fix warning

main.nf

@@ -108,5 +108,4 @@ workflow {
     else{
         run_multi()
     }
-
 }

modules/gene_demulti/freemuxlet.nf

@@ -75,7 +75,7 @@ process freemuxlet {
         mkdir freemuxlet_${sampleId}/plp
         touch freemuxlet_${sampleId}/params.csv
         barcode_num=\$(wc -l < "${group_list}")
-        echo -e "Argument,Value \n samfile,${sam} \n tag_group,${tag_group} \n tag_UMI,${tag_UMI} \n vcf_file,${vcf} \n sm,${sm} \n sm_list_file,${sm_list_file_name} \n sam_verbose,${sam_verbose} \n vcf_verbose,${vcf_verbose} \n skip_umi,${skip_umi} \n cap_BQ,${cap_BQ} \n min_BQ,${min_BQ} \n min_MQ,${min_MQ} \n min_TD,${min_TD} \n excl_flag,${excl_flag} \n grouplist,${grouplist_name}_\${barcode_num} \n min_total,${min_total} \n min_uniq,${min_uniq} \n min_umi,${min_umi} \n min_snp,${min_snp} \n init_cluster,${init_cluster} \n nsample,${nsample} \n aux_files,${aux_files} \n verbose,${verbose} \n doublet_prior,${doublet_prior} \n bf_thres,${bf_thres} \n frac_init_clust,${frac_init_clust} \n iter_init,${iter_init} \n keep_init_missing,${keep_init_missing}" >> freemuxlet_${sampleId}/params.csv
+        echo -e "Argument,Value \n samfile,${sam} \n tag_group,${tag_group} \n tag_UMI,${tag_UMI} \n vcf_file,${vcf} \n sm,${sm} \n sm_list_file,${sm_list_file_name} \n sam_verbose,${sam_verbose} \n vcf_verbose,${vcf_verbose} \n skip_umi,${skip_umi} \n cap_BQ,${cap_BQ} \n min_BQ,${min_BQ} \n min_MQ,${min_MQ} \n min_TD,${min_TD} \n excl_flag,${excl_flag} \n grouplist,${grouplist.name}_\${barcode_num} \n min_total,${min_total} \n min_uniq,${min_uniq} \n min_umi,${min_umi} \n min_snp,${min_snp} \n init_cluster,${init_cluster} \n nsample,${nsample} \n aux_files,${aux_files} \n verbose,${verbose} \n doublet_prior,${doublet_prior} \n bf_thres,${bf_thres} \n frac_init_clust,${frac_init_clust} \n iter_init,${iter_init} \n keep_init_missing,${keep_init_missing}" >> freemuxlet_${sampleId}/params.csv
         
         popscle dsc-pileup $samfile ${taggroup} ${tagUMI} $vcffile ${smlist} ${sm_list_file} ${samverbose} ${vcfverbose} \
             ${skipumi} ${capBQ} ${minBQ} ${minMQ} ${minTD} ${exclflag} ${grouplist} ${mintotal} ${minuniq} ${minsnp} \

modules/hash_demulti/bff.nf

@@ -34,10 +34,10 @@ process bff{
         """
         mkdir bff_${sampleId}
         bff.R --fileHto hto_data --methods $methods --methodsForConsensus $methodsForConsensus \
-        --cellbarcodeWhitelist $cellbarcodeWhitelist --cellbarcodeWhitelist $cellbarcodeWhitelist --metricsFile bff_${task.index}_$metricsFile \
+        --cellbarcodeWhitelist $cellbarcodeWhitelist --metricsFile bff_${task.index}_$metricsFile \
         --doTSNE $doTSNE --doHeatmap $doHeatmap --perCellSaturation $perCellSaturation --majorityConsensusThreshold $majorityConsensusThreshold \
-        --chemistry $chemistry --callerDisagreementThreshold $callerDisagreementThreshold --outputdir bff_${sampleId} --assignmentOutBff $assignmentOutBff \ 
-        --preprocess $preprocess_bff --barcodeWhitelist $barcodeWhitelist
+        --chemistry $chemistry --callerDisagreementThreshold $callerDisagreementThreshold --outputdir bff_${sampleId} \
+        --assignmentOutBff $assignmentOutBff --preprocess $preprocess_bff --barcodeWhitelist $barcodeWhitelist
         """
 
 }
@@ -69,7 +69,9 @@ workflow bff_hashing{
         preprocess_bff = split_input(params.preprocess_bff)
         barcodeWhitelist = split_input(params.barcodeWhitelist)
 
-        bff(hto_matrix, methods, methodsForConsensus, metricsFile,cellbarcodeWhitelist,doTSNE,doHeatmap,perCellSaturation,majorityConsensusThreshold,chemistry,callerDisagreementThreshold,assignmentOutBff,preprocess_bff,barcodeWhitelist)
+        bff(hto_matrix, methods, methodsForConsensus, cellbarcodeWhitelist, metricsFile, doTSNE, doHeatmap, 
+            perCellSaturation, majorityConsensusThreshold, chemistry, callerDisagreementThreshold, assignmentOutBff,
+            preprocess_bff, barcodeWhitelist)
 
   emit:
         bff.out.collect()

modules/hash_demulti/demuxem.nf

@@ -20,7 +20,7 @@ process demuxem{
         val random_state
         val generate_gender_plot
         val objectOutDemuxem
-        each filter_demuxem
+        val filter_demuxem
     output:
         path "demuxem_${sampleId}"
 
@@ -31,8 +31,7 @@ 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
         
         """
 

modules/hash_demulti/demuxmix.nf

@@ -35,7 +35,7 @@ process demuxmix{
         mkdir demuxmix_${sampleId}
 
         demuxmix.R --fileUmi rna_data --fileHto hto_data --rna_available $rna_available --assay $assay --ndelim $ndelim --model $model --alpha_demuxmix $alpha_demuxmix \
-            --beta_demuxmix $beta_demuxmix --tol_demuxmix $tol_demuxmix --maxIter_demuxmix $maxIter_demuxmix --correctTails $correctTails\
+            --beta_demuxmix $beta_demuxmix --tol_demuxmix $tol_demuxmix --maxIter_demuxmix $maxIter_demuxmix --correctTails $correctTails \
             --k_hto $k_hto  --k_rna $k_rna --outputdir demuxmix_${sampleId} --assignmentOutDemuxmix $assignmentOutDemuxmix
         """
 

modules/hash_demulti/hashedDrops.nf

@@ -53,7 +53,7 @@ process hashedDrops{
             --assignmentOutEmptyDrops $assignmentOutEmptyDrops --minProp $minProp --pseudoCount $pseudoCount \
             --doubletNmads $doubletNmads --doubletMin $doubletMin --confidentNmads $confidentNmads \
             --confidenMin $confidenMin --objectOutHashedDrops $objectOutHashedDrops \
-            --outputdir hashedDrops_${sampleId} --assignmentOutHashedDrops ${assignmentOutHashedDrops}\
+            --outputdir hashedDrops_${sampleId} --assignmentOutHashedDrops ${assignmentOutHashedDrops} \
             ${testAmb}${ign}${alp}${rou}${byR}${constantAmb}${doubletMix}${amb}${comb}
         """
 

modules/single/hash_demulti/demuxem.nf

@@ -31,8 +31,7 @@ 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 $objectOutDemuxem --outputdir demuxem_${task.index} \
-            --filter_demuxem $filter_demuxem
+            --n_threads $threads $generateGenderPlot --objectOutDemuxem $objectOutDemuxem --outputdir demuxem_${task.index} --filter_demuxem $filter_demuxem
         
         """
 
@@ -65,7 +64,7 @@ workflow demuxem_hashing{
         filter_demuxem = split_input(params.filter_demuxem)
 
         demuxem(rna_matrix, hto_matrix, threads, alpha, alpha_noise, tol, min_num_genes, min_num_umis, 
-                min_signal, random_state, generate_gender_plot, objectOutDemuxem,filter_demuxem)
+                min_signal, random_state, generate_gender_plot, objectOutDemuxem, filter_demuxem)
 
   emit:
         demuxem.out.collect()