Merge pull request #1008 from drpatelh/updates

Small fixes for 3.11.2 patch release

Author: drpatelh

CHANGELOG.md

@@ -3,10 +3,20 @@
 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).
 
-## [Unpublished Version / DEV]
+## [[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 code contributions to the release:
+
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
+- [W. Lee Pang](https://github.com/wleepang)
 
 ### 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

@@ -19,29 +19,21 @@ params {
     max_memory = '6.GB'
     max_time   = '6.h'
 
+
     // Input data
-    // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/samplesheet/v3.10/samplesheet_test.csv
+    // 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
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/genome.fasta
     fasta              = "${params.test_data_base}/reference/genome.fasta"
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz
     gtf                = "${params.test_data_base}/reference/genes.gtf.gz"
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz
     gff                = "${params.test_data_base}/reference/genes.gff.gz"
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta
     transcript_fasta   = "${params.test_data_base}/reference/transcriptome.fasta"
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz
     additional_fasta   = "${params.test_data_base}/reference/gfp.fa.gz"
 
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt
     bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt"
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz
     hisat2_index       = "${params.test_data_base}/reference/hisat2.tar.gz"
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz
     salmon_index       = "${params.test_data_base}/reference/salmon.tar.gz"
-    //                   https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz
     rsem_index         = "${params.test_data_base}/reference/rsem.tar.gz"
 
     // Other parameters

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         = '3.12.0dev'
+    version         = '3.11.2'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }