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update config to enable usage of a custom config #1955

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update config to enable usage of a custom config

update config to enable usage of a custom config #1955

Run time

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Job Run time
Run pipeline with test data (23.04.0)
11m 3s
Run pipeline with test data (latest-everything)
10m 51s
Test STAR RSEM with workflow parameters (--skip_qc)
17m 49s
Test Salmon with workflow parameters (--skip_qc)
8m 17s
Test STAR RSEM with workflow parameters (--rsem_index false)
9m 52s
Test HISAT2 with workflow parameters (--skip_qc)
11m 29s
Test Salmon with workflow parameters (--skip_alignment --skip_pseudo_alignment)
6m 1s
Test HISAT2 with workflow parameters (--hisat2_index false)
16m 40s
Test Salmon with workflow parameters (--salmon_index false --transcript_fasta false)
25m 37s
Test STAR Salmon with workflow parameters (--skip_qc)
8m 10s
Test STAR Salmon with workflow parameters (--skip_trimming)
19m 57s
Test STAR Salmon with workflow parameters (--gtf false)
21m 16s
Test STAR Salmon with workflow parameters (--star_index false)
10m 37s
Test STAR Salmon with workflow parameters (--transcript_fasta false)
21m 46s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
19m 25s
Test STAR Salmon with workflow parameters (--with_umi)
12m 0s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
11m 17s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
50m 10s
Test STAR Salmon with workflow parameters (--bam_csi_index)
10m 22s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
25m 19s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
19m 8s
Test STAR Salmon with workflow parameters (--trimmer fastp)
10m 46s
5h 57m 52s