Merge remote-tracking branch 'origin/dev' into dev

nf-core · Mar 13, 2024 · fc47a34 · fc47a34
2 parents ec19912 + ae5b28b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.6.0dev - [date]
 
-- [[#91](https://github.com/nf-core/scrnaseq/issues/91)] - Change from pytests to nf-test
+- Change from pytests to nf-test ([#291](https://github.com/nf-core/scrnaseq/pull/291))
+- Update template to v2.13.1 ([#309](https://github.com/nf-core/scrnaseq/pull/309))
+- Update to kallisto|bustools v0.28.2 ([#294](https://github.com/nf-core/scrnaseq/pull/294))
 
 ## v2.5.1
 

diff --git a/modules/local/gene_map.nf b/modules/local/gene_map.nf
diff --git a/modules/local/mtx_to_h5ad.nf b/modules/local/mtx_to_h5ad.nf
@@ -27,7 +27,7 @@ process MTX_TO_H5AD {
     if (params.aligner == 'kallisto') {
         mtx_matrix   = "*count/counts_unfiltered/*.mtx"
         barcodes_tsv = "*count/counts_unfiltered/*.barcodes.txt"
-        features_tsv = "*count/counts_unfiltered/*.genes.txt"
+        features_tsv = "*count/counts_unfiltered/*.genes.names.txt"
     } else if (params.aligner == 'alevin') {
         mtx_matrix   = "*_alevin_results/af_quant/alevin/quants_mat.mtx"
         barcodes_tsv = "*_alevin_results/af_quant/alevin/quants_mat_rows.txt"
@@ -54,13 +54,13 @@ process MTX_TO_H5AD {
     else if (params.aligner == 'kallisto' && params.kb_workflow != 'standard')
     """
     # convert file types
-    for input_type in spliced unspliced ; do
+    for input_type in nascent ambiguous mature ; do
         mtx_to_h5ad.py \\
             --aligner ${params.aligner} \\
             --sample ${meta.id} \\
-            --input *count/counts_unfiltered/\${input_type}.mtx \\
-            --barcode *count/counts_unfiltered/\${input_type}.barcodes.txt \\
-            --feature *count/counts_unfiltered/\${input_type}.genes.txt \\
+            --input *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
+            --barcode $barcodes_tsv \\
+            --feature $features_tsv \\
             --txp2gene ${txp2gene} \\
             --star_index ${star_index} \\
             --out ${meta.id}/${meta.id}_\${input_type}_matrix.h5ad ;

diff --git a/modules/local/mtx_to_seurat.nf b/modules/local/mtx_to_seurat.nf
@@ -26,7 +26,7 @@ process MTX_TO_SEURAT {
     } else if (params.aligner == "kallisto") {
         matrix   = "*count/counts_unfiltered/*.mtx"
         barcodes = "*count/counts_unfiltered/*.barcodes.txt"
-        features = "*count/counts_unfiltered/*.genes.txt"
+        features = "*count/counts_unfiltered/*.genes.names.txt"
     } else if (params.aligner == "alevin") {
         matrix   = "*_alevin_results/af_quant/alevin/quants_mat.mtx"
         barcodes = "*_alevin_results/af_quant/alevin/quants_mat_rows.txt"
@@ -43,11 +43,11 @@ process MTX_TO_SEURAT {
     if (params.aligner == 'kallisto' && params.kb_workflow != 'standard')
     """
     # convert file types
-    for input_type in spliced unspliced ; do
+    for input_type in nascent ambiguous mature ; do
         mtx_to_seurat.R \\
-            *count/counts_unfiltered/\${input_type}.mtx \\
-            *count/counts_unfiltered/\${input_type}.barcodes.txt \\
-            *count/counts_unfiltered/\${input_type}.genes.txt \\
+            *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
+            $barcodes \\
+            $features \\
             ${meta.id}/${meta.id}_\${input_type}_matrix.rds \\
             ${aligner}
     done

diff --git a/nextflow.config b/nextflow.config
@@ -19,17 +19,18 @@ params {
     // reference files
     genome            = null
     transcript_fasta  = null
+    txp2gene          = null
 
     // salmon alevin parameters (simpleaf)
     simpleaf_rlen     = 91
     barcode_whitelist = null
-    txp2gene          = null
     salmon_index      = null
 
-    // kallist bustools parameters
-    kallisto_gene_map = null
+    // kallisto bustools parameters
     kallisto_index    = null
     kb_workflow       = "standard"
+    kb_t1c            = null
+    kb_t2c            = null
 
     // STARsolo parameters
     star_index          = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -214,26 +214,35 @@
             "type": "object",
             "description": "Params related to Kallisto/BUS tool",
             "default": "",
-            "fa_icon": "fas fa-fish",
+            "fa_icon": "fas fa-rainbow",
             "properties": {
-                "kallisto_gene_map": {
-                    "type": "string",
-                    "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"
-                },
                 "kallisto_index": {
                     "type": "string",
                     "description": "Specify a path to the precomputed Kallisto index.",
-                    "fa_icon": "fas fa-fish",
+                    "fa_icon": "fas fa-rainbow",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "kb_t1c": {
+                    "type": "string",
+                    "description": "Specify a path to the cDNA transcripts-to-capture.",
+                    "fa_icon": "fas fa-rainbow",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "kb_t2c": {
+                    "type": "string",
+                    "description": "Specify a path to the intron transcripts-to-capture.",
+                    "fa_icon": "fas fa-rainbow",
                     "format": "file-path",
                     "exists": true
                 },
                 "kb_workflow": {
                     "type": "string",
                     "default": "standard",
-                    "description": "Type of workflow. Use `lamanno` for RNA velocity based on La Manno et al. 2018 logic. Use `nucleus` for RNA velocity on single-nucleus RNA-seq reads. Use `kite` for feature barcoding. Use `kite: 10xFB` for 10x Genomics Feature Barcoding technology. (default: standard)",
-                    "fa_icon": "fas fa-fish",
-                    "enum": ["standard", "lamanno", "nucleus", "kite", "kite: 10xFB"]
+                    "description": "Type of workflow. Use `nac` for an index type that can quantify nascent and mature RNA. Use `lamanno` for RNA velocity based on La Manno et al. 2018 logic. (default: standard)",
+                    "fa_icon": "fas fa-rainbow",
+                    "enum": ["standard", "lamanno", "nac"]
                 }
             }
         },

diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
@@ -1,5 +1,4 @@
 /* --    IMPORT LOCAL MODULES/SUBWORKFLOWS     -- */
-include { GENE_MAP }                          from '../../modules/local/gene_map'
 include {KALLISTOBUSTOOLS_COUNT }             from '../../modules/nf-core/kallistobustools/count/main'
 
 /* --    IMPORT NF-CORE MODULES/SUBWORKFLOWS   -- */
@@ -14,33 +13,22 @@ workflow KALLISTO_BUSTOOLS {
     gtf
     kallisto_index
     txp2gene
+    t1c
+    t2c
     protocol
     kb_workflow
     ch_fastq
 
     main:
     ch_versions = Channel.empty()
 
-    assert kallisto_index || (genome_fasta && gtf):
+    assert (txp2gene && kallisto_index) || (genome_fasta && gtf):
         "Must provide a genome fasta file ('--fasta') and a gtf file ('--gtf') if no index is given!"
 
-    assert txp2gene || gtf:
-        "Must provide either a GTF file ('--gtf') or kallisto gene map ('--kallisto_gene_map') to align with kallisto bustools!"
-
-    /*
-    * Generate Kallisto Gene Map if not supplied and index is given
-    * If no index is given, the gene map will be generated in the 'kb ref' step
-    */
-    if (!txp2gene && kallisto_index) {
-        GENE_MAP( gtf )
-        txp2gene = GENE_MAP.out.gene_map
-        ch_versions = ch_versions.mix(GENE_MAP.out.versions)
-    }
-
     /*
-    * Generate kallisto index
+    * Generate kallisto index and t2g if not already present
     */
-    if (!kallisto_index) {
+    if (!(txp2gene && kallisto_index)) {
         KALLISTOBUSTOOLS_REF( genome_fasta, gtf, kb_workflow )
         txp2gene = KALLISTOBUSTOOLS_REF.out.t2g.collect()
         kallisto_index = KALLISTOBUSTOOLS_REF.out.index.collect()
@@ -58,15 +46,16 @@ workflow KALLISTO_BUSTOOLS {
         txp2gene,
         t1c,
         t2c,
-        protocol
+        protocol,
+        kb_workflow
     )
 
     ch_versions = ch_versions.mix(KALLISTOBUSTOOLS_COUNT.out.versions)
 
     emit:
     ch_versions
     counts = KALLISTOBUSTOOLS_COUNT.out.count
-    txp2gene = txp2gene.collect()
+    txp2gene
 
 
 }
diff --git a/tests/.nf-test.log b/tests/.nf-test.log
@@ -0,0 +1,21 @@
+Feb-27 21:54:09.971 [main] INFO  com.askimed.nf.test.App - nf-test 0.8.4
+Feb-27 21:54:09.988 [main] INFO  com.askimed.nf.test.App - Arguments: [test, tests/main_pipeline_kallisto.test, --update-snapshot]
+Feb-27 21:54:10.670 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 23.10.1
+Feb-27 21:54:10.674 [main] WARN  com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found.
+Feb-27 21:54:10.674 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files.
+Feb-27 21:54:10.676 [main] ERROR com.askimed.nf.test.commands.RunTestsCommand - Running tests failed.
+java.lang.Exception: Test file '/home/ec2-user/scrnaseq/tests/tests/main_pipeline_kallisto.test' not found.
+	at com.askimed.nf.test.core.TestExecutionEngine.parse(TestExecutionEngine.java:116)
+	at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:159)
+	at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:184)
+	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43)
+	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18)
+	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
+	at picocli.CommandLine.access$1300(CommandLine.java:145)
+	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
+	at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
+	at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
+	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
+	at picocli.CommandLine.execute(CommandLine.java:2078)
+	at com.askimed.nf.test.App.run(App.java:44)
+	at com.askimed.nf.test.App.main(App.java:51)
diff --git a/tests/main_pipeline_kallisto.test.snap b/tests/main_pipeline_kallisto.test.snap
@@ -20,15 +20,15 @@
                 "name": "workflow",
                 "success": true
             },
-            "cells_x_genes.barcodes.txt:md5,18be561873e435d4587f6b3f95a0e301",
+            "cells_x_genes.barcodes.txt:md5,72d78bb1c1ee7cb174520b30f695aa48",
             "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
-            "cells_x_genes.mtx:md5,37d2cd8c712f9c70463e87485bf6cd36",
-            "cells_x_genes.barcodes.txt:md5,488437e1f5477243697efb93366e5676",
+            "cells_x_genes.mtx:md5,894d60da192e3788de11fa8fc1fa711d",
+            "cells_x_genes.barcodes.txt:md5,a8cf7ea4b2d075296a94bf066a64b7a4",
             "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
-            "cells_x_genes.mtx:md5,af90e05b404490f6cb133ab7f62949f8",
-            "Sample_X_matrix.rds:md5,f0e43f69403f4b2e7704065421592ad0",
-            "Sample_Y_matrix.rds:md5,61809156e64dbdaf254cbc1c3456588e"
+            "cells_x_genes.mtx:md5,abd83de117204d0a77df3c92d00cc025",
+            "Sample_X_matrix.rds:md5,0938f4189b7a7fd1030abfcee798741c",
+            "Sample_Y_matrix.rds:md5,93c12abe283ab37c5f37e5cd3cb25302"
         ],
-        "timestamp": "2024-01-23T12:19:47.921508953"
+        "timestamp": "2024-02-27T12:19:47.921508953"
     }
 }
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -43,6 +43,12 @@ workflow SCRNASEQ {
         ch_barcode_whitelist = []
     }
 
+    //kallisto params
+    ch_kallisto_index = params.kallisto_index ? file(params.kallisto_index) : []
+    kb_workflow = params.kb_workflow
+    kb_t1c = params.kb_t1c ? file(params.kb_t1c) : []
+    kb_t2c = params.kb_t2c ? file(params.kb_t2c) : []
+
     // samplesheet - this is passed to the MTX conversion functions to add metadata to the
     // AnnData objects.
     ch_input = file(params.input)
@@ -83,6 +89,8 @@ workflow SCRNASEQ {
             ch_filter_gtf,
             ch_kallisto_index,
             ch_txp2gene,
+            kb_t1c,
+            kb_t2c,
             protocol_config['protocol'],
             kb_workflow,
             ch_fastq