minor changes

theislab · Nov 6, 2023 · 99589b6 · 99589b6
1 parent b5f02b2
commit 99589b6
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Showing 4 changed files with 9 additions and 8 deletions.
diff --git a/main.nf b/main.nf
@@ -88,15 +88,15 @@ workflow run_single{
             donor_match(summary_all.out)
             if (params.generate_anndata == "True" || params.generate_mudata == "True" ){
                 generate_data(donor_match.out, params.generate_anndata, params.generate_mudata, 
-                    params.rna_matrix_filtered, params.hto_matrix_filtered)
+                params.rna_matrix_filtered, params.hto_matrix_filtered)
             }
         }
     }
     else if (params.mode == "donor_match"){
         donor_match(params.demultiplexing_result)
         if (params.generate_anndata == "True" || params.generate_mudata == "True" ){
             generate_data(donor_match.out, params.generate_anndata, params.generate_mudata, 
-                params.rna_matrix_filtered, params.hto_matrix_filtered)
+            params.rna_matrix_filtered, params.hto_matrix_filtered)
         }
     }
 }

diff --git a/modules/gene_demultiplexing.nf b/modules/gene_demultiplexing.nf
@@ -59,16 +59,16 @@ process summary{
             scsplit_files =  "--scsplit ${scsplit_res}"
         }
         if (generate_anndata == "True"){
-            if(rna_matrix == "None"){
+            if(rna_matrix.name == "None"){
                 error "Error: RNA count matrix is not given."
             }
             generate_adata = "--generate_anndata --read_rna_mtx $rna_matrix"
         }
         if (generate_mudata == "True"){
-            if(rna_matrix == "None"){
+            if(rna_matrix.name == "None"){
                 error "Error: RNA count matrix is not given."
             }
-            if(hto_matrix == "None"){
+            if(hto_matrix.name == "None"){
                 error "Error: HTO count matrix is not given."
             }
             generate_mdata = "--generate_mudata --read_rna_mtx $rna_matrix --read_hto_mtx $hto_matrix"

diff --git a/modules/hash_demulti/demuxem.nf b/modules/hash_demulti/demuxem.nf
@@ -31,7 +31,8 @@ process demuxem{
         demuxem.py --rna_matrix_dir rna_data_${params.rna_matrix_demuxem} --hto_matrix_dir hto_data_${params.hto_matrix_demuxem} \
             --randomState $random_state --min_signal $min_signal --tol $tol \
             --min_num_genes $min_num_genes --min_num_umis $min_num_umis --alpha $alpha --alpha_noise $alpha_noise \
-            --n_threads $threads $generateGenderPlot --objectOutDemuxem $objectOutDemuxem --outputdir demuxem_${sampleId} --filter_demuxem $filter_demuxem
+            --n_threads $threads $generateGenderPlot --objectOutDemuxem $objectOutDemuxem --outputdir demuxem_${sampleId} \
+            --filter_demuxem $filter_demuxem
         
         """
 

diff --git a/modules/hash_demulti/hashedDrops.nf b/modules/hash_demulti/hashedDrops.nf
@@ -36,11 +36,11 @@ process hashedDrops{
         path "hashedDrops_${sampleId}"
 
     script:
-	    def testAmb = testAmbient != 'False' ? " --testAmbient" : ''
+        def testAmb = testAmbient != 'False' ? " --testAmbient" : ''
         def rou = round != 'False' ? " --round" : ''
         def constantAmb = constantAmbient != 'False' ? " --constantAmbient" : ''
         def doubletMix = doubletMixture != 'False' ?  " --doubletMixture" : ''
-	    def ign = ignore != "None" ? " --ignore ${ignore}" : ''
+        def ign = ignore != "None" ? " --ignore ${ignore}" : ''
         def alp = alpha != "None" ? " --alpha ${alpha}" : ''
         def byR = byRank != "None" ? " --by.rank ${byRank}" : ''
         def amb = ambient != 'False' ? " --ambient" : ''