Add cellranger_mkref (#164) #1435

Run time

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Job	Run time
test / List components to test	43s
test / Test (rsem_calculate_expression, rsem, src/rsem/rsem_calculate_expression/config.vsh.yaml, src/rs...	2m 57s
test / Test (rsem_prepare_reference, rsem, src/rsem/rsem_prepare_reference/config.vsh.yaml, src/rsem/rse...	11m 9s
test / Test (trimgalore, src/trimgalore/config.vsh.yaml, src/trimgalore/, bash_script, trimgalore)	1m 0s
test / Test (snpeff, src/snpeff/config.vsh.yaml, src/snpeff/, bash_script, snpeff)	2m 14s
test / Test (nanoplot, src/nanoplot/config.vsh.yaml, src/nanoplot/, bash_script, nanoplot)	3m 3s
test / Test (bbmap_bbsplit, bbmap, src/bbmap/bbmap_bbsplit/config.vsh.yaml, src/bbmap/bbmap_bbsplit/, ba...	3m 37s
test / Test (salmon_quant, salmon, src/salmon/salmon_quant/config.vsh.yaml, src/salmon/salmon_quant/, ba...	1m 16s
test / Test (salmon_index, salmon, src/salmon/salmon_index/config.vsh.yaml, src/salmon/salmon_index/, ba...	1m 54s
test / Test (seqtk_subseq, seqtk, src/seqtk/seqtk_subseq/config.vsh.yaml, src/seqtk/seqtk_subseq/, bash_...	2m 25s
test / Test (seqtk_sample, seqtk, src/seqtk/seqtk_sample/config.vsh.yaml, src/seqtk/seqtk_sample/, bash_...	41s
test / Test (qualimap_rnaseq, qualimap, src/qualimap/qualimap_rnaseq/config.vsh.yaml, src/qualimap/quali...	3m 3s
test / Test (rseqc_inferexperiment, rseqc, src/rseqc/rseqc_inferexperiment/config.vsh.yaml, src/rseqc/rs...	2m 38s
test / Test (rseqc_inner_distance, rseqc, src/rseqc/rseqc_inner_distance/config.vsh.yaml, src/rseqc/rseq...	3m 6s
test / Test (rseqc_bamstat, rseqc, src/rseqc/rseqc_bamstat/config.vsh.yaml, src/rseqc/rseqc_bamstat/, ba...	1m 26s
test / Test (cutadapt, src/cutadapt/config.vsh.yaml, src/cutadapt/, bash_script, cutadapt)	1m 1s
test / Test (bedtools_links, bedtools, src/bedtools/bedtools_links/config.vsh.yaml, src/bedtools/bedtool...	42s
test / Test (bedtools_bed12tobed6, bedtools, src/bedtools/bedtools_bed12tobed6/config.vsh.yaml, src/bedt...	1m 59s
test / Test (bedtools_genomecov, bedtools, src/bedtools/bedtools_genomecov/config.vsh.yaml, src/bedtools...	1m 38s
test / Test (bedtools_sort, bedtools, src/bedtools/bedtools_sort/config.vsh.yaml, src/bedtools/bedtools_...	1m 57s
test / Test (bedtools_groupby, bedtools, src/bedtools/bedtools_groupby/config.vsh.yaml, src/bedtools/bed...	42s
test / Test (bedtools_merge, bedtools, src/bedtools/bedtools_merge/config.vsh.yaml, src/bedtools/bedtool...	44s
test / Test (bedtools_bamtofastq, bedtools, src/bedtools/bedtools_bamtofastq/config.vsh.yaml, src/bedtoo...	42s
test / Test (bedtools_getfasta, bedtools, src/bedtools/bedtools_getfasta/config.vsh.yaml, src/bedtools/b...	54s
test / Test (bedtools_bedtobam, bedtools, src/bedtools/bedtools_bedtobam/config.vsh.yaml, src/bedtools/b...	2m 48s
test / Test (bedtools_intersect, bedtools, src/bedtools/bedtools_intersect/config.vsh.yaml, src/bedtools...	49s
test / Test (bedtools_bamtobed, bedtools, src/bedtools/bedtools_bamtobed/config.vsh.yaml, src/bedtools/b...	2m 2s
test / Test (featurecounts, src/featurecounts/config.vsh.yaml, src/featurecounts/, bash_script, featurec...	3m 9s
test / Test (fastqc, src/fastqc/config.vsh.yaml, src/fastqc/, bash_script, fastqc)	2m 40s
test / Test (multiqc, src/multiqc/config.vsh.yaml, src/multiqc/, bash_script, multiqc)	2m 32s
test / Test (fq_subsample, src/fq_subsample/config.vsh.yaml, src/fq_subsample/, bash_script, fq_subsample)	1m 34s
test / Test (falco, src/falco/config.vsh.yaml, src/falco/, bash_script, falco)	1m 7s
test / Test (bd_rhapsody_sequence_analysis, bd_rhapsody, src/bd_rhapsody/bd_rhapsody_sequence_analysis/c...	11m 3s
test / Test (bd_rhapsody_make_reference, bd_rhapsody, src/bd_rhapsody/bd_rhapsody_make_reference/config....	2m 58s
test / Test (agat_convert_sp_gxf2gxf, agat, src/agat/agat_convert_sp_gxf2gxf/config.vsh.yaml, src/agat/a...	3m 37s
test / Test (agat_sp_merge_annotations, agat, src/agat/agat_sp_merge_annotations/config.vsh.yaml, src/ag...	1m 10s
test / Test (agat_convert_sp_gff2tsv, agat, src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml, src/agat/a...	1m 1s
test / Test (agat_convert_genscan2gff, agat, src/agat/agat_convert_genscan2gff/config.vsh.yaml, src/agat...	1m 2s
test / Test (agat_sp_filter_feature_from_kill_list, agat, src/agat/agat_sp_filter_feature_from_kill_list...	2m 16s
test / Test (agat_sp_add_introns, agat, src/agat/agat_sp_add_introns/config.vsh.yaml, src/agat/agat_sp_a...	1m 1s
test / Test (agat_convert_bed2gff, agat, src/agat/agat_convert_bed2gff/config.vsh.yaml, src/agat/agat_co...	56s
test / Test (agat_sp_statistics, agat, src/agat/agat_sp_statistics/config.vsh.yaml, src/agat/agat_sp_sta...	1m 3s
test / Test (agat_convert_mfannot2gff, agat, src/agat/agat_convert_mfannot2gff/config.vsh.yaml, src/agat...	58s
test / Test (agat_convert_embl2gff, agat, src/agat/agat_convert_embl2gff/config.vsh.yaml, src/agat/agat_...	2m 53s
test / Test (agat_sq_stat_basic, agat, src/agat/agat_sq_stat_basic/config.vsh.yaml, src/agat/agat_sq_sta...	57s
test / Test (agat_convert_sp_gff2gtf, agat, src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml, src/agat/a...	1m 18s
test / Test (cellranger_mkref, cellranger, src/cellranger/cellranger_mkref/config.vsh.yaml, src/cellrang...	1m 22s
test / Test (umi_tools_prepareforrsem, umi_tools, src/umi_tools/umi_tools_prepareforrsem/config.vsh.yaml...	1m 3s
test / Test (umi_tools_extract, umi_tools, src/umi_tools/umi_tools_extract/config.vsh.yaml, src/umi_tool...	55s
test / Test (umi_tools_dedup, umi_tools, src/umi_tools/umi_tools_dedup/config.vsh.yaml, src/umi_tools/um...	2m 42s
test / Test (arriba, src/arriba/config.vsh.yaml, src/arriba/, bash_script, arriba)	1m 24s
test / Test (gffread, src/gffread/config.vsh.yaml, src/gffread/, bash_script, gffread)	47s
test / Test (lofreq_indelqual, lofreq, src/lofreq/indelqual/config.vsh.yaml, src/lofreq/indelqual/, bash...	1m 49s
test / Test (lofreq_call, lofreq, src/lofreq/call/config.vsh.yaml, src/lofreq/call/, bash_script, lofreq...	49s
test / Test (bcl_convert, src/bcl_convert/config.vsh.yaml, src/bcl_convert/, bash_script, bcl_convert)	2m 46s
test / Test (samtools_faidx, samtools, src/samtools/samtools_faidx/config.vsh.yaml, src/samtools/samtool...	43s
test / Test (samtools_collate, samtools, src/samtools/samtools_collate/config.vsh.yaml, src/samtools/sam...	2m 21s
test / Test (samtools_sort, samtools, src/samtools/samtools_sort/config.vsh.yaml, src/samtools/samtools_...	2m 39s
test / Test (samtools_flagstat, samtools, src/samtools/samtools_flagstat/config.vsh.yaml, src/samtools/s...	46s
test / Test (samtools_fastq, samtools, src/samtools/samtools_fastq/config.vsh.yaml, src/samtools/samtool...	41s
test / Test (samtools_view, samtools, src/samtools/samtools_view/config.vsh.yaml, src/samtools/samtools_...	45s
test / Test (samtools_idxstats, samtools, src/samtools/samtools_idxstats/config.vsh.yaml, src/samtools/s...	41s
test / Test (samtools_fasta, samtools, src/samtools/samtools_fasta/config.vsh.yaml, src/samtools/samtool...	36s
test / Test (samtools_stats, samtools, src/samtools/samtools_stats/config.vsh.yaml, src/samtools/samtool...	43s
test / Test (samtools_index, samtools, src/samtools/samtools_index/config.vsh.yaml, src/samtools/samtool...	46s
test / Test (pear, src/pear/config.vsh.yaml, src/pear/, bash_script, pear)	43s
test / Test (kallisto_index, kallisto, src/kallisto/kallisto_index/config.vsh.yaml, src/kallisto/kallist...	1m 56s
test / Test (kallisto_quant, kallisto, src/kallisto/kallisto_quant/config.vsh.yaml, src/kallisto/kallist...	3m 13s
test / Test (star_genome_generate, star, src/star/star_genome_generate/config.vsh.yaml, src/star/star_ge...	5m 7s
test / Test (star_align_reads, star, src/star/star_align_reads/config.vsh.yaml, src/star/star_align_read...	4m 1s
test / Test (busco_list_datasets, busco, src/busco/busco_list_datasets/config.vsh.yaml, src/busco/busco_...	1m 20s
test / Test (busco_download_datasets, busco, src/busco/busco_download_datasets/config.vsh.yaml, src/busc...	1m 24s
test / Test (busco_run, busco, src/busco/busco_run/config.vsh.yaml, src/busco/busco_run/, bash_script, b...	6m 33s
test / Test (fastp, src/fastp/config.vsh.yaml, src/fastp/, bash_script, fastp)	41s
test / Test (bcftools_norm, bcftools, src/bcftools/bcftools_norm/config.vsh.yaml, src/bcftools/bcftools_...	2m 28s
test / Test (bcftools_annotate, bcftools, src/bcftools/bcftools_annotate/config.vsh.yaml, src/bcftools/b...	46s
test / Test (bcftools_concat, bcftools, src/bcftools/bcftools_concat/config.vsh.yaml, src/bcftools/bcfto...	2m 9s
test / Test (bcftools_stats, bcftools, src/bcftools/bcftools_stats/config.vsh.yaml, src/bcftools/bcftool...	1m 13s
test / Test (bcftools_sort, bcftools, src/bcftools/bcftools_sort/config.vsh.yaml, src/bcftools/bcftools_...	1m 44s
test / Test (sortmerna, src/sortmerna/config.vsh.yaml, src/sortmerna/, bash_script, sortmerna)	2m 36s
	2h 40m 37s

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Add cellranger_mkref (#164) #1435

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Add cellranger_mkref (#164) #1435

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