Merge pull request #1382 from nf-core/rnaseq_propro_trimfail_fix

Slight fixes for rnaseq preprocessing
nf-core · Sep 16, 2024 · 8def328 · 8def328
2 parents 087a3a7 + 5703690
commit 8def328
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev
 - [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names
 - [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules
+- [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing
 
 ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04
 

diff --git a/modules.json b/modules.json
@@ -325,7 +325,7 @@
                     },
                     "fastq_qc_trim_filter_setstrandedness": {
                         "branch": "master",
-                        "git_sha": "8c47be6a114b82a6e6d2f5320b3b5c67579956c0",
+                        "git_sha": "ee3b8b84da02320fff5f3f2dc1d6f9b72d7cd5af",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {

diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
@@ -167,25 +167,6 @@ workflow RNASEQ {
             meta, num_reads ->
                 return [ meta.id, num_reads > params.min_trimmed_reads.toFloat() ]
         }
-    //
-    // Get list of samples that failed trimming threshold for MultiQC report
-    //
-    ch_trim_read_count
-        .map {
-            meta, num_reads ->
-                if (num_reads <= params.min_trimmed_reads.toFloat()) {
-                    return [ "$meta.id\t$num_reads" ]
-                }
-        }
-        .collect()
-        .map {
-            tsv_data ->
-                def header = ["Sample", "Reads after trimming"]
-                sample_status_header_multiqc.text + multiqcTsvFromList(tsv_data, header)
-        }
-        .set { ch_fail_trimming_multiqc }
-
-    ch_multiqc_files = ch_multiqc_files.mix(ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv'))
 
     //
     // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon