diff --git a/main.nf b/main.nf index 32c0007..239683a 100644 --- a/main.nf +++ b/main.nf @@ -108,5 +108,4 @@ workflow { else{ run_multi() } - } \ No newline at end of file diff --git a/modules/gene_demulti/freemuxlet.nf b/modules/gene_demulti/freemuxlet.nf index 037f5b5..6fa84c8 100755 --- a/modules/gene_demulti/freemuxlet.nf +++ b/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} ${minsnp} \ diff --git a/modules/hash_demulti/bff.nf b/modules/hash_demulti/bff.nf index db9dbb1..0c093f7 100644 --- a/modules/hash_demulti/bff.nf +++ b/modules/hash_demulti/bff.nf @@ -34,10 +34,10 @@ process bff{ """ mkdir bff_${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 $barcodeWhitelist """ } @@ -69,7 +69,9 @@ workflow bff_hashing{ preprocess_bff = split_input(params.preprocess_bff) barcodeWhitelist = split_input(params.barcodeWhitelist) - bff(hto_matrix, methods, methodsForConsensus, metricsFile,cellbarcodeWhitelist,doTSNE,doHeatmap,perCellSaturation,majorityConsensusThreshold,chemistry,callerDisagreementThreshold,assignmentOutBff,preprocess_bff,barcodeWhitelist) + bff(hto_matrix, methods, methodsForConsensus, cellbarcodeWhitelist, metricsFile, doTSNE, doHeatmap, + perCellSaturation, majorityConsensusThreshold, chemistry, callerDisagreementThreshold, assignmentOutBff, + preprocess_bff, barcodeWhitelist) emit: bff.out.collect() diff --git a/modules/hash_demulti/demuxem.nf b/modules/hash_demulti/demuxem.nf index 9b49f05..4190b7d 100644 --- a/modules/hash_demulti/demuxem.nf +++ b/modules/hash_demulti/demuxem.nf @@ -20,7 +20,7 @@ process demuxem{ val random_state val generate_gender_plot val objectOutDemuxem - each filter_demuxem + val filter_demuxem output: path "demuxem_${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 $filter_demuxem """ diff --git a/modules/hash_demulti/demuxmix.nf b/modules/hash_demulti/demuxmix.nf index 5325d6d..18f83d9 100644 --- a/modules/hash_demulti/demuxmix.nf +++ b/modules/hash_demulti/demuxmix.nf @@ -35,7 +35,7 @@ process demuxmix{ mkdir demuxmix_${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 """ diff --git a/modules/hash_demulti/hashedDrops.nf b/modules/hash_demulti/hashedDrops.nf index decc286..6e10cb0 100755 --- a/modules/hash_demulti/hashedDrops.nf +++ b/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}${comb} """ diff --git a/modules/single/hash_demulti/demuxem.nf b/modules/single/hash_demulti/demuxem.nf index 7d2d86d..e47ec40 100644 --- a/modules/single/hash_demulti/demuxem.nf +++ b/modules/single/hash_demulti/demuxem.nf @@ -31,8 +31,7 @@ process demuxem{ demuxem.py --rna_matrix_dir rna_data_${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()