Merge pull request #1009 from nf-core/dev

Dev -> Master for 3.11.2 release

Author: drpatelh

CHANGELOG.md

@@ -3,6 +3,23 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.11.2](https://github.com/nf-core/rnaseq/releases/tag/3.11.2)] - 2023-04-25
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
+- [W. Lee Pang](https://github.com/wleepang)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [[#1003](https://github.com/nf-core/rnaseq/pull/1003)] - `FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX` is launched multiple times and fails
+
 ## [[3.11.1](https://github.com/nf-core/rnaseq/releases/tag/3.11.1)] - 2023-03-31
 
 ### Credits

conf/test.config

@@ -19,7 +19,9 @@ params {
     max_memory = '6.GB'
     max_time   = '6.h'
 
+
     // Input data
+    // params.test_data_base (default) = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/'
     input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv"
 
     // Genome references

modules.json

@@ -17,7 +17,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "b6d4d476aee074311c89d82a69c1921bd70c8180",
+                        "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b",
                         "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
@@ -77,7 +77,7 @@
                     },
                     "qualimap/rnaseq": {
                         "branch": "master",
-                        "git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6",
+                        "git_sha": "0a9c4eb264cce197707491861ce058a4c79d9c4f",
                         "installed_by": ["modules"]
                     },
                     "rsem/calculateexpression": {

modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

@@ -261,7 +261,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '3.11.1'
+    version         = '3.11.2'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 

modules/nf-core/qualimap/rnaseq/main.nf

@@ -247,6 +247,7 @@ workflow RNASEQ {
     PREPARE_GENOME.out.fasta
         .combine(ch_strand_fastq.auto_strand)
         .map { it.first() }
+        .first()
         .set { ch_genome_fasta }
 
     FASTQ_SUBSAMPLE_FQ_SALMON (
@@ -321,7 +322,7 @@ workflow RNASEQ {
 
     //
     // Get list of samples that failed trimming threshold for MultiQC report
-    //        
+    //
     ch_trim_read_count
         .map {
             meta, num_reads ->
@@ -332,7 +333,7 @@ workflow RNASEQ {
                 }
         }
         .collect()
-        .map { 
+        .map {
             tsv_data ->
                 def header = ["Sample", "Reads after trimming"]
                 WorkflowRnaseq.multiqcTsvFromList(tsv_data, header)
@@ -604,7 +605,7 @@ workflow RNASEQ {
         ch_pass_fail_mapped
             .fail
             .collect()
-            .map { 
+            .map {
                 tsv_data ->
                     def header = ["Sample", "STAR uniquely mapped reads (%)"]
                     WorkflowRnaseq.multiqcTsvFromList(tsv_data, header)
@@ -765,7 +766,7 @@ workflow RNASEQ {
             ch_versions = ch_versions.mix(BAM_RSEQC.out.versions)
 
             ch_inferexperiment_multiqc
-                .map { 
+                .map {
                     meta, strand_log ->
                         def inferred_strand = WorkflowRnaseq.getInferexperimentStrandedness(strand_log, 30)
                         pass_strand_check[meta.id] = true
@@ -775,7 +776,7 @@ workflow RNASEQ {
                         }
                 }
                 .collect()
-                .map { 
+                .map {
                     tsv_data ->
                         def header = [
                             "Sample",