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Ensure pseudoaligner is set if pseudoalignment is not skipped #2054

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Ensure pseudoaligner is set if pseudoalignment is not skipped

Ensure pseudoaligner is set if pseudoalignment is not skipped #2054

Run time

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Job Run time
Test STAR RSEM with workflow parameters (--skip_qc)
7m 16s
Test HISAT2 with workflow parameters (--skip_qc)
5m 49s
Test STAR RSEM with workflow parameters (--rsem_index false)
10m 3s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
8m 6s
Test HISAT2 with workflow parameters (--hisat2_index false)
8m 7s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
3m 33s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
10m 46s
Test STAR Salmon with workflow parameters (--skip_qc)
8m 21s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
8m 15s
Run pipeline with test data (23.04.0)
11m 8s
Test STAR Salmon with workflow parameters (--skip_trimming)
10m 59s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
3m 33s
Run pipeline with test data (latest-everything)
10m 53s
Test STAR Salmon with workflow parameters (--gtf false)
10m 34s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index false --...
11m 4s
Test STAR Salmon with workflow parameters (--star_index false)
11m 7s
Test STAR Salmon with workflow parameters (--transcript_fasta false)
11m 13s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
10m 0s
Test STAR Salmon with workflow parameters (--with_umi)
11m 52s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
11m 5s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
18m 27s
Test STAR Salmon with workflow parameters (--bam_csi_index)
10m 50s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
10m 35s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
10m 43s
Test STAR Salmon with workflow parameters (--trimmer fastp)
10m 39s
4h 4m 58s