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Reorganise arguments for clearer syntax #1896

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Reorganise arguments for clearer syntax

Reorganise arguments for clearer syntax #1896

Run time

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Job Run time
Run pipeline with test data (23.04.0)
13m 57s
Run pipeline with test data (latest-everything)
13m 59s
Test HISAT2 with workflow parameters (--skip_qc)
11m 55s
Test Salmon with workflow parameters (--skip_qc)
13m 50s
Test STAR RSEM with workflow parameters (--skip_qc)
13m 50s
Test HISAT2 with workflow parameters (--hisat2_index false)
13m 57s
Test Salmon with workflow parameters (--skip_alignment --skip_pseudo_alignment)
6m 3s
Test STAR RSEM with workflow parameters (--rsem_index false)
13m 56s
Test Salmon with workflow parameters (--salmon_index false --transcript_fasta false)
13m 57s
Test STAR Salmon with workflow parameters (--skip_qc)
13m 8s
Test STAR Salmon with workflow parameters (--skip_trimming)
13m 7s
Test STAR Salmon with workflow parameters (--gtf false)
13m 37s
Test STAR Salmon with workflow parameters (--star_index false)
13m 3s
Test STAR Salmon with workflow parameters (--transcript_fasta false)
13m 8s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
13m 35s
Test STAR Salmon with workflow parameters (--with_umi)
13m 5s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
13m 7s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
13m 20s
Test STAR Salmon with workflow parameters (--bam_csi_index)
13m 47s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
13m 7s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
13m 46s
Test STAR Salmon with workflow parameters (--trimmer fastp)
13m 7s
4h 48m 21s