Merge pull request #1261 from adamrtalbot/dev

Add more tests for PREPARE_GENOME

Author: adamrtalbot

.github/workflows/ci.yml

@@ -28,9 +28,6 @@ jobs:
         parameters:
           - "--skip_qc"
           - "--skip_trimming"
-          - "--gtf false"
-          - "--star_index false"
-          - "--transcript_fasta false"
           - "--min_mapped_reads 90"
           - "--with_umi"
           - "--with_umi --skip_trimming"
@@ -59,7 +56,6 @@ jobs:
       matrix:
         parameters:
           - "--skip_qc"
-          - "--rsem_index false"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4
@@ -79,7 +75,6 @@ jobs:
       matrix:
         parameters:
           - "--skip_qc"
-          - "--hisat2_index false"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4
@@ -100,10 +95,8 @@ jobs:
         parameters:
           - "--pseudo_aligner salmon --skip_qc"
           - "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
-          - "--pseudo_aligner salmon --salmon_index false --transcript_fasta false"
           - "--pseudo_aligner kallisto --skip_qc"
           - "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
-          - "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4

CHANGELOG.md

@@ -58,7 +58,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1247](https://github.com/nf-core/rnaseq/pull/1247) - nf-test prepare_genome
 - [PR #1249](https://github.com/nf-core/rnaseq/pull/1249) - Include nf-tests for rsem_merge_counts module
 - [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed
-- [PR #1251](https://github.com/nf-core/rnaseq/pull/1251) - Replace deseq2_qc paths
+- [PR #1251](https://github.com/nf-core/rnaseq/pull/1251) - Replace deseq2qc paths
+- [PR #1261](https://github.com/nf-core/rnaseq/pull/1261) - Add more tests for PREPARE_GENOME
 - [PR #1265](https://github.com/nf-core/rnaseq/pull/1265) - Small updates noticed during code review
 - [PR #1266](https://github.com/nf-core/rnaseq/pull/1266) - Delete unecessary tags from nf.test files for modules and subworkflows
 

subworkflows/local/prepare_genome/main.nf

@@ -51,7 +51,7 @@ workflow PREPARE_GENOME {
     salmon_index             // directory: /path/to/salmon/index/
     kallisto_index           // directory: /path/to/kallisto/index/
     hisat2_index             // directory: /path/to/hisat2/index/
-    bbsplit_index            // directory: /path/to/rsem/index/
+    bbsplit_index            // directory: /path/to/bbsplit/index/
     sortmerna_index          // directory: /path/to/sortmerna/index/
     gencode                  //   boolean: whether the genome is from GENCODE
     featurecounts_group_type //    string: The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts