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Update sortmerna usage #2290

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Update sortmerna usage

Update sortmerna usage #2290

Run time

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Job Run time
Test STAR RSEM with workflow parameters (--skip_qc)
22s
Test STAR RSEM with workflow parameters (--rsem_index false)
20s
Test STAR Salmon with workflow parameters (--skip_qc)
21s
Test STAR Salmon with workflow parameters (--skip_trimming)
11s
Test HISAT2 with workflow parameters (--skip_qc)
21s
Test STAR Salmon with workflow parameters (--gtf false)
24s
Test HISAT2 with workflow parameters (--hisat2_index false)
22s
Test STAR Salmon with workflow parameters (--star_index false)
21s
Test STAR Salmon with workflow parameters (--transcript_fasta false)
7s
Check for changes
6s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
22s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
22s
Test STAR Salmon with workflow parameters (--with_umi)
2s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
20s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
1s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
22s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
18s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
21s
Test STAR Salmon with workflow parameters (--bam_csi_index)
20s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
21s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index false --...
21s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
21s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
18s
Test STAR Salmon with workflow parameters (--trimmer fastp)
1s
BAM_RSEQC docker NF-23.04.0
1m 20s
RSEQC_JUNCTIONANNOTATION docker NF-23.04.0
58s
FASTQ_FASTQC_UMITOOLS_TRIMGALORE docker NF-23.04.0
1m 43s
SAMTOOLS_IDXSTATS docker NF-23.04.0
49s
SALMON_INDEX docker NF-23.04.0
36s
SAMTOOLS_SORT docker NF-23.04.0
41s
BAM_SORT_STATS_SAMTOOLS docker NF-23.04.0
56s
RSEQC_TIN docker NF-23.04.0
54s
FQ_SUBSAMPLE docker NF-23.04.0
1m 6s
UTILS_NFVALIDATION_PLUGIN docker NF-23.04.0
49s
SAMTOOLS_FLAGSTAT docker NF-23.04.0
44s
MULTIQC docker NF-23.04.0
1m 56s
PIPELINE docker NF-23.04.0
38s
HISAT2_EXTRACTSPLICESITES docker NF-23.04.0
35s
BAM_MARKDUPLICATES_PICARD docker NF-23.04.0
1m 23s
CUSTOM_GETCHROMSIZES docker NF-23.04.0
53s
GUNZIP docker NF-23.04.0
31s
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS docker NF-23.04.0
50s
BAM_STATS_SAMTOOLS docker NF-23.04.0
2m 59s
CAT_FASTQ docker NF-23.04.0
1m 24s
SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT docker NF-23.04.0
3m 40s
UMITOOLS_EXTRACT docker NF-23.04.0
1m 58s
FASTQC docker NF-23.04.0
3m 8s
PRESEQ_LCEXTRAP docker NF-23.04.0
1m 3s
UTILS_NFCORE_PIPELINE docker NF-23.04.0
1m 9s
BBMAP_BBSPLIT docker NF-23.04.0
51s
UTILS_NEXTFLOW_PIPELINE docker NF-23.04.0
1m 14s
RSEQC_INNERDISTANCE docker NF-23.04.0
52s
RSEQC_BAMSTAT docker NF-23.04.0
52s
HISAT2_ALIGN docker NF-23.04.0
2m 8s
SUBREAD_FEATURECOUNTS docker NF-23.04.0
59s
STRINGTIE_STRINGTIE docker NF-23.04.0
1m 22s
UMITOOLS_PREPAREFORRSEM docker NF-23.04.0
1m 4s
CUSTOM_CATADDITIONALFASTA docker NF-23.04.0
33s
RSEQC_READDUPLICATION docker NF-23.04.0
46s
UNTAR docker NF-23.04.0
4m 53s
BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG docker NF-23.04.0
33s
HISAT2_BUILD docker NF-23.04.0
49s
UCSC_BEDCLIP docker NF-23.04.0
40s
PICARD_MARKDUPLICATES docker NF-23.04.0
1m 38s
RSEQC_INFEREXPERIMENT docker NF-23.04.0
57s
TXIMETA_TXIMPORT docker NF-23.04.0
1m 58s
SAMTOOLS_STATS docker NF-23.04.0
1m 5s
CUSTOM_TX2GENE docker NF-23.04.0
58s
UCSC_BEDGRAPHTOBIGWIG docker NF-23.04.0
43s
QUALIMAP_RNASEQ docker NF-23.04.0
1m 6s
KALLISTO_INDEX docker NF-23.04.0
44s
KALLISTO_QUANT docker NF-23.04.0
44s
UMITOOLS_DEDUP docker NF-23.04.0
1m 31s
SALMON_QUANT docker NF-23.04.0
1m 17s
SAMTOOLS_INDEX docker NF-23.04.0
1m 1s
STAR_ALIGN docker NF-23.04.0
8m 53s
FASTQ_ALIGN_HISAT2 docker NF-23.04.0
1m 14s
FASTQ_SUBSAMPLE_FQ_SALMON docker NF-23.04.0
49s
SORTMERNA docker NF-23.04.0
2m 1s
RSEQC_JUNCTIONSATURATION docker NF-23.04.0
49s
RSEM_PREPAREREFERENCE docker NF-23.04.0
52s
GFFREAD docker NF-23.04.0
56s
TRIMGALORE docker NF-23.04.0
1m 59s
RSEM_CALCULATEEXPRESSION docker NF-23.04.0
2m 23s
FASTQ_FASTQC_UMITOOLS_FASTP docker NF-23.04.0
56s
FASTP docker NF-23.04.0
2m 50s
RSEQC_READDISTRIBUTION docker NF-23.04.0
52s
STAR_GENOMEGENERATE docker NF-23.04.0
1m 13s
confirm-pass
1s
1h 36m 34s