Merge pull request #978 from drpatelh/fixes

Fix #975 and replace System.exit(1) calls in template
nf-core · Mar 28, 2023 · 8e68c07 · 8e68c07
2 parents 1b1714d + 7fd78ca
commit 8e68c07
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Showing 6 changed files with 40 additions and 40 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -3,4 +3,5 @@ lint:
   files_unchanged:
     - assets/email_template.html
     - assets/email_template.txt
+    - lib/NfcoreSchema.groovy
     - lib/NfcoreTemplate.groovy
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-27
+## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-29
 
 ### Credits
 
@@ -24,16 +24,17 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
   - Users can now select between `--trimmer trimgalore` (default) and `--trimmer fastp`.
   - Trim Galore! specific pipeline parameters have been deprecated: `--clip_r1`, `--clip_r2`, `--three_prime_clip_r1`, `--three_prime_clip_r2` and `--trim_nextseq`
   - Any additional options can now be specified via the `--extra_trimgalore_args` and `--extra_fastp_args` parameters, respectively.
-- [[#663](https://github.com/nf-core/rnaseq/pull/663)] - Alternative trimming step for polyA/T removal
-- [[#781](https://github.com/nf-core/rnaseq/pull/781)] - Add Warning for poly(A) libraries
-- [[#878](https://github.com/nf-core/rnaseq/pull/878)] - Allow tabs in fasta header when creating decoys for salmon index
-- [[#931](https://github.com/nf-core/rnaseq/pull/931)] - Save transcriptome BAM files when using `--save_umi_intermeds` / `--save_align_intermeds`
+- [[#663](https://github.com/nf-core/rnaseq/issues/663)] - Alternative trimming step for polyA/T removal
+- [[#781](https://github.com/nf-core/rnaseq/issues/781)] - Add Warning for poly(A) libraries
+- [[#878](https://github.com/nf-core/rnaseq/issues/878)] - Allow tabs in fasta header when creating decoys for salmon index
+- [[#931](https://github.com/nf-core/rnaseq/issues/931)] - Save transcriptome BAM files when using `--save_umi_intermeds` / `--save_align_intermeds`
 - [[#934](https://github.com/nf-core/rnaseq/pull/934)] - Union of `ext.args` and `params.extra_star_align_args` prevents parameter clashes in the STAR module
-- [[#940](https://github.com/nf-core/rnaseq/issues/940)] - Bugfix in `salmon_summarizedexperiment.r` to ensure `rbind` doesn't fail when `rowdata` has no `tx` column. See ([[#941](https://github.com/nf-core/rnaseq/pull/941)]) for details.
+- [[#940](https://github.com/nf-core/rnaseq/issues/940)] - Bugfix in `salmon_summarizedexperiment.r` to ensure `rbind` doesn't fail when `rowdata` has no `tx` column.
 - [[#944](https://github.com/nf-core/rnaseq/issues/944)] - Read clipping using clip_r1, clip_r2, three_prime_clip_r1, three_prime_clip_r2 disabled in 3.10
 - [[#956](https://github.com/nf-core/rnaseq/pull/956)] - Implement 'auto' as default strandedness argument in `fastq_dir_to_samplesheet.py` script
-- [[#960](https://github.com/nf-core/rnaseq/pull/960)] - Failure with awsbatch when running processes that are using `executor: local`
-- [[#961](https://github.com/nf-core/rnaseq/pull/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
+- [[#960](https://github.com/nf-core/rnaseq/issues/960)] - Failure with awsbatch when running processes that are using `executor: local`
+- [[#961](https://github.com/nf-core/rnaseq/issues/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
+- [[#975](https://github.com/nf-core/rnaseq/issues/975)] - `SALMON_INDEX` runs when using `--aligner star_rsem` even if samples have explicit strandedness
 - Remove HISAT2 from automated AWS full-sized tests
 
 ### Parameters

diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
@@ -2,6 +2,7 @@
 // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
 //
 
+import nextflow.Nextflow
 import org.everit.json.schema.Schema
 import org.everit.json.schema.loader.SchemaLoader
 import org.everit.json.schema.ValidationException
@@ -177,7 +178,7 @@ class NfcoreSchema {
         }
 
         if (has_error) {
-            System.exit(1)
+            Nextflow.error('Exiting!')
         }
     }
 

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -2,6 +2,8 @@
 // This file holds several functions specific to the main.nf workflow in the nf-core/rnaseq pipeline
 //
 
+import nextflow.Nextflow
+
 class WorkflowMain {
 
     //
@@ -83,8 +85,7 @@ class WorkflowMain {
 
         // Check input has been provided
         if (!params.input) {
-            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
-            System.exit(1)
+            Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
         }
     }
     //

diff --git a/lib/WorkflowRnaseq.groovy b/lib/WorkflowRnaseq.groovy
@@ -2,6 +2,7 @@
 // This file holds several functions specific to the workflow/rnaseq.nf in the nf-core/rnaseq pipeline
 //
 
+import nextflow.Nextflow
 import groovy.json.JsonSlurper
 import groovy.text.SimpleTemplateEngine
 
@@ -15,13 +16,11 @@ class WorkflowRnaseq {
 
 
         if (!params.fasta) {
-            log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-            System.exit(1)
+            Nextflow.error("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.")
         }
 
         if (!params.gtf && !params.gff) {
-            log.error "No GTF or GFF3 annotation specified! The pipeline requires at least one of these files."
-            System.exit(1)
+            Nextflow.error("No GTF or GFF3 annotation specified! The pipeline requires at least one of these files.")
         }
 
         if (params.gtf) {
@@ -41,51 +40,43 @@ class WorkflowRnaseq {
         }
 
         if (!params.skip_bbsplit && !params.bbsplit_index && !params.bbsplit_fasta_list) {
-            log.error "Please provide either --bbsplit_fasta_list / --bbsplit_index to run BBSplit."
-            System.exit(1)
+            Nextflow.error("Please provide either --bbsplit_fasta_list / --bbsplit_index to run BBSplit.")
         }
 
         if (params.remove_ribo_rna && !params.ribo_database_manifest) {
-            log.error "Please provide --ribo_database_manifest to remove ribosomal RNA with SortMeRNA."
-            System.exit(1)
+            Nextflow.error("Please provide --ribo_database_manifest to remove ribosomal RNA with SortMeRNA.")
         }
 
 
         if (params.with_umi && !params.skip_umi_extract) {
             if (!params.umitools_bc_pattern && !params.umitools_bc_pattern2) {
-                log.error "UMI-tools requires a barcode pattern to extract barcodes from the reads."
-                System.exit(1)
+                Nextflow.error("UMI-tools requires a barcode pattern to extract barcodes from the reads.")
             }
         }
 
         if (!params.skip_trimming) {
             if (!valid_params['trimmers'].contains(params.trimmer)) {
-                log.error "Invalid option: '${params.trimmer}'. Valid options for '--trimmer': ${valid_params['trimmers'].join(', ')}."
-                System.exit(1)
+                Nextflow.error("Invalid option: '${params.trimmer}'. Valid options for '--trimmer': ${valid_params['trimmers'].join(', ')}.")
             }
         }
 
         if (!params.skip_alignment) {
             if (!valid_params['aligners'].contains(params.aligner)) {
-                log.error "Invalid option: '${params.aligner}'. Valid options for '--aligner': ${valid_params['aligners'].join(', ')}."
-                System.exit(1)
+                Nextflow.error("Invalid option: '${params.aligner}'. Valid options for '--aligner': ${valid_params['aligners'].join(', ')}.")
             }
         } else {
             if (!params.pseudo_aligner) {
-                log.error "--skip_alignment specified without --pseudo_aligner...please specify e.g. --pseudo_aligner ${valid_params['pseudoaligners'][0]}."
-                System.exit(1)
+                Nextflow.error("--skip_alignment specified without --pseudo_aligner...please specify e.g. --pseudo_aligner ${valid_params['pseudoaligners'][0]}.")
             }
             skipAlignmentWarn(log)
         }
 
         if (params.pseudo_aligner) {
             if (!valid_params['pseudoaligners'].contains(params.pseudo_aligner)) {
-                log.error "Invalid option: '${params.pseudo_aligner}'. Valid options for '--pseudo_aligner': ${valid_params['pseudoaligners'].join(', ')}."
-                System.exit(1)
+                Nextflow.error("Invalid option: '${params.pseudo_aligner}'. Valid options for '--pseudo_aligner': ${valid_params['pseudoaligners'].join(', ')}.")
             } else {
                 if (!(params.salmon_index || params.transcript_fasta || (params.fasta && (params.gtf || params.gff)))) {
-                    log.error "To use `--pseudo_aligner 'salmon'`, you must provide either --salmon_index or --transcript_fasta or both --fasta and --gtf / --gff."
-                    System.exit(1)
+                    Nextflow.error("To use `--pseudo_aligner 'salmon'`, you must provide either --salmon_index or --transcript_fasta or both --fasta and --gtf / --gff.")
                 }
             }
         }
@@ -120,8 +111,7 @@ class WorkflowRnaseq {
         // Check which RSeQC modules we are running
         def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
         if ((valid_params['rseqc_modules'] + rseqc_modules).unique().size() != valid_params['rseqc_modules'].size()) {
-            log.error "Invalid option: ${params.rseqc_modules}. Valid options for '--rseqc_modules': ${valid_params['rseqc_modules'].join(', ')}"
-            System.exit(1)
+            Nextflow.error("Invalid option: ${params.rseqc_modules}. Valid options for '--rseqc_modules': ${valid_params['rseqc_modules'].join(', ')}")
         }
     }
 
@@ -159,14 +149,14 @@ class WorkflowRnaseq {
             def chrom = lspl[0]
             def size  = lspl[1]
             if (size.toInteger() > max_size) {
-                log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+                def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                     "  Contig longer than ${max_size}bp found in reference genome!\n\n" +
                     "  ${chrom}: ${size}\n\n" +
                     "  Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.\n\n" +
                     "  Please see:\n" +
                     "  https://github.com/nf-core/rnaseq/issues/744\n" +
                     "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-                System.exit(1)
+                Nextflow.error(error_string)
             }
         }
     }
@@ -313,12 +303,12 @@ class WorkflowRnaseq {
     //
     private static void genomeExistsError(params, log) {
         if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                 "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
                 "  Currently, the available genome keys are:\n" +
                 "  ${params.genomes.keySet().join(", ")}\n" +
                 "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-            System.exit(1)
+            Nextflow.error(error_string)
         }
     }
 
@@ -384,13 +374,13 @@ class WorkflowRnaseq {
     // Print a warning if using '--aligner star_rsem' and '--with_umi'
     //
     private static void rsemUmiError(log) {
-        log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
             "  When using '--aligner star_rsem', STAR is run by RSEM itself and so it is\n" +
             "  not possible to remove UMIs before the quantification.\n\n" +
             "  If you would like to remove UMI barcodes using the '--with_umi' option\n" +
             "  please use either '--aligner star_salmon' or '--aligner hisat2'.\n" +
             "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        System.exit(1)
+        Nextflow.error(error_string)
     }
 
     //

diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
@@ -243,9 +243,15 @@ workflow RNASEQ {
     //
     // SUBWORKFLOW: Sub-sample FastQ files and pseudo-align with Salmon to auto-infer strandedness
     //
+    // Return empty channel if ch_strand_fastq.auto_strand is empty so salmon index isn't created
+    PREPARE_GENOME.out.fasta
+        .combine(ch_strand_fastq.auto_strand)
+        .map { it.first() }
+        .set { ch_genome_fasta }
+
     FASTQ_SUBSAMPLE_FQ_SALMON (
         ch_strand_fastq.auto_strand,
-        PREPARE_GENOME.out.fasta,
+        ch_genome_fasta,
         PREPARE_GENOME.out.transcript_fasta,
         PREPARE_GENOME.out.gtf,
         PREPARE_GENOME.out.salmon_index,