Fix #922

Author: drpatelh

CHANGELOG.md

@@ -3,11 +3,12 @@
 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](https://github.com/nf-core/rnaseq/releases/tag/3.11)] - 2023-01-05
+## [[3.10.1](https://github.com/nf-core/rnaseq/releases/tag/3.10.1)] - 2023-01-05
 
 ### Enhancements & fixes
 
 - [[#919](https://github.com/nf-core/rnaseq/issues/919)] - Salmon quant not run after FastQ subsampling if index not provided
+- [[#922](https://github.com/nf-core/rnaseq/issues/922)] - Passing TrimGalore `--hardtrim3` / `--hardtrim5` via custom config raises missing output filename error
 
 ## [[3.10](https://github.com/nf-core/rnaseq/releases/tag/3.10)] - 2022-12-21
 

modules.json

@@ -192,7 +192,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "72ffbd7128015a1d4b65b95ff8d37be8fee2f981",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore"]
                     },
                     "ucsc/bedclip": {
@@ -265,7 +265,7 @@
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "b51a69e30973c71950225c817ad07a3337d22c40",
+                        "git_sha": "72ffbd7128015a1d4b65b95ff8d37be8fee2f981",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {

modules/nf-core/trimgalore/main.nf

@@ -254,7 +254,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '3.11'
+    version         = '3.10.1'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 

modules/nf-core/trimgalore/meta.yml

@@ -270,16 +270,20 @@ workflow RNASEQ {
     ch_filtered_reads = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.reads
     if (!params.skip_trimming) {
         ch_filtered_reads
-            .join(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log)
+            .join(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log, remainder: true)
             .map {
                 meta, reads, trim_log ->
-                    if (!meta.single_end) {
-                        trim_log = trim_log[-1]
+                    if (trim_log) {
+                        if (!meta.single_end) {
+                            trim_log = trim_log[-1]
+                        }
+                        num_reads = WorkflowRnaseq.getTrimGaloreReadsAfterFiltering(trim_log)
+                        [ meta, reads, num_reads ]
+                    } else {
+                        [ meta, reads, params.min_trimmed_reads + 1 ]
                     }
-                    num_reads = WorkflowRnaseq.getTrimGaloreReadsAfterFiltering(trim_log)
-                    [ meta, reads, num_reads ]
             }
-            .set { ch_num_trimmed_reads  }
+            .set { ch_num_trimmed_reads }
 
         ch_num_trimmed_reads
             .map { meta, reads, num_reads -> if (num_reads > params.min_trimmed_reads) [ meta, reads ] }