remove name of grouplist

theislab · Nov 27, 2023 · e3c949c · e3c949c
1 parent 2e240ad
commit e3c949c
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/modules/gene_demulti/freemuxlet.nf b/modules/gene_demulti/freemuxlet.nf
@@ -74,8 +74,7 @@ process freemuxlet {
         mkdir freemuxlet_${sampleId}
         mkdir freemuxlet_${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,${excl_flag} \n grouplist,${group_list} \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} \