Follow the lead, Timmy

nf-core · Jan 11, 2024 · e1b232f · e1b232f
1 parent cd69374
commit e1b232f
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Showing 3 changed files with 19 additions and 107 deletions.
diff --git a/subworkflows/local/umi_dedup.nf b/subworkflows/local/umi_dedup.nf
@@ -1,10 +1,10 @@
-// 
+//
 // Deduplicate the UMI reads by mapping them to the complete genome.
 //
 
 include { INDEX_GENOME                        } from '../../modules/local/bowtie_genome'
 include { BOWTIE_MAP_SEQ as UMI_MAP_GENOME    } from '../../modules/local/bowtie_map_mirna'
-include { BAM_SORT_SAMTOOLS                   } from '../../subworkflows/nf-core/bam_sort_samtools'
+include { BAM_SORT_STATS_SAMTOOLS             } from '../../subworkflows/nf-core/bam_sort_stats_samtools'
 include { UMITOOLS_DEDUP                      } from '../../modules/nf-core/modules/umitools/dedup/main'
 include { SAMTOOLS_BAM2FQ                     } from '../../modules/nf-core/modules/samtools/bam2fq/main'
 include { CAT_CAT                             } from '../../modules/nf-core/modules/cat/cat/main'
@@ -31,7 +31,7 @@ workflow DEDUPLICATE_UMIS {
     }
 
     if (bt_index){
-        
+
         UMI_MAP_GENOME ( reads, bt_index.collect() )
         ch_versions = ch_versions.mix(UMI_MAP_GENOME.out.versions)
 
@@ -54,7 +54,7 @@ workflow DEDUPLICATE_UMIS {
                 .join(UMI_MAP_GENOME.out.unmapped)
                 .map { meta, file1, file2 -> [meta, [file1, file2]]}
                 .set { ch_cat }
-    
+
             CAT_CAT ( ch_cat )
             ch_dedup_reads = CAT_CAT.out.file_out
         }

diff --git a/subworkflows/nf-core/fastqc_umitools_trimgalore.nf b/subworkflows/nf-core/fastqc_umitools_trimgalore.nf
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
@@ -64,14 +64,14 @@ if (!params.mirgenedb) {
     if (params.mirgenedb_gff) { mirna_gtf = file(params.mirgenedb_gff, checkIfExists: true) } else { exit 1, "MirGeneDB gff file not found: ${params.mirgenedb_gff}"}
 }
 
-include { INPUT_CHECK        } from '../subworkflows/local/input_check'
-include { FASTQC_UMITOOLS_FASTP } from '../subworkflows/nf-core/fastqc_umitools_trimgalore'
-include { DEDUPLICATE_UMIS           } from '../subworkflows/local/umi_dedup'
-include { CONTAMINANT_FILTER } from '../subworkflows/local/contaminant_filter'
-include { MIRNA_QUANT        } from '../subworkflows/local/mirna_quant'
-include { GENOME_QUANT       } from '../subworkflows/local/genome_quant'
-include { MIRTRACE           } from '../subworkflows/local/mirtrace'
-include { MIRDEEP2           } from '../subworkflows/local/mirdeep2'
+include { INPUT_CHECK           } from '../subworkflows/local/input_check'
+include { FASTQ_FASTQC_UMITOOLS_FASTP } from '../subworkflows/nf-core/fastq_fastqc_umitools_fastp'
+include { DEDUPLICATE_UMIS      } from '../subworkflows/local/umi_dedup'
+include { CONTAMINANT_FILTER    } from '../subworkflows/local/contaminant_filter'
+include { MIRNA_QUANT           } from '../subworkflows/local/mirna_quant'
+include { GENOME_QUANT          } from '../subworkflows/local/genome_quant'
+include { MIRTRACE              } from '../subworkflows/local/mirtrace'
+include { MIRDEEP2              } from '../subworkflows/local/mirdeep2'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -132,22 +132,19 @@ workflow SMRNASEQ {
     ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))
 
     //
-    // SUBWORKFLOW: Read QC and trim adapters
+    // SUBWORKFLOW: Read QC, extract UMI and trim adapters & dedup UMIs if necessary / desired by the user
     //
 
-    //
-    // SUBWORKFLOW: Read QC, extract UMI and trim adapters
-    //
-    FASTQC_UMITOOLS_FASTP (
+    FASTQ_FASTQC_UMITOOLS_FASTP (
         ch_cat_fastq,
         params.skip_fastqc || params.skip_qc,
         params.with_umi,
         params.skip_trimming,
         params.umi_discard_read
     )
-    ch_versions = ch_versions.mix(FASTQC_UMITOOLS_FASTP.out.versions)
+    ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions)
 
-    reads_for_mirna = FASTQC_UMITOOLS_FASTP.out.reads
+    reads_for_mirna = FASTQ_FASTQC_UMITOOLS_FASTP.out.reads
 
     //
     // SUBWORKFLOW: Deduplicate UMIs by mapping them to the genome
@@ -156,27 +153,20 @@ workflow SMRNASEQ {
         if (fasta){
             fasta_ch = file(fasta)
             DEDUPLICATE_UMIS (
-                fasta_ch, 
-                bt_index, 
+                fasta_ch,
+                bt_index,
                 FASTQC_UMITOOLS_FASTP.out.reads
             )
             reads_for_mirna = DEDUPLICATE_UMIS.out.reads
             ch_versions = ch_versions.mix(DEDUPLICATE_UMIS.out.versions)
         }
     }
 
-    FASTQC_UMITOOLS_FASTP (
-        ch_cat_fastq,
-        ch_fastp_adapters,
-        false,
-        false
-    )
-    ch_versions = ch_versions.mix(FASTQC_FASTP.out.versions)
 
     //
     // SUBWORKFLOW: mirtrace QC
     //
-    FASTQC_FASTP.out.adapterseq
+    FASTQ_FASTQC_UMITOOLS_FASTP.out.adapterseq
     .join( FASTQC_FASTP.out.reads )
     .map { meta, adapterseq, reads -> [adapterseq, meta.id, reads] }
     .groupTuple()