Merge pull request #811 from drpatelh/fixes

Fix #798, #799, #802

Author: drpatelh

CHANGELOG.md

@@ -9,6 +9,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - [[#791](https://github.com/nf-core/rnaseq/issues/791)] - Add outputs for umitools dedup summary stats
+- [[#798](https://github.com/nf-core/rnaseq/issues/798)] - Decompress transcript fasta error
+- [[#799](https://github.com/nf-core/rnaseq/issues/799)] - Issue with using `--retain_unpaired` with the `FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE` module
+- [[#802](https://github.com/nf-core/rnaseq/issues/802)] - `--bam_csi_index` error generated if `--skip_alignment` specified
 - [[#808](https://github.com/nf-core/rnaseq/issues/808)] - Auto-detect usage of Illumina iGenomes reference
 - Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 

modules.json

@@ -103,7 +103,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "trimgalore": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "85ec13ff1fc2196c5a507ea497de468101baabed"
             },
             "ucsc/bedclip": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

modules/nf-core/modules/trimgalore/main.nf

@@ -106,7 +106,7 @@ workflow PREPARE_GENOME {
     //
     if (params.transcript_fasta) {
         if (params.transcript_fasta.endsWith('.gz')) {
-            ch_transcript_fasta = GUNZIP_TRANSCRIPT_FASTA ( [:], params.transcript_fasta ).gunzip.map { it[1] }
+            ch_transcript_fasta = GUNZIP_TRANSCRIPT_FASTA ( [ [:], params.transcript_fasta ] ).gunzip.map { it[1] }
             ch_versions         = ch_versions.mix(GUNZIP_TRANSCRIPT_FASTA.out.versions)
         } else {
             ch_transcript_fasta = file(params.transcript_fasta)

modules/nf-core/modules/trimgalore/meta.yml

@@ -177,10 +177,12 @@ workflow RNASEQ {
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     // Check if contigs in genome fasta file > 512 Mbp
-    PREPARE_GENOME
-        .out
-        .fai
-        .map { WorkflowRnaseq.checkMaxContigSize(it, log) }
+    if (!params.skip_alignment) {
+        PREPARE_GENOME
+            .out
+            .fai
+            .map { WorkflowRnaseq.checkMaxContigSize(it, log) }
+    }
 
     //
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files