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Delete lib directory and replace with utils_* subworkflows #2161

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Delete lib directory and replace with utils_* subworkflows

Delete lib directory and replace with utils_* subworkflows #2161

Run time

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Job Run time
Run pipeline with test data (23.04.0)
10m 50s
Run pipeline with test data (latest-everything)
10m 10s
Test STAR Salmon with workflow parameters (--skip_qc)
7m 42s
Test STAR Salmon with workflow parameters (--skip_trimming)
10m 2s
Test STAR RSEM with workflow parameters (--skip_qc)
7m 21s
Test STAR Salmon with workflow parameters (--gtf false)
10m 16s
Test STAR RSEM with workflow parameters (--rsem_index false)
9m 40s
Test STAR Salmon with workflow parameters (--star_index false)
10m 32s
Test STAR Salmon with workflow parameters (--transcript_fasta false)
10m 19s
Test HISAT2 with workflow parameters (--skip_qc)
5m 17s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
8m 9s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
9m 56s
Test HISAT2 with workflow parameters (--hisat2_index false)
8m 6s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
3m 58s
Test STAR Salmon with workflow parameters (--with_umi)
11m 24s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
10m 31s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
10m 55s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
7m 48s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
17m 43s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
3m 21s
Test STAR Salmon with workflow parameters (--bam_csi_index)
9m 59s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index false --...
10m 34s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
10m 24s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
10m 12s
Test STAR Salmon with workflow parameters (--trimmer fastp)
10m 17s
3h 55m 26s