Add nf-test for all components in pipeline

[maxulysse]

Tests for components from nf-core modules

• Merging Add all nf-core modules and CI/CD and all nf-tests to everything #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:

• my_module (@drpatelh; #1213411)

modules

• bedtools_genomecov MIGRATE - @pinin4fjords Migrate bedtools/genome_cov to nf-core/modules #1161 Switch to genomecov from nf-core  #1234
• deseq2_qc @adamrtalbot Add nf-tests for deseq2_qc local module #1241
• deseq2_qc @adamrtalbot proper file paths Replace deseq2qc paths #1251
• dupradar MIGRATE - @pinin4fjords Migrate DUPRADAR to nf-core/modules #1164 Add new dupradar module with tests modules#5075 Swtich to dupradar from nf-core #1242
• gtf2bed - @pinin4fjords Migrate gtf2bed to nf-core/modules #1165 Add gtf2bed tests #1244
• gtf_filter @adamrtalbot Add nf-test to local module GTF_FILTER #1236
• multiqc_custom_biotype @adamrtalbot nf-test for module MULTIQC_CUSTOM_BIOTYPE #1243
• preprocess_transcripts_fasta_gencode @adamrtalbot nf-test for PREPROCESS_TRANSCRIPTS_FASTA_GENCODE #1238
• rsem_merge_counts @robsyme Include nf-tests for rsem_merge_counts module #1249
• star_align_igenomes - @maxulysse add nf-tests for star_align_igenomes #1233
• star_genomegenerate_igenomes - @maxulysse Adding tests for star_genomegenerate_igenomes #1232

subworkflows

• align_star - @maxulysse - ALIGN_STAR - add nf-test tests #1239
• prepare_genome - @maxulysse - nf-test prepare_genome #1247
• quantify_pseudo_alignment @adamrtalbot nf-test quantify pseudoalignment #1246
• quantify_rsem @adamrtalbot nf test quantify rsem #1245
• utils_nfcore_rnaseq_pipeline @adamrtalbot nf-test: utils_nfcore_rnaseq_pipeline tests #1235

Workflow(s)

• workflow/rnaseq.nf