fixing branching of contigs

Joon-Klaps · Aug 7, 2023 · 5069022 · 5069022
1 parent abf7167
commit 5069022
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Showing 3 changed files with 6 additions and 8 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -412,7 +412,7 @@ process {
             publishDir = [
                 path: { "${params.outdir}/consensus_qc/checkv/" },
                 mode: params.publish_dir_mode,
-                pattern: "**.{tsv/fna}"
+                pattern: "**.{tsv,fna}"
             ]
         }
 
@@ -429,7 +429,7 @@ process {
             publishDir = [
                 path: { "${params.outdir}/consensus_qc/quast/" },
                 mode: params.publish_dir_mode,
-                pattern: "checkv_db"
+                pattern: "*.tsv"
             ]
         }
     }

diff --git a/subworkflows/local/clust_seq_extract.nf b/subworkflows/local/clust_seq_extract.nf
@@ -69,7 +69,7 @@ def create_member_ref_channel(ArrayList row) {
     sample             = String.valueOf(row[0].id) // just to make sure we don't pass by reference
     regex              = (members =~ /.*\/.*_([0-9]+)_n([0-9]+)_members.txt/) // try and extract the correct cluster ID and size associated to the sample
     cluster            = regex[0][1]
-    cluster_size       = regex[0][2]
+    cluster_size       = regex[0][2] as int
     id                 = "${sample}_${cluster}"
 
     new_meta = row[0] + [ id: id, cluster: cluster, cluster_size: cluster_size, sample: sample]

diff --git a/workflows/viralgenie.nf b/workflows/viralgenie.nf
@@ -134,6 +134,7 @@ workflow VIRALGENIE {
     }
 
     // Assembly
+    ch_consensus = Channel.empty()
     if (!params.skip_assembly) {
         FASTQ_SPADES_TRINITY_MEGAHIT(
             PREPROCESSING_ILLUMINA.out.reads,
@@ -163,15 +164,12 @@ workflow VIRALGENIE {
                 }
                 .set{ch_centroids_members}
             ch_versions = ch_versions.mix(FASTA_BLAST_CLUST.out.versions)
-
-            //TODO: ch_centroids_members.multiple still not working properly
-            ch_centroids_members.multiple.view()
-            //ch_centroids_members.singletons.view()
 
             ALIGN_COLLAPSE_CONTIGS(
-                FASTA_BLAST_CLUST.out.centroids_members,
+                ch_centroids_members.multiple,
                 params.contig_align_method
                 )
+
             ch_versions = ch_versions.mix(ALIGN_COLLAPSE_CONTIGS.out.versions)
             ch_consensus = ALIGN_COLLAPSE_CONTIGS.out.consensus