Improvements to channel handling

nf-core · Jan 11, 2024 · 2828bd2 · 2828bd2
1 parent e1b232f
commit 2828bd2
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Showing 2 changed files with 16 additions and 8 deletions.
diff --git a/subworkflows/local/umi_dedup.nf b/subworkflows/local/umi_dedup.nf
@@ -5,9 +5,10 @@
 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_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'
+include { UMITOOLS_DEDUP                      } from '../../modules/nf-core/umitools/dedup/main'
+include { SAMTOOLS_BAM2FQ                     } from '../../modules/nf-core/samtools/bam2fq/main'
+include { CAT_CAT                             } from '../../modules/nf-core/cat/cat/main'
+
 
 workflow DEDUPLICATE_UMIS {
     take:

diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
@@ -137,14 +137,21 @@ workflow SMRNASEQ {
 
     FASTQ_FASTQC_UMITOOLS_FASTP (
         ch_cat_fastq,
-        params.skip_fastqc || params.skip_qc,
+        params.skip_fastqc,
         params.with_umi,
+        params.skip_umi_extract,
+        params.umi_discard_read,
         params.skip_trimming,
-        params.umi_discard_read
+        params.umi_discard_read,
+        params.skip_trimming,
+        params.adapter_fasta,
+        params.save_trimmed_fail,
+        params.save_merged,
+        params.min_trimmed_reads
     )
     ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions)
 
-    reads_for_mirna = FASTQ_FASTQC_UMITOOLS_FASTP.out.reads
+    reads_for_mirna = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads
 
     //
     // SUBWORKFLOW: Deduplicate UMIs by mapping them to the genome
@@ -155,7 +162,7 @@ workflow SMRNASEQ {
             DEDUPLICATE_UMIS (
                 fasta_ch,
                 bt_index,
-                FASTQC_UMITOOLS_FASTP.out.reads
+                FASTQC_UMITOOLS_FASTP.out.trim_reads
             )
             reads_for_mirna = DEDUPLICATE_UMIS.out.reads
             ch_versions = ch_versions.mix(DEDUPLICATE_UMIS.out.versions)
@@ -167,7 +174,7 @@ workflow SMRNASEQ {
     // SUBWORKFLOW: mirtrace QC
     //
     FASTQ_FASTQC_UMITOOLS_FASTP.out.adapterseq
-    .join( FASTQC_FASTP.out.reads )
+    .join( FASTQ_FASTQC_UMITOOLS_FASTP.out.reads )
     .map { meta, adapterseq, reads -> [adapterseq, meta.id, reads] }
     .groupTuple()
     .set { ch_mirtrace_inputs }