Add nf-test for all components in pipeline

[maxulysse]

Tests for components from nf-core modules

• [x] Merging #1221 should add tests for all nf-core/modules, nf-core/subworkflows and pipeline level tests. (see comment)

Tests for local components

Please edit this comment and assign yourself to the component you will be adding tests for and link in the PR. For example:

• [x] my_module (@drpatelh; #1213411)

modules

• [x] bedtools_genomecov MIGRATE - @pinin4fjords https://github.com/nf-core/rnaseq/issues/1161 https://github.com/nf-core/rnaseq/pull/1234
• [x] deseq2_qc @adamrtalbot https://github.com/nf-core/rnaseq/pull/1241
• [x] deseq2_qc @adamrtalbot proper file paths https://github.com/nf-core/rnaseq/pull/1251
• [x] dupradar MIGRATE - @pinin4fjords https://github.com/nf-core/rnaseq/issues/1164 https://github.com/nf-core/modules/pull/5075 https://github.com/nf-core/rnaseq/pull/1242
• [x] gtf2bed - @pinin4fjords https://github.com/nf-core/rnaseq/issues/1165 https://github.com/nf-core/rnaseq/pull/1244
• [x] gtf_filter @adamrtalbot https://github.com/nf-core/rnaseq/pull/1236
• [x] multiqc_custom_biotype @adamrtalbot https://github.com/nf-core/rnaseq/pull/1243
• [x] preprocess_transcripts_fasta_gencode @adamrtalbot https://github.com/nf-core/rnaseq/pull/1238
• [x] rsem_merge_counts @robsyme https://github.com/nf-core/rnaseq/pull/1249
• [x] star_align_igenomes - @maxulysse https://github.com/nf-core/rnaseq/pull/1233
• [x] star_genomegenerate_igenomes - @maxulysse https://github.com/nf-core/rnaseq/pull/1232

subworkflows

• [x] align_star - @maxulysse - https://github.com/nf-core/rnaseq/pull/1239
• [x] prepare_genome - @maxulysse - https://github.com/nf-core/rnaseq/pull/1247
• [x] quantify_pseudo_alignment @adamrtalbot https://github.com/nf-core/rnaseq/pull/1246
• [x] quantify_rsem @adamrtalbot https://github.com/nf-core/rnaseq/pull/1245
• [x] utils_nfcore_rnaseq_pipeline @adamrtalbot https://github.com/nf-core/rnaseq/pull/1235

Workflow(s)

• [ ] workflow/rnaseq.nf