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- bedtools/genomecov
- bracken/bracken
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- cat/fastq
- tests
- custom
- catadditionalfasta/tests
- getchromsizes
- tests
- tx2gene/tests
- dupradar
- tests
- fastp
- tests
- fastqc
- tests
- fq
- lint
- tests
- subsample
- tests
- gffread
- tests
- gunzip
- tests
- hisat2
- align
- tests
- build
- tests
- extractsplicesites
- tests
- kallisto
- index
- tests
- quant
- tests
- kraken2/kraken2
- tests
- multiqc
- tests
- picard/markduplicates
- tests
- preseq/lcextrap
- tests
- qualimap/rnaseq
- tests
- rsem/calculateexpression
- tests
- rseqc
- bamstat
- tests
- inferexperiment
- tests
- innerdistance
- tests
- junctionannotation
- tests
- junctionsaturation
- tests
- readdistribution
- tests
- readduplication
- tests
- tin
- tests
- salmon
- index
- quant
- tests
- samtools
- flagstat
- tests
- idxstats
- tests
- index/tests
- sort/tests
- stats
- tests
- sortmerna
- tests
- star
- align
- genomegenerate
- stringtie/stringtie
- tests
- subread/featurecounts
- tests
- summarizedexperiment/summarizedexperiment
- tests
- trimgalore
- tests
- tximeta/tximport
- tests
- ucsc
- bedclip
- tests
- bedgraphtobigwig
- tests
- umicollapse
- tests
- umitools
- dedup
- tests
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- tests
- prepareforrsem
- tests
- untar
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- subworkflows/nf-core
- bam_dedup_stats_samtools_umicollapse/tests
- bam_dedup_stats_samtools_umitools/tests
- bam_dedup_umi/tests
- bam_markduplicates_picard/tests
- bam_rseqc/tests
- bam_sort_stats_samtools/tests
- bam_stats_samtools/tests
- bedgraph_bedclip_bedgraphtobigwig/tests
- fastq_align_hisat2
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- fastq_fastqc_umitools_fastp
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- fastq_fastqc_umitools_trimgalore
- tests
- fastq_qc_trim_filter_setstrandedness
- tests
- fastq_subsample_fq_salmon/tests
- quantify_pseudo_alignment
- tests
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