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Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage #1981

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Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage

Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage #1981

Run time

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Job Run time
Test HISAT2 with workflow parameters (--skip_qc)
6m 7s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
7m 56s
Test HISAT2 with workflow parameters (--hisat2_index false)
8m 21s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
3m 41s
Test STAR RSEM with workflow parameters (--skip_qc)
7m 9s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
10m 51s
Test STAR RSEM with workflow parameters (--rsem_index false)
9m 54s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
8m 19s
Test STAR Salmon with workflow parameters (--skip_qc)
8m 30s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
3m 42s
Test STAR Salmon with workflow parameters (--skip_trimming)
10m 33s
Run pipeline with test data (23.04.0)
11m 4s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index false --...
10m 43s
Test STAR Salmon with workflow parameters (--gtf false)
10m 49s
Run pipeline with test data (latest-everything)
11m 10s
Test STAR Salmon with workflow parameters (--star_index false)
10m 38s
Test STAR Salmon with workflow parameters (--transcript_fasta false)
10m 55s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
9m 50s
Test STAR Salmon with workflow parameters (--with_umi)
12m 9s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
11m 26s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
19m 15s
Test STAR Salmon with workflow parameters (--bam_csi_index)
10m 33s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
11m 5s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
10m 45s
Test STAR Salmon with workflow parameters (--trimmer fastp)
10m 8s
4h 5m 33s