Merge pull request #294 from gennadyFauna/kb_update

kallisto|bustools 0.28.2 update
nf-core · Mar 7, 2024 · ae5b28b · ae5b28b
2 parents 6ff7a83 + 600619f
commit 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.json b/modules.json
@@ -52,12 +52,12 @@
                     },
                     "kallistobustools/count": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "de8215983defba48cd81961d620a9e844f11c7e7",
                         "installed_by": ["modules"]
                     },
                     "kallistobustools/ref": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "de8215983defba48cd81961d620a9e844f11c7e7",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {

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/modules/nf-core/kallistobustools/count/environment.yml b/modules/nf-core/kallistobustools/count/environment.yml
diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test b/modules/nf-core/kallistobustools/count/tests/main.nf.test