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Merge branch 'feat-2-0' into update-star/align

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nf-core linting on: pull_request 2

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nf-core

nf-test on: pull_request 139

nf-test tests (23.04.3, docker, test, genome_no_chrom_sizes)

nf-test tests (23.04.3, docker, test, genome_fasta_raw)

nf-test tests (23.04.3, docker, test, genome_fasta_gz)

nf-test tests (23.04.3, docker, test, genome_fasta_fai)

nf-test tests (23.04.3, docker, test, genome_ncrna_fasta_gz)

nf-test tests (23.04.3, docker, test, genome_ncrna_fasta)

nf-test tests (23.04.3, docker, test, genome_ncrna_fasta_fai)

nf-test tests (23.04.3, docker, test, genome_gtf_raw)

nf-test tests (23.04.3, docker, test, genome_gtf_gz)

nf-test tests (23.04.3, docker, test, genome_gtf_filt)

nf-test tests (23.04.3, docker, test, genome_gtf_filt_seg)

nf-test tests (23.04.3, docker, test, genome_gtf_seg)

nf-test tests (23.04.3, docker, test, genome_gtf_resolve_unanno)

nf-test tests (23.04.3, docker, test, genome_gtf_resolve_unanno_region)

nf-test tests (23.04.3, docker, test, genome_gtf_resolve_unanno_genic)

nf-test tests (23.04.3, docker, test, genome_gtf_resolve_unanno_region_genic)

nf-test tests (23.04.3, docker, test, genome_star_build_index)

nf-test tests (23.04.3, docker, test, genome_bt_build_index)

nf-test tests (23.04.3, docker, test, genome_no_longest_transcript)

nf-test tests (23.04.3, docker, test, genome_preset)

nf-test tests (23.04.3, docker, test, only_input_primary)

nf-test tests (23.04.3, docker, test, only_preprocessing_primary)

nf-test tests (23.04.3, docker, test, only_preprocessing_skip_fastqc)

nf-test tests (23.04.3, docker, test, only_preprocessing_skip_umi_extract)

nf-test tests (23.04.3, docker, test, only_preprocessing_skip_trimming)

nf-test tests (23.04.3, docker, test, only_alignment_primary)

nf-test tests (23.04.3, docker, test, only_alignment_false_outputs)

nf-test tests (23.04.3, docker, test, only_dedup_primary)

nf-test tests (23.04.3, docker, test, only_crosslinking_primary)

nf-test tests (23.04.3, docker, test, only_peakcalling_primary)

nf-test tests (23.04.3, docker, test, only_peakcalling_caller_param_fail)

nf-test tests (23.04.3, docker, test, only_peakcalling_clippy)

nf-test tests (23.04.3, docker, test, only_peakcalling_icount)

nf-test tests (23.04.3, docker, test, only_peakcalling_paraclu)

nf-test tests (23.04.3, docker, test, only_peakcalling_paraclu_clippy)

nf-test tests (latest-everything, docker, test, genome_no_chrom_sizes)

nf-test tests (latest-everything, docker, test, genome_fasta_raw)

nf-test tests (latest-everything, docker, test, genome_fasta_gz)

nf-test tests (latest-everything, docker, test, genome_fasta_fai)

nf-test tests (latest-everything, docker, test, genome_ncrna_fasta_gz)

nf-test tests (latest-everything, docker, test, genome_ncrna_fasta)

nf-test tests (latest-everything, docker, test, genome_ncrna_fasta_fai)

nf-test tests (latest-everything, docker, test, genome_gtf_raw)

nf-test tests (latest-everything, docker, test, genome_gtf_gz)

nf-test tests (latest-everything, docker, test, genome_gtf_filt)

nf-test tests (latest-everything, docker, test, genome_gtf_filt_seg)

nf-test tests (latest-everything, docker, test, genome_gtf_seg)

nf-test tests (latest-everything, docker, test, genome_gtf_resolve_unanno)

nf-test tests (latest-everything, docker, test, genome_gtf_resolve_unanno_region)

nf-test tests (latest-everything, docker, test, genome_gtf_resolve_unanno_genic)

nf-test tests (latest-everything, docker, test, genome_gtf_resolve_unanno_region_genic)

nf-test tests (latest-everything, docker, test, genome_star_build_index)

nf-test tests (latest-everything, docker, test, genome_bt_build_index)

nf-test tests (latest-everything, docker, test, genome_no_longest_transcript)

nf-test tests (latest-everything, docker, test, genome_preset)

nf-test tests (latest-everything, docker, test, only_input_primary)

nf-test tests (latest-everything, docker, test, only_preprocessing_primary)

nf-test tests (latest-everything, docker, test, only_preprocessing_skip_fastqc)

nf-test tests (latest-everything, docker, test, only_preprocessing_skip_umi_extract)

nf-test tests (latest-everything, docker, test, only_preprocessing_skip_trimming)

nf-test tests (latest-everything, docker, test, only_alignment_primary)

nf-test tests (latest-everything, docker, test, only_alignment_false_outputs)

nf-test tests (latest-everything, docker, test, only_dedup_primary)

nf-test tests (latest-everything, docker, test, only_crosslinking_primary)

nf-test tests (latest-everything, docker, test, only_peakcalling_primary)

nf-test tests (latest-everything, docker, test, only_peakcalling_caller_param_fail)

nf-test tests (latest-everything, docker, test, only_peakcalling_clippy)

nf-test tests (latest-everything, docker, test, only_peakcalling_icount)

nf-test tests (latest-everything, docker, test, only_peakcalling_paraclu)

nf-test tests (latest-everything, docker, test, only_peakcalling_paraclu_clippy)

nf-core CI on: pull_request 3

Run pipeline with test data (24.04.2 | test | docker)

Run pipeline with test data (latest-everything | test | docker)

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