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Update trimming subworkflow to include more tests #2459

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Update trimming subworkflow to include more tests

Update trimming subworkflow to include more tests #2459

Run time

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Job Run time
Test STAR Salmon with workflow parameters (--skip_qc)
1m 4s
Test STAR Salmon with workflow parameters (--skip_qc)
7m 44s
Test STAR Salmon with workflow parameters (--skip_trimming)
1m 8s
Test STAR Salmon with workflow parameters (--skip_trimming)
9m 50s
Test STAR RSEM with workflow parameters (--skip_qc)
5m 39s
Test STAR RSEM with workflow parameters (--skip_qc)
7m 4s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
45s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
9m 29s
Test STAR Salmon with workflow parameters (--with_umi)
1m 5s
Test STAR Salmon with workflow parameters (--with_umi)
10m 49s
Test HISAT2 with workflow parameters (--skip_qc)
5m 37s
Test HISAT2 with workflow parameters (--skip_qc)
6m 1s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
49s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
10m 37s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
1m 4s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
12m 39s
Test STAR Salmon with workflow parameters (--bam_csi_index)
1m 2s
Test STAR Salmon with workflow parameters (--bam_csi_index)
10m 16s
Check for changes
10s
Check for changes
10s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
1m 13s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
10m 32s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
1m 15s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
10m 23s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
51s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
7m 45s
Test STAR Salmon with workflow parameters (--trimmer fastp)
1m 33s
Test STAR Salmon with workflow parameters (--trimmer fastp)
9m 34s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
1m 9s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
3m 32s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
1m 9s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
7m 50s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
1m 7s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
4m 8s
FASTP docker NF-23.04.0
5m 35s
FASTP docker NF-23.04.0
5m 35s
FASTQ_FASTQC_UMITOOLS_FASTP docker NF-23.04.0
3m 16s
FASTQ_FASTQC_UMITOOLS_FASTP docker NF-23.04.0
3m 16s
confirm-pass
1s
confirm-pass
1s
3h 2m 47s