Merge pull request #921 from drpatelh/fixes

Fix #919
nf-core · Jan 5, 2023 · a147b4e · a147b4e
2 parents a5e1920 + d7cd968
commit a147b4e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,10 +3,13 @@
 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-## [Unpublished Version / DEV]
+## [[3.10.1](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
 
 ### Enhancements & fixes

diff --git a/main.nf b/main.nf
@@ -17,15 +17,17 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta         = WorkflowMain.getGenomeAttribute(params, 'fasta')
-params.gtf           = WorkflowMain.getGenomeAttribute(params, 'gtf')
-params.gff           = WorkflowMain.getGenomeAttribute(params, 'gff')
-params.gene_bed      = WorkflowMain.getGenomeAttribute(params, 'bed12')
-params.bbsplit_index = WorkflowMain.getGenomeAttribute(params, 'bbsplit')
-params.star_index    = WorkflowMain.getGenomeAttribute(params, 'star')
-params.hisat2_index  = WorkflowMain.getGenomeAttribute(params, 'hisat2')
-params.rsem_index    = WorkflowMain.getGenomeAttribute(params, 'rsem')
-params.salmon_index  = WorkflowMain.getGenomeAttribute(params, 'salmon')
+params.fasta            = WorkflowMain.getGenomeAttribute(params, 'fasta')
+params.transcript_fasta = WorkflowMain.getGenomeAttribute(params, 'transcript_fasta')
+params.additional_fasta = WorkflowMain.getGenomeAttribute(params, 'additional_fasta')
+params.gtf              = WorkflowMain.getGenomeAttribute(params, 'gtf')
+params.gff              = WorkflowMain.getGenomeAttribute(params, 'gff')
+params.gene_bed         = WorkflowMain.getGenomeAttribute(params, 'bed12')
+params.bbsplit_index    = WorkflowMain.getGenomeAttribute(params, 'bbsplit')
+params.star_index       = WorkflowMain.getGenomeAttribute(params, 'star')
+params.hisat2_index     = WorkflowMain.getGenomeAttribute(params, 'hisat2')
+params.rsem_index       = WorkflowMain.getGenomeAttribute(params, 'rsem')
+params.salmon_index     = WorkflowMain.getGenomeAttribute(params, 'salmon')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/modules.json b/modules.json
@@ -129,7 +129,7 @@
                     "salmon/index": {
                         "branch": "master",
                         "git_sha": "94b06f1683ddf893cf06525f6e7f0573ad8fbf83",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_subsample_fq_salmon"]
                     },
                     "salmon/quant": {
                         "branch": "master",
@@ -192,7 +192,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "72ffbd7128015a1d4b65b95ff8d37be8fee2f981",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore"]
                     },
                     "ucsc/bedclip": {
@@ -265,12 +265,12 @@
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "b51a69e30973c71950225c817ad07a3337d22c40",
+                        "git_sha": "72ffbd7128015a1d4b65b95ff8d37be8fee2f981",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {
                         "branch": "master",
-                        "git_sha": "0098bc93f6219c6194f443f0feb089ba83717384",
+                        "git_sha": "82d60046b4519e9dbef4a934371a53fa7666eabc",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -14,8 +14,6 @@ params {
 
     // References
     genome                     = null
-    transcript_fasta           = null
-    additional_fasta           = null
     splicesites                = null
     gtf_extra_attributes       = 'gene_name'
     gtf_group_features         = 'gene_id'
@@ -256,7 +254,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '3.11dev'
+    version         = '3.10.1'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 

diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
@@ -230,15 +230,15 @@ workflow PREPARE_GENOME {
     // Uncompress Salmon index or generate from scratch if required
     //
     ch_salmon_index = Channel.empty()
-    if ('salmon' in prepare_tool_indices) {
-        if (params.salmon_index) {
-            if (params.salmon_index.endsWith('.tar.gz')) {
-                ch_salmon_index = UNTAR_SALMON_INDEX ( [ [:], params.salmon_index ] ).untar.map { it[1] }
-                ch_versions     = ch_versions.mix(UNTAR_SALMON_INDEX.out.versions)
-            } else {
-                ch_salmon_index = file(params.salmon_index)
-            }
+    if (params.salmon_index) {
+        if (params.salmon_index.endsWith('.tar.gz')) {
+            ch_salmon_index = UNTAR_SALMON_INDEX ( [ [:], params.salmon_index ] ).untar.map { it[1] }
+            ch_versions     = ch_versions.mix(UNTAR_SALMON_INDEX.out.versions)
         } else {
+            ch_salmon_index = file(params.salmon_index)
+        }
+    } else {
+        if ('salmon' in prepare_tool_indices) {
             ch_salmon_index = SALMON_INDEX ( ch_fasta, ch_transcript_fasta ).index
             ch_versions     = ch_versions.mix(SALMON_INDEX.out.versions)
         }

diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf b/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml b/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
@@ -232,9 +232,11 @@ workflow RNASEQ {
     //
     FASTQ_SUBSAMPLE_FQ_SALMON (
         ch_strand_fastq.auto_strand,
+        PREPARE_GENOME.out.fasta,
+        PREPARE_GENOME.out.transcript_fasta,
+        PREPARE_GENOME.out.gtf,
         PREPARE_GENOME.out.salmon_index,
-        ch_dummy_file,
-        PREPARE_GENOME.out.gtf
+        !params.salmon_index && !('salmon' in prepareToolIndices)
     )
     ch_versions = ch_versions.mix(FASTQ_SUBSAMPLE_FQ_SALMON.out.versions)
 
@@ -268,16 +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 ] }