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lines changed- modules/nf-core
- bbmap/bbsplit
- tests
- bedtools/genomecov
- bracken/bracken
- tests
- cat/fastq
- tests
- custom
- catadditionalfasta
- templates
- tests
- getchromsizes
- tests
- tx2gene
- tests
- dupradar
- fastp
- fq/subsample
- tests
- gffread
- gunzip
- hisat2
- align
- build
- extractsplicesites
- kallisto
- index
- tests
- quant
- tests
- kraken2/kraken2
- tests
- preseq/lcextrap
- tests
- qualimap/rnaseq
- rsem
- calculateexpression
- preparereference
- rseqc
- bamstat
- tests
- inferexperiment
- innerdistance
- junctionannotation
- junctionsaturation
- readdistribution
- readduplication
- tin
- salmon
- index
- tests
- quant
- tests
- samtools
- flagstat
- tests
- idxstats
- tests
- index
- tests
- sort
- tests
- stats
- tests
- sortmerna
- tests
- star
- align
- tests
- genomegenerate
- stringtie/stringtie
- tests
- subread/featurecounts
- tests
- summarizedexperiment/summarizedexperiment
- tests
- trimgalore
- tests
- tximeta/tximport
- ucsc
- bedclip
- bedgraphtobigwig
- tests
- umitools
- dedup
- prepareforrsem
- untar
- subworkflows
- local
- align_star/tests
- prepare_genome/tests
- quantify_rsem/tests
- nf-core
- bam_dedup_stats_samtools_umitools/tests
- bam_markduplicates_picard/tests
- bam_sort_stats_samtools/tests
- bam_stats_samtools/tests
- bedgraph_bedclip_bedgraphtobigwig/tests
- fastq_align_hisat2/tests
- fastq_fastqc_umitools_fastp/tests
- fastq_fastqc_umitools_trimgalore/tests
- fastq_subsample_fq_salmon/tests
- quantify_pseudo_alignment/tests
- utils_nfschema_plugin/tests
- tests
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