Merge pull request #223 from nf-core/dev

Dev -> Master for v2.3.0 release
nf-core · May 3, 2023 · cfada12 · cfada12
2 parents c6ec217 + 5035215
commit cfada12
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Showing 6 changed files with 18 additions and 28 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,11 @@
 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).
 
+## v2.3.0 Steelblue Waspaloy Dachshund
+
+- Fix problem on samplesheet check related to amount of columns ([[#211](https://github.com/nf-core/scrnaseq/issues/211)])
+- Fixed bug in starsolo output cardinality.
+
 ## v2.2.0
 
 - Added support to output 10x count files in text format.

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -104,7 +104,8 @@ def check_samplesheet(file_in, file_out):
                 min_header_count = min_header_count + 1
             colmap[h] = i
             i = i + 1
-        if unknown_header or min_header_count < len(MIN_HEADER):
+        if min_header_count < len(MIN_HEADER):
+            # code was checking for unknown_header or min_header_count however looking at the ifelse, unknown_header does not seem that it should be tested
             given = ",".join(header)
             wanted = ",".join(MIN_HEADER)
             print(f"ERROR: Please check samplesheet header -> {given} != {wanted}")

diff --git a/nextflow.config b/nextflow.config
@@ -11,7 +11,6 @@ params {
 
     // generic options
     aligner           = 'alevin'
-    bustools_correct  = true
     outdir            = null
     input             = null
     save_reference    = false
@@ -30,7 +29,6 @@ params {
     // kallist bustools parameters
     kallisto_gene_map = null
     kallisto_index    = null
-    skip_bustools     = false
     kb_workflow       = "standard"
 
     // STARsolo parameters
@@ -43,11 +41,11 @@ params {
     cellranger_index    = null
 
     // UniverSC paramaters
-    universc_index    = null
+    universc_index      = null
     universc_technology = '10x'
 
     // Template Boilerplate options
-    skip_multiqc                = false
+    skip_multiqc               = false
 
     // References
     genome                     = null
@@ -225,7 +223,7 @@ manifest {
     description     = """Pipeline for processing 10x Genomics single cell rnaseq data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '2.2.0'
+    version         = '2.3.0'
     doi             = '10.5281/zenodo.3568187'
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -182,8 +182,7 @@
                 },
                 "seq_center": {
                     "type": "string",
-                    "description": "Name of sequencing center for BAM read group tag.",
-                    "default": "None"
+                    "description": "Name of sequencing center for BAM read group tag."
                 },
                 "star_feature": {
                     "type": "string",
@@ -207,16 +206,6 @@
                     "description": "Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.",
                     "fa_icon": "fas fa-fish"
                 },
-                "bustools_correct": {
-                    "type": "boolean",
-                    "description": "If set to false, skip the correct steps after mapping with Kallisto.",
-                    "fa_icon": "fas fa-bus-alt"
-                },
-                "skip_bustools": {
-                    "type": "boolean",
-                    "description": "Skip BUStools entirely in workflow",
-                    "fa_icon": "fas fa-forward"
-                },
                 "kallisto_index": {
                     "type": "string",
                     "description": "Specify a path to the precomputed Kallisto index.",
@@ -251,11 +240,12 @@
             "properties": {
                 "universc_index": {
                     "type": "string",
-                    "description": "Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website. "
+                    "description": "Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website."
                 },
                 "universc_technology": {
                     "type": "string",
-                    "description": "Specify a single-cell technology, vendor, or platform. See the UniverSC documentation or GitHub repository for more details. "
+                    "description": "Specify a single-cell technology, vendor, or platform. See the UniverSC documentation or GitHub repository for more details.",
+                    "default": "10x"
                 }
             }
         },

diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf
@@ -56,7 +56,5 @@ workflow STARSOLO {
     star_index  = star_index
     star_result = STAR_ALIGN.out.tab
     star_counts = STAR_ALIGN.out.counts
-    for_multiqc = STAR_ALIGN.out.log_final.collect{it[1]}.ifEmpty([])
-
-
+    for_multiqc = STAR_ALIGN.out.log_final
 }
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -104,8 +104,6 @@ ch_cellranger_index = params.cellranger_index ? file(params.cellranger_index) :
 
 //universc params
 ch_universc_index = params.universc_index ? file(params.universc_index) : []
-ch_universc_technology = params.universc_technology
-
 
 workflow SCRNASEQ {
 
@@ -201,7 +199,7 @@ workflow SCRNASEQ {
             ch_genome_fasta,
             ch_filter_gtf,
             ch_universc_index,
-            ch_universc_technology,
+            params.universc_technology,
             ch_fastq
         )
         ch_versions = ch_versions.mix(UNIVERSC_ALIGN.out.ch_versions)
@@ -238,8 +236,8 @@ workflow SCRNASEQ {
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_fastqc.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_alevin.collect{it[1]}.ifEmpty([])),
-    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_star.collect{it[1]}.ifEmpty([])),
+    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_alevin.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_star.collect{it[1]}.ifEmpty([]))
 
     MULTIQC (
         ch_multiqc_files.collect(),