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Update all nf-core/modules in pipeline #1905

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Update all nf-core/modules in pipeline

Update all nf-core/modules in pipeline #1905

Run time

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Job Run time
Test HISAT2 with workflow parameters (--skip_qc)
11m 42s
Test Salmon with workflow parameters (--skip_qc)
21m 14s
Test STAR RSEM with workflow parameters (--skip_qc)
15m 19s
Test HISAT2 with workflow parameters (--hisat2_index false)
15m 5s
Test Salmon with workflow parameters (--skip_alignment --skip_pseudo_alignment)
6m 55s
Test STAR RSEM with workflow parameters (--rsem_index false)
17m 15s
Test Salmon with workflow parameters (--salmon_index false --transcript_fasta false)
21m 15s
Test STAR Salmon with workflow parameters (--skip_qc)
16m 18s
Run pipeline with test data (23.04.0)
21m 42s
Test STAR Salmon with workflow parameters (--skip_trimming)
19m 50s
Run pipeline with test data (latest-everything)
19m 25s
Test STAR Salmon with workflow parameters (--gtf false)
19m 58s
Test STAR Salmon with workflow parameters (--star_index false)
19m 28s
Test STAR Salmon with workflow parameters (--transcript_fasta false)
24m 59s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
23m 29s
Test STAR Salmon with workflow parameters (--with_umi)
26m 29s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
20m 49s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
45m 21s
Test STAR Salmon with workflow parameters (--bam_csi_index)
20m 30s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
20m 39s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
25m 22s
Test STAR Salmon with workflow parameters (--trimmer fastp)
19m 34s
7h 32m 38s