cleanup

nf-core · Oct 11, 2022 · 7f7d69e · 7f7d69e
1 parent 9130564
commit 7f7d69e
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Showing 2 changed files with 4 additions and 31 deletions.
diff --git a/modules/local/h5ad_to_10x.nf b/modules/local/h5ad_to_10x.nf
@@ -1,14 +1,7 @@
 process H5AD_TO_10X {
     label 'process_low'
 
-    // conda (params.enable_conda ? "conda-forge::scanpy conda-forge::python-igraph conda-forge::leidenalg" : null)
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    //     'https://depot.galaxyproject.org/singularity/scanpy:1.7.2--pyhdfd78af_0' :
-    //     'quay.io/biocontainers/scanpy:1.7.2--pyhdfd78af_0' }"
-
     input:
-    // inputs from cellranger nf-core module does not come in a single sample dir
-    // for each sample, the sub-folders and files come directly in array.
     path h5ad_file
     path t2g_file
 
@@ -17,23 +10,6 @@ process H5AD_TO_10X {
 
 
     script:
-    // def file paths for aligners (except cellranger)
-    // if (params.aligner == 'kallisto') {
-    //     mtx_matrix   = "*count/counts_unfiltered/*.mtx"
-    //     barcodes_tsv = "*count/counts_unfiltered/*.barcodes.txt"
-    //     features_tsv = "*count/counts_unfiltered/*.genes.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"
-    //     features_tsv = "*_alevin_results/af_quant/alevin/quants_mat_cols.txt"
-    // } else if (params.aligner == 'star') {
-    //     mtx_matrix   = "*.Solo.out/Gene*/filtered/matrix.mtx.gz"
-    //     barcodes_tsv = "*.Solo.out/Gene*/filtered/barcodes.tsv.gz"
-    //     features_tsv = "*.Solo.out/Gene*/filtered/features.tsv.gz"
-    // }
-    //
-    // run script
-    //
     """
     # convert file types
     sampleName=`basename ${h5ad_file} .h5ad`

diff --git a/subworkflows/local/mtx_conversion.nf b/subworkflows/local/mtx_conversion.nf
@@ -25,16 +25,13 @@ workflow MTX_CONVERSION {
             mtx_matrices
         )
 
-        //
-        // Convert h5ad files to 10x counts format
-        //
-        // if (!txp2gene) {
-        //     GENE_MAP( gtf )
-        //     txp2gene = GENE_MAP.out.gene_map
-        // }
+        // Generate the t2g file to enrich the 10x files with gene names
         KALLISTOBUSTOOLS_REF( genome_fasta, gtf, 'standard' )
         txp2gene = KALLISTOBUSTOOLS_REF.out.t2g.collect()
 
+        //
+        // Convert h5ad files to 10x counts format
+        //
         H5AD_TO_10X (
             MTX_TO_H5AD.out.h5ad, // gather all sample-specific files
             txp2gene