solve warning

nf-core · May 28, 2024 · ee7c264 · ee7c264
1 parent 22f410d
commit ee7c264
Showing 1 changed file with 22 additions and 22 deletions.
diff --git a/subworkflows/local/presto_umi.nf b/subworkflows/local/presto_umi.nf
@@ -7,28 +7,28 @@ include { FASTP                                          } from '../../modules/n
 
 
 //PRESTO
-include { PRESTO_FILTERSEQ      as  PRESTO_FILTERSEQ_UMI }      from '../../modules/local/presto/presto_filterseq'
-include { PRESTO_MASKPRIMERS    as  PRESTO_MASKPRIMERS_UMI }    from '../../modules/local/presto/presto_maskprimers'
-include { PRESTO_MASKPRIMERS_ALIGN }                            from '../../modules/local/presto/presto_maskprimers_align'
-include { PRESTO_MASKPRIMERS_EXTRACT }                          from '../../modules/local/presto/presto_maskprimers_extract'
-include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_CREGION }    from '../../modules/local/presto/presto_maskprimers_align'
-include { PRESTO_PAIRSEQ        as  PRESTO_PAIRSEQ_UMI }        from '../../modules/local/presto/presto_pairseq'
-include { PRESTO_PAIRSEQ        as  PRESTO_PAIRSEQ_ALIGN } from '../../modules/local/presto/presto_pairseq'
-include { PRESTO_CLUSTERSETS    as  PRESTO_CLUSTERSETS_UMI }    from '../../modules/local/presto/presto_clustersets'
-include { PRESTO_PARSE_CLUSTER  as  PRESTO_PARSE_CLUSTER_UMI }  from '../../modules/local/presto/presto_parse_cluster'
-include { PRESTO_BUILDCONSENSUS as  PRESTO_BUILDCONSENSUS_UMI } from '../../modules/local/presto/presto_buildconsensus'
-include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_ALIGN } from '../../modules/local/presto/presto_buildconsensus'
+include { PRESTO_FILTERSEQ      as  PRESTO_FILTERSEQ_UMI     }    from '../../modules/local/presto/presto_filterseq'
+include { PRESTO_MASKPRIMERS    as  PRESTO_MASKPRIMERS_UMI   }    from '../../modules/local/presto/presto_maskprimers'
+include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_PRIMERS   }    from '../../modules/local/presto/presto_maskprimers_align'
+include { PRESTO_MASKPRIMERS_EXTRACT                         }    from '../../modules/local/presto/presto_maskprimers_extract'
+include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_CREGION   }    from '../../modules/local/presto/presto_maskprimers_align'
+include { PRESTO_PAIRSEQ        as  PRESTO_PAIRSEQ_UMI       }    from '../../modules/local/presto/presto_pairseq'
+include { PRESTO_PAIRSEQ        as  PRESTO_PAIRSEQ_ALIGN     }    from '../../modules/local/presto/presto_pairseq'
+include { PRESTO_CLUSTERSETS    as  PRESTO_CLUSTERSETS_UMI   }    from '../../modules/local/presto/presto_clustersets'
+include { PRESTO_PARSE_CLUSTER  as  PRESTO_PARSE_CLUSTER_UMI }    from '../../modules/local/presto/presto_parse_cluster'
+include { PRESTO_BUILDCONSENSUS as  PRESTO_BUILDCONSENSUS_UMI}    from '../../modules/local/presto/presto_buildconsensus'
+include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_ALIGN }  from '../../modules/local/presto/presto_buildconsensus'
 include { PRESTO_POSTCONSENSUS_PAIRSEQ as PRESTO_POSTCONSENSUS_PAIRSEQ_UMI }    from '../../modules/local/presto/presto_postconsensus_pairseq'
-include { PRESTO_ASSEMBLEPAIRS  as  PRESTO_ASSEMBLEPAIRS_UMI }  from '../../modules/local/presto/presto_assemblepairs'
-include { PRESTO_ASSEMBLEPAIRS_SEQUENTIAL }                     from '../../modules/local/presto/presto_assemblepairs_sequential'
+include { PRESTO_ASSEMBLEPAIRS  as  PRESTO_ASSEMBLEPAIRS_UMI }    from '../../modules/local/presto/presto_assemblepairs'
+include { PRESTO_ASSEMBLEPAIRS_SEQUENTIAL                    }    from '../../modules/local/presto/presto_assemblepairs_sequential'
 include { PRESTO_PARSEHEADERS   as  PRESTO_PARSEHEADERS_COLLAPSE_UMI } from '../../modules/local/presto/presto_parseheaders'
-include { PRESTO_PARSEHEADERS   as  PRESTO_PARSEHEADERS_CREGION }   from '../../modules/local/presto/presto_parseheaders'
+include { PRESTO_PARSEHEADERS   as  PRESTO_PARSEHEADERS_CREGION } from '../../modules/local/presto/presto_parseheaders'
 include { PRESTO_PARSEHEADERS_PRIMERS   as PRESTO_PARSEHEADERS_PRIMERS_UMI }    from '../../modules/local/presto/presto_parseheaders_primers'
 include { PRESTO_PARSEHEADERS_METADATA  as PRESTO_PARSEHEADERS_METADATA_UMI }   from '../../modules/local/presto/presto_parseheaders_metadata'
-include { PRESTO_COLLAPSESEQ    as PRESTO_COLLAPSESEQ_UMI }     from '../../modules/local/presto/presto_collapseseq'
-include { PRESTO_COLLAPSESEQ    as PRESTO_COLLAPSESEQ_ALIGN }   from '../../modules/local/presto/presto_collapseseq'
-include { PRESTO_COLLAPSESEQ    as PRESTO_COLLAPSESEQ_CREGION } from '../../modules/local/presto/presto_collapseseq'
-include { PRESTO_SPLITSEQ       as PRESTO_SPLITSEQ_UMI}         from '../../modules/local/presto/presto_splitseq'
+include { PRESTO_COLLAPSESEQ    as PRESTO_COLLAPSESEQ_UMI    }    from '../../modules/local/presto/presto_collapseseq'
+include { PRESTO_COLLAPSESEQ    as PRESTO_COLLAPSESEQ_ALIGN  }    from '../../modules/local/presto/presto_collapseseq'
+include { PRESTO_COLLAPSESEQ    as PRESTO_COLLAPSESEQ_CREGION}    from '../../modules/local/presto/presto_collapseseq'
+include { PRESTO_SPLITSEQ       as PRESTO_SPLITSEQ_UMI       }    from '../../modules/local/presto/presto_splitseq'
 
 
 workflow PRESTO_UMI {
@@ -108,7 +108,7 @@ workflow PRESTO_UMI {
                                             .map{ reads -> [reads[0], reads[1]] }.dump(tag: 'ch_reads_R1')
         ch_reads_R2 = PRESTO_FILTERSEQ_UMI.out.reads
                                             .map{ reads -> [reads[0], reads[2]] }.dump(tag: 'ch_reads_R2')
-        PRESTO_MASKPRIMERS_ALIGN(
+        PRESTO_ALIGN_PRIMERS(
             ch_reads_R1,
             ch_cprimers.collect(),
             params.primer_maxlen,
@@ -119,15 +119,15 @@ workflow PRESTO_UMI {
             ch_reads_R2
         )
 
-        ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_ALIGN.out.versions)
+        ch_versions = ch_versions.mix(PRESTO_ALIGN_PRIMERS.out.versions)
         ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_EXTRACT.out.versions)
         // Merge again R1 and R2 by sample ID.
-        ch_maskprimers_reads_R1 = PRESTO_MASKPRIMERS_ALIGN.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R1')
+        ch_maskprimers_reads_R1 = PRESTO_ALIGN_PRIMERS.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R1')
         ch_maskprimers_reads_R2 = PRESTO_MASKPRIMERS_EXTRACT.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R2')
         ch_maskprimers_reads = ch_maskprimers_reads_R1.join(ch_maskprimers_reads_R2)
                                                         .map{ it -> [it[1], it[2], it[4]] }.dump(tag: 'ch_maskprimers_reads_after_remerge')
 
-        ch_maskprimers_logs = PRESTO_MASKPRIMERS_ALIGN.out.logs
+        ch_maskprimers_logs = PRESTO_ALIGN_PRIMERS.out.logs
         ch_maskprimers_logs = ch_maskprimers_logs.mix(PRESTO_MASKPRIMERS_EXTRACT.out.logs)
 
         PRESTO_PAIRSEQ_ALIGN( ch_maskprimers_reads )