Fix issues due to meta2

nf-core · Sep 28, 2023 · 79d0146 · 79d0146
1 parent dca40cb
commit 79d0146
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Showing 4 changed files with 16 additions and 4 deletions.
diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
@@ -13,7 +13,7 @@ process STAR_ALIGN {
     // Input array for a sample is created in the same order reads appear in samplesheet as pairs from replicates are appended to array.
     //
     tuple val(meta), path(reads)
-    path  index
+    tuple val(meta2), path(index)
     path  gtf
     path whitelist
     val protocol

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -130,6 +130,14 @@
                     "type": "boolean",
                     "description": "Specify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.",
                     "fa_icon": "fas fa-bookmark"
+                },
+                "igenomes_base": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "Directory / URL base for iGenomes references.",
+                    "default": "s3://ngi-igenomes/igenomes",
+                    "fa_icon": "fas fa-cloud-download-alt",
+                    "hidden": true
                 }
             }
         },

diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf
@@ -31,7 +31,10 @@ workflow STARSOLO {
     * Build STAR index if not supplied
     */
     if (!star_index) {
-        STAR_GENOMEGENERATE( genome_fasta, gtf )
+        STAR_GENOMEGENERATE(
+            genome_fasta.map{ f -> [[id: f.baseName], f]},
+            gtf.map{ g -> [[id: g.baseName], g]}
+        )
         star_index = STAR_GENOMEGENERATE.out.index.collect()
         ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
     }
@@ -53,7 +56,8 @@ workflow STARSOLO {
 
     emit:
     ch_versions
-    star_index  = star_index
+    // get rid of meta for star index
+    star_index  = star_index.map{ meta, index -> index}
     star_result = STAR_ALIGN.out.tab
     star_counts = STAR_ALIGN.out.counts
     for_multiqc = STAR_ALIGN.out.log_final

diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -72,7 +72,7 @@ ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
 
 // general input and params
 ch_input = file(params.input)
-ch_genome_fasta = params.fasta ? file(params.fasta) : []
+ch_genome_fasta = Channel.value(params.fasta ? file(params.fasta) : [])
 ch_gtf = params.gtf ? file(params.gtf) : []
 ch_transcript_fasta = params.transcript_fasta ? file(params.transcript_fasta): []
 ch_txp2gene = params.txp2gene ? file(params.txp2gene) : []