 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_arriba_output_directory' is greater than 23 characters
2022-10-31 17:27:36,336 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_fastq_list_csv_step' is greater than 23 characters
2022-10-31 17:27:36,362 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_transcriptome_step' is greater than 23 characters

workflows/dragen-transcriptome-pipeline/3.8.4/dragen-transcriptome-pipeline__3.8.4.cwl

2022-10-31 17:28:41,746 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_arriba_output_directory' is greater than 23 characters
2022-10-31 17:28:41,773 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_fastq_list_csv_step' is greater than 23 characters
2022-10-31 17:28:41,802 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_transcriptome_step' is greater than 23 characters

workflows/dragen-transcriptome-pipeline/3.9.3/dragen-transcriptome-pipeline__3.9.3.cwl

2022-10-31 17:29:49,058 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_arriba_output_directory' is greater than 23 characters
2022-10-31 17:29:49,097 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_transcriptome_step' is greater than 23 characters

workflows/dragen-wgs-qc-pipeline/3.7.5/dragen-wgs-qc-pipeline__3.7.5.cwl

2022-10-31 17:31:18,031 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_fastq_list_csv_step' is greater than 23 characters
2022-10-31 17:31:18,059 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_alignment_step' is greater than 23 characters

workflows/dragen-wgs-qc-pipeline/3.9.3/dragen-wgs-qc-pipeline__3.9.3.cwl

2022-10-31 17:31:55,131 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_alignment_step' is greater than 23 characters

workflows/dragen-wts-qc-pipeline/3.9.3/dragen-wts-qc-pipeline__3.9.3.cwl

2022-10-31 17:32:27,072 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_transcriptome_step' is greater than 23 characters

workflows/get-hla-regions-bed/1.0.0/get-hla-regions-bed__1.0.0.cwl

2022-10-31 17:33:08,682 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_regions_bed_for_chr_6_hla_region_step' is greater than 23 characters
2022-10-31 17:33:08,721 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_regions_bed_for_hla_contigs_step' is greater than 23 characters

workflows/ghif-qc/1.0.0/ghif-qc__1.0.0.cwl

workflows/ghif-qc/1.0.1/ghif-qc__1.0.1.cwl

workflows/optitype-pipeline/1.3.5/optitype-pipeline__1.3.5.cwl

2022-10-31 17:35:31,295 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_bam_slice_from_bed_step' is greater than 23 characters
2022-10-31 17:35:31,309 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_unmapped_file_from_sorted_bam_step' is greater than 23 characters
2022-10-31 17:35:31,324 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'merge_hla_and_unmapped_bam_files_step' is greater than 23 characters
2022-10-31 17:35:31,367 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'sort_merged_bam_by_name_step' is greater than 23 characters
2022-10-31 17:35:31,403 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'unmapped_and_hla_bam_to_fastq_step' is greater than 23 characters

workflows/tso500-ctdna/1.1.0--120/tso500-ctdna__1.1.0--120.cwl

2022-10-31 17:36:45,662 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'add_sample_type_and_pair_id_to_samplesheet_step' is greater than 23 characters
2022-10-31 17:36:45,706 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_tso500_ctdna_analysis_workflow_step' is greater than 23 characters
2022-10-31 17:36:45,724 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_tso500_ctdna_demultiplex_workflow_step' is greater than 23 characters
2022-10-31 17:36:45,746 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_tso500_ctdna_reporting_workflow_step' is greater than 23 characters

workflows/tso500-ctdna-post-processing-pipeline/1.0.0/tso500-ctdna-post-processing-pipeline__1.0.0.cwl

2022-10-31 17:38:54,642 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'compress_reporting_jsons_with_gzip_step' is greater than 23 characters
2022-10-31 17:38:54,680 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'convert_metric_csvs_into_json_gzip_step' is greater than 23 characters
2022-10-31 17:38:54,766 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'dragen_metrics_to_json_step' is greater than 23 characters
2022-10-31 17:38:54,784 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'gather_compressed_metric_json_files_into_tar_step' is greater than 23 characters
2022-10-31 17:38:54,806 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'gather_compressed_reporting_json_files_into_tar_step' is greater than 23 characters
2022-10-31 17:38:54,828 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'gather_compressed_vcf_files_into_tar_step' is greater than 23 characters
2022-10-31 17:38:55,084 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'make_exon_coverage_qc_step' is greater than 23 characters
2022-10-31 17:38:55,110 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'make_per_coverage_threshold_qc_step' is greater than 23 characters
2022-10-31 17:38:55,173 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_multiqc_on_align_collapse_fusion_caller_dir_step' is greater than 23 characters

workflows/tso500-ctdna-with-post-processing-pipeline/1.1.0--1.0.0/tso500-ctdna-with-post-processing-pipeline__1.1.0--1.0.0.cwl

2022-10-31 17:45:20,622 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_final_output_directory' is greater than 23 characters
2022-10-31 17:46:12,997 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'add_sample_type_and_pair_id_to_samplesheet_step' is greater than 23 characters
2022-10-31 17:46:13,081 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_tso500_ctdna_analysis_workflow_step' is greater than 23 characters
2022-10-31 17:46:13,106 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_tso500_ctdna_demultiplex_workflow_step' is greater than 23 characters
2022-10-31 17:46:13,129 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_tso500_ctdna_reporting_workflow_step' is greater than 23 characters
2022-10-31 17:46:13,512 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'compress_reporting_jsons_with_gzip_step' is greater than 23 characters
2022-10-31 17:46:13,555 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'convert_metric_csvs_into_json_gzip_step' is greater than 23 characters
2022-10-31 17:46:13,667 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'dragen_metrics_to_json_step' is greater than 23 characters
2022-10-31 17:46:13,685 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'gather_compressed_metric_json_files_into_tar_step' is greater than 23 characters
2022-10-31 17:46:13,704 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'gather_compressed_reporting_json_files_into_tar_step' is greater than 23 characters
2022-10-31 17:46:13,728 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'gather_compressed_vcf_files_into_tar_step' is greater than 23 characters
2022-10-31 17:46:13,960 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'make_exon_coverage_qc_step' is greater than 23 characters
2022-10-31 17:46:13,979 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'make_per_coverage_threshold_qc_step' is greater than 23 characters
2022-10-31 17:46:14,019 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_multiqc_on_align_collapse_fusion_caller_dir_step' is greater than 23 characters

workflows/umccrise-pipeline/1.2.1--0/umccrise-pipeline__1.2.1--0.cwl

2022-10-31 17:47:28,932 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_umccrise_tsv_step' is greater than 23 characters

workflows/umccrise-pipeline/1.2.2--0/umccrise-pipeline__1.2.2--0.cwl

2022-10-31 17:48:20,087 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'create_umccrise_tsv_step' is greater than 23 characters

workflows/umccrise-with-dragen-germline-pipeline/2.0.0--3.9.3/umccrise-with-dragen-germline-pipeline__2.0.0--3.9.3.cwl

2022-10-31 17:49:14,292 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_tumor_name_from_bam_header' is greater than 23 characters
2022-10-31 17:49:14,323 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_umccrise_pipeline_step' is greater than 23 characters
2022-10-31 17:49:28,813 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters

workflows/umccrise-with-dragen-germline-pipeline/2.0.1--3.9.3/umccrise-with-dragen-germline-pipeline__2.0.1--3.9.3.cwl

2022-10-31 17:50:09,462 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_tumor_name_from_bam_header' is greater than 23 characters
2022-10-31 17:50:09,490 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_umccrise_pipeline_step' is greater than 23 characters
2022-10-31 17:50:25,008 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters

workflows/umccrise-with-dragen-germline-pipeline/2.0.2--3.9.3/umccrise-with-dragen-germline-pipeline__2.0.2--3.9.3.cwl

2022-10-31 17:51:04,614 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_tumor_name_from_bam_header' is greater than 23 characters
2022-10-31 17:51:04,650 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_umccrise_pipeline_step' is greater than 23 characters
2022-10-31 17:51:19,967 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters

workflows/umccrise-with-dragen-germline-pipeline/2.1.0--3.9.3/umccrise-with-dragen-germline-pipeline__2.1.0--3.9.3.cwl

2022-10-31 17:51:55,384 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_tumor_name_from_bam_header' is greater than 23 characters
2022-10-31 17:51:55,414 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_umccrise_pipeline_step' is greater than 23 characters
2022-10-31 17:52:10,323 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters

workflows/umccrise-with-dragen-germline-pipeline/2.1.1--3.9.3/umccrise-with-dragen-germline-pipeline__2.1.1--3.9.3.cwl

2022-10-31 17:52:46,137 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_tumor_name_from_bam_header' is greater than 23 characters
2022-10-31 17:52:46,168 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_umccrise_pipeline_step' is greater than 23 characters
2022-10-31 17:53:01,123 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters

workflows/umccrise-with-dragen-germline-pipeline/2.2.0--3.9.3/umccrise-with-dragen-germline-pipeline__2.2.0--3.9.3.cwl

2022-10-31 17:53:37,885 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_tumor_name_from_bam_header' is greater than 23 characters
2022-10-31 17:53:37,920 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_umccrise_pipeline_step' is greater than 23 characters
2022-10-31 17:53:56,561 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters

workflows/umccrise-with-dragen-germline-pipeline/2.2.1--3.9.3/umccrise-with-dragen-germline-pipeline__2.2.1--3.9.3.cwl

2022-10-31 17:54:36,645 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'get_tumor_name_from_bam_header' is greater than 23 characters
2022-10-31 17:54:36,674 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_umccrise_pipeline_step' is greater than 23 characters
2022-10-31 17:54:52,636 - WARNING  - cwl_workflow_helper_utils - check_workflow_step_lengths              : LineNo. 109  - Step name 'run_dragen_germline_step' is greater than 23 characters
alexiswl commented 1 year ago

Have added this warning to the cwl-ica icav2-zip-workflow subcommand in https://github.com/umccr/cwl-ica-cli/pull/69

alexiswl commented 1 year ago

So happy to adjust workflows as required rather than edit everything in existence.

alexiswl commented 1 year ago

Closing this, will update workflows as we move them to v2 on a case-by-case basis.