Fix tags entries and rename pipeline level tests

CHANGELOG.md

@@ -60,31 +60,47 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [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 deseq2qc paths
+- [PR #1252](https://github.com/nf-core/rnaseq/pull/1252) - Fix genomeAttribute usage
 - [PR #1253](https://github.com/nf-core/rnaseq/pull/1253) - Use nf-test files as matrix to test over in CI/CD for efficiency
+- [PR #1260](https://github.com/nf-core/rnaseq/pull/1260) - Update CHANGELOG
 - [PR #1261](https://github.com/nf-core/rnaseq/pull/1261) - Add more tests for PREPARE_GENOME
+- [PR #1262](https://github.com/nf-core/rnaseq/pull/1262) - Fix CI pipeline
+- [PR #1264](https://github.com/nf-core/rnaseq/pull/1264) - Add GHA files back into include statement of Github workflow change detection
 - [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
+- [PR #1271](https://github.com/nf-core/rnaseq/pull/1271) - Update trimming subworkflow to include more tests
+- [PR #1272](https://github.com/nf-core/rnaseq/pull/1272) - Simple pipeline level nf-tests
+- [PR #1274](https://github.com/nf-core/rnaseq/pull/1274) - Update bam_markduplicates_picard subworkflow
 - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow
+- [PR #1279](https://github.com/nf-core/rnaseq/pull/1279) - Add psueudoaligner pipeline level tests to test suite
 - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure
+- [PR #1282](https://github.com/nf-core/rnaseq/pull/1282) - Fix CHANGELOG error
 - [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot
 - [PR #1293](https://github.com/nf-core/rnaseq/pull/1293) - Update subworkflow utils_nfcore_pipeline
 - [PR #1297](https://github.com/nf-core/rnaseq/pull/1297) - Important! Template update for nf-core/tools v2.14.1
 - [PR #1302](https://github.com/nf-core/rnaseq/pull/1302) - Add missing files from Tximport processing
 - [PR #1304](https://github.com/nf-core/rnaseq/pull/1304) - Remove redundant gene TPM outputs
+- [PR #1306](https://github.com/nf-core/rnaseq/pull/1306) - Overhaul strandedness detection / comparison
 - [PR #1307](https://github.com/nf-core/rnaseq/pull/1307) - Clarify infer strandedness step in subway map and text
-- [PR #1317](https://github.com/nf-core/rnaseq/pull/1317) - Strip problematic ifEmpty()
-- [PR #1319](https://github.com/nf-core/rnaseq/pull/1319) - Reinstate oncomplete error messages
-- [PR #1310](https://github.com/nf-core/rnaseq/pull/1310) - Reinstate pseudoalignment subworkflow config
 - [PR #1309](https://github.com/nf-core/rnaseq/pull/1309) - Document FASTP sampling
+- [PR #1310](https://github.com/nf-core/rnaseq/pull/1310) - Reinstate pseudoalignment subworkflow config
 - [PR #1312](https://github.com/nf-core/rnaseq/pull/1312) - Fix issues with unzipping of GTF/ GFF files without absolute paths
+- [PR #1317](https://github.com/nf-core/rnaseq/pull/1317) - Strip problematic ifEmpty()
+- [PR #1319](https://github.com/nf-core/rnaseq/pull/1319) - Reinstate oncomplete error messages
+- [PR #1321](https://github.com/nf-core/rnaseq/pull/1321) - Remove push and release triggers from CI
 - [PR #1322](https://github.com/nf-core/rnaseq/pull/1322) - Use pre-built Github Action to detect nf-test changes
-- [PR #1306](https://github.com/nf-core/rnaseq/pull/1306) - Overhaul strandedness detection / comparison
+- [PR #1323](https://github.com/nf-core/rnaseq/pull/1323) - Update actions/checkout to v4
+- [PR #1324](https://github.com/nf-core/rnaseq/pull/1324) - Fix tags entries and rename pipeline level tests
 
 ### Parameters
 
-| Old parameter | New parameter       |
-| ------------- | ------------------- |
-|               | `--sortmerna_index` |
+| Old parameter      | New parameter                    |
+| ------------------ | -------------------------------- |
+|                    | `--pipelines_testdata_base_path` |
+|                    | `--sortmerna_index`              |
+|                    | `--stranded_threshold`           |
+|                    | `--unstranded_threshold`         |
+| `--test_data_base` |                                  |
 
 ### Software dependencies
 

main.nf

@@ -17,19 +17,19 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.additional_fasta = getGenomeAttribute('additional_fasta')
-params.bbsplit_index    = getGenomeAttribute('bbsplit')
-params.gene_bed         = getGenomeAttribute('bed12')
 params.fasta            = getGenomeAttribute('fasta')
+params.additional_fasta = getGenomeAttribute('additional_fasta')
+params.transcript_fasta = getGenomeAttribute('transcript_fasta')
 params.gff              = getGenomeAttribute('gff')
 params.gtf              = getGenomeAttribute('gtf')
-params.hisat2_index     = getGenomeAttribute('hisat2')
-params.kallisto_index   = getGenomeAttribute('kallisto')
-params.rsem_index       = getGenomeAttribute('rsem')
-params.salmon_index     = getGenomeAttribute('salmon')
+params.gene_bed         = getGenomeAttribute('bed12')
+params.bbsplit_index    = getGenomeAttribute('bbsplit')
 params.sortmerna_index  = getGenomeAttribute('sortmerna')
 params.star_index       = getGenomeAttribute('star')
-params.transcript_fasta = getGenomeAttribute('transcript_fasta')
+params.rsem_index       = getGenomeAttribute('rsem')
+params.hisat2_index     = getGenomeAttribute('hisat2')
+params.salmon_index     = getGenomeAttribute('salmon')
+params.kallisto_index   = getGenomeAttribute('kallisto')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

modules/local/star_align_igenomes/tests/main.nf.test

@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process STAR_ALIGN_IGENOMES"
     script "../main.nf"
     process "STAR_ALIGN_IGENOMES"
-    tag "STAR_ALIGN_IGENOMES"
     tag "STAR_GENOMEGENERATE_IGENOMES"
 
     setup {

nextflow_schema.json

@@ -411,7 +411,7 @@
                 },
                 "min_mapped_reads": {
                     "type": "number",
-                    "default": 5,
+                    "default": 5.0,
                     "fa_icon": "fas fa-percentage",
                     "description": "Minimum percentage of uniquely mapped reads below which samples are removed from further processing.",
                     "help_text": "Some downstream steps in the pipeline will fail if this threshold is too low."

subworkflows/local/align_star/tests/main.nf.test

@@ -4,7 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     workflow "ALIGN_STAR"
     config "./nextflow.config"
-
     tag "STAR_GENOMEGENERATE"
     tag "STAR_GENOMEGENERATE_IGENOMES"
     tag "STAR_ALIGN"

subworkflows/local/prepare_genome/tests/main.nf.test

@@ -4,7 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     workflow "PREPARE_GENOME"
     config "./nextflow.config"
-
     tag "BBMAP_BBSPLIT"
     tag "CUSTOM_CATADDITIONALFASTA"
     tag "CUSTOM_GETCHROMSIZES"
@@ -79,7 +78,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -147,7 +145,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -215,7 +212,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -283,7 +279,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -351,7 +346,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -419,7 +413,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -487,7 +480,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -555,7 +547,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -623,7 +614,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -691,7 +681,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -759,7 +748,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -827,7 +815,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -895,7 +882,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -962,7 +948,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -1030,7 +1015,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -1098,7 +1082,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -1166,7 +1149,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -1234,7 +1216,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -1302,7 +1283,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,
@@ -1370,7 +1350,6 @@ nextflow_workflow {
                     workflow.out.gene_bed,
                     workflow.out.chrom_sizes,
                     workflow.out.splicesites,
-                    // workflow.out.bbsplit_index,
                     workflow.out.sortmerna_index,
                     workflow.out.star_index,
                     workflow.out.rsem_index,

subworkflows/local/quantify_rsem/tests/main.nf.test

@@ -4,7 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     workflow "QUANTIFY_RSEM"
     config "./nextflow.config"
-
     tag "RSEM_PREPAREREFERENCE"
     tag "RSEM_CALCULATEEXPRESSION"
     tag "RSEM_MERGE_COUNTS"

subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf

@@ -552,7 +552,6 @@ def biotypeInGtf(gtf_file, biotype) {
 // Function to determine library type by comparing type counts. Consistent
 // between Salmon and RSeQC
 //
-
 def calculateStrandedness(forwardFragments, reverseFragments, unstrandedFragments, stranded_threshold=0.8, unstranded_threshold=0.1) {
     def totalFragments = forwardFragments + reverseFragments + unstrandedFragments
     def totalStrandedFragments = forwardFragments + reverseFragments
@@ -583,7 +582,6 @@ def calculateStrandedness(forwardFragments, reverseFragments, unstrandedFragment
 //
 // Function that parses Salmon quant 'lib_format_counts.json' output file to get inferred strandedness
 //
-
 def getSalmonInferredStrandedness(json_file, stranded_threshold = 0.8, unstranded_threshold = 0.1) {
     // Parse the JSON content of the file
     def libCounts = new JsonSlurper().parseText(json_file.text)
@@ -610,7 +608,6 @@ def getSalmonInferredStrandedness(json_file, stranded_threshold = 0.8, unstrande
 //
 // Function that parses RSeQC infer_experiment output file to get inferred strandedness
 //
-
 def getInferexperimentStrandedness(inferexperiment_file, stranded_threshold = 0.8, unstranded_threshold = 0.1) {
     def forwardFragments = 0
     def reverseFragments = 0