Fixing warning message produced by nanocomp so that files are passed …

…in correctly
nf-core · Mar 13, 2024 · 6e358bc · 6e358bc
1 parent 2714573
commit 6e358bc
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Showing 2 changed files with 6 additions and 9 deletions.
diff --git a/modules/local/nanocomp.nf b/modules/local/nanocomp.nf
@@ -7,7 +7,8 @@ process NANOCOMP {
         'biocontainers/nanocomp:1.20.0--pyhdfd78af_0' }"
 
     input:
-    tuple path(ont_files), path(ont_files_idx)
+    path(ont_files)
+    path(idx_files)
 
     output:
     path "*.html"       , emit: html

diff --git a/workflows/scnanoseq.nf b/workflows/scnanoseq.nf
@@ -197,11 +197,9 @@ workflow SCNANOSEQ {
     ch_nanocomp_fastq_html = Channel.empty()
     ch_nanocomp_fastq_txt = Channel.empty()
     if (!params.skip_qc && !params.skip_fastq_nanocomp) {
-        ch_nanocomp_fastqs = ch_cat_fastq
-                                 .collect{it[1]}
-                                 .combine( ch_dummy_file )
 
-        NANOCOMP_FASTQ ( ch_nanocomp_fastqs )
+        NANOCOMP_FASTQ ( ch_cat_fastq.collect{it[1]},
+                         ch_dummy_file )
         ch_nanocomp_fastq_html = NANOCOMP_FASTQ.out.html
         ch_nanocomp_fastq_txt = NANOCOMP_FASTQ.out.txt
 
@@ -437,11 +435,9 @@ workflow SCNANOSEQ {
     ch_nanocomp_bam_txt = Channel.empty()
 
     if (!params.skip_qc && !params.skip_bam_nanocomp) {
-        ch_nanocomp_bams = ch_minimap_sorted_bam
-                               .collect{it[1]}
-                               .join( ch_minimap_sorted_bai, by: 0 )
 
-        NANOCOMP_BAM ( ch_nanocomp_bams )
+        NANOCOMP_BAM ( ch_minimap_sorted_bam.collect{it[1]},
+                       ch_minimap_sorted_bai.collect{it[1]})
 
         ch_nanocomp_bam_html = NANOCOMP_BAM.out.html
         ch_nanocomp_bam_txt = NANOCOMP_BAM.out.txt