Merge pull request #278 from replikation/master

Update ww-porecov branch to latest master
replikation · Dec 16, 2024 · 210f73a · 210f73a
2 parents 7d674f6 + b3b8620
commit 210f73a
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/poreCov.nf b/poreCov.nf
@@ -443,7 +443,7 @@ workflow {
                     read_screening_lsc_wf(filtered_reads_ch)
                 }
                 if (params.freyja) {
-                    read_screening_freyja_wf(artic_ncov_wf.out.binary_alignment.combine(reference_for_qc_input_ch))
+                    read_screening_freyja_wf(artic_ncov_wf.out.trimmed_bam.map{it -> [it[0], it[1]]}.combine(reference_for_qc_input_ch))
                 }
             }
             alignments_ch = align_to_reference(filtered_reads_ch.combine(reference_for_qc_input_ch))