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Add all nf-core modules and CI/CD and all nf-tests to everything #2288

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Add all nf-core modules and CI/CD and all nf-tests to everything

Add all nf-core modules and CI/CD and all nf-tests to everything #2288

Run time

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Job Run time
Test STAR RSEM with workflow parameters (--skip_qc)
7m 40s
Test STAR Salmon with workflow parameters (--skip_qc)
7m 47s
Test STAR RSEM with workflow parameters (--rsem_index false)
9m 56s
Check for changes
7s
Test STAR Salmon with workflow parameters (--skip_trimming)
10m 39s
Test HISAT2 with workflow parameters (--skip_qc)
5m 39s
Test STAR Salmon with workflow parameters (--gtf false)
10m 31s
Test HISAT2 with workflow parameters (--hisat2_index false)
7m 49s
Test STAR Salmon with workflow parameters (--star_index false)
10m 22s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
8m 11s
Test STAR Salmon with workflow parameters (--transcript_fasta false)
11m 1s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
3m 43s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
13m 46s
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
10m 6s
Test STAR Salmon with workflow parameters (--with_umi)
11m 1s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
7m 44s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
11m 8s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
3m 46s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
17m 19s
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index false --...
10m 21s
Test STAR Salmon with workflow parameters (--bam_csi_index)
10m 8s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
10m 31s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
10m 9s
Test STAR Salmon with workflow parameters (--trimmer fastp)
9m 52s
UCSC_BEDGRAPHTOBIGWIG docker NF-23.04.0
39s
RSEQC_BAMSTAT docker NF-23.04.0
44s
UTILS_NEXTFLOW_PIPELINE docker NF-23.04.0
1m 6s
RSEQC_TIN docker NF-23.04.0
48s
UMITOOLS_PREPAREFORRSEM docker NF-23.04.0
56s
PIPELINE docker NF-23.04.0
10m 34s
BAM_RSEQC docker NF-23.04.0
1m 5s
SAMTOOLS_IDXSTATS docker NF-23.04.0
47s
RSEQC_INNERDISTANCE docker NF-23.04.0
1m 3s
SAMTOOLS_STATS docker NF-23.04.0
3m 41s
HISAT2_BUILD docker NF-23.04.0
46s
SALMON_INDEX docker NF-23.04.0
50s
FASTP docker NF-23.04.0
2m 26s
FASTQC docker NF-23.04.0
3m 10s
PICARD_MARKDUPLICATES docker NF-23.04.0
1m 25s
UMITOOLS_DEDUP docker NF-23.04.0
1m 25s
SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT docker NF-23.04.0
3m 25s
UCSC_BEDCLIP docker NF-23.04.0
31s
CAT_FASTQ docker NF-23.04.0
1m 13s
TRIMGALORE docker NF-23.04.0
2m 0s
BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG docker NF-23.04.0
42s
SUBREAD_FEATURECOUNTS docker NF-23.04.0
53s
RSEQC_READDUPLICATION docker NF-23.04.0
53s
QUALIMAP_RNASEQ docker NF-23.04.0
1m 49s
STAR_ALIGN docker NF-23.04.0
8m 20s
HISAT2_EXTRACTSPLICESITES docker NF-23.04.0
35s
RSEM_PREPAREREFERENCE docker NF-23.04.0
49s
SAMTOOLS_INDEX docker NF-23.04.0
1m 6s
RSEM_CALCULATEEXPRESSION docker NF-23.04.0
2m 44s
CUSTOM_CATADDITIONALFASTA docker NF-23.04.0
43s
BAM_STATS_SAMTOOLS docker NF-23.04.0
2m 34s
SAMTOOLS_FLAGSTAT docker NF-23.04.0
42s
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS docker NF-23.04.0
1m 0s
RSEQC_INFEREXPERIMENT docker NF-23.04.0
47s
PRESEQ_LCEXTRAP docker NF-23.04.0
41s
MULTIQC docker NF-23.04.0
1m 33s
TXIMETA_TXIMPORT docker NF-23.04.0
1m 45s
UTILS_NFCORE_PIPELINE docker NF-23.04.0
1m 16s
UTILS_NFVALIDATION_PLUGIN docker NF-23.04.0
54s
GFFREAD docker NF-23.04.0
44s
STAR_GENOMEGENERATE docker NF-23.04.0
1m 6s
RSEQC_READDISTRIBUTION docker NF-23.04.0
55s
FQ_SUBSAMPLE docker NF-23.04.0
1m 7s
SORTMERNA docker NF-23.04.0
2m 1s
KALLISTO_INDEX docker NF-23.04.0
42s
FASTQ_SUBSAMPLE_FQ_SALMON docker NF-23.04.0
1m 2s
FASTQ_FASTQC_UMITOOLS_FASTP docker NF-23.04.0
54s
UNTAR docker NF-23.04.0
5m 11s
CUSTOM_TX2GENE docker NF-23.04.0
1m 2s
RSEQC_JUNCTIONANNOTATION docker NF-23.04.0
46s
BAM_SORT_STATS_SAMTOOLS docker NF-23.04.0
1m 4s
KALLISTO_QUANT docker NF-23.04.0
58s
BBMAP_BBSPLIT docker NF-23.04.0
47s
UMITOOLS_EXTRACT docker NF-23.04.0
1m 49s
FASTQ_FASTQC_UMITOOLS_TRIMGALORE docker NF-23.04.0
1m 44s
RSEQC_JUNCTIONSATURATION docker NF-23.04.0
50s
GUNZIP docker NF-23.04.0
42s
SAMTOOLS_SORT docker NF-23.04.0
46s
STRINGTIE_STRINGTIE docker NF-23.04.0
1m 5s
SALMON_QUANT docker NF-23.04.0
1m 25s
CUSTOM_GETCHROMSIZES docker NF-23.04.0
43s
HISAT2_ALIGN docker NF-23.04.0
1m 25s
FASTQ_ALIGN_HISAT2 docker NF-23.04.0
1m 10s
BAM_MARKDUPLICATES_PICARD docker NF-23.04.0
1m 22s
confirm-pass
1s
5h 18m 57s