Merge branch 'CW-7332' into 'dev'

IGV tracks mismatch index when there is one BAM per sample [CW-7332,CW-7349]

Closes CW-7332

See merge request epi2melabs/workflows/wf-transcriptomes!332

.gitlab-ci.yml

@@ -12,7 +12,7 @@ variables:
               PYTEST_TESTS_PATH: "bin/workflow_glue/tests/common"
               RTEST_CONTAINER_NAME: "wf-transcriptomes-core"
               RTEST_CONTAINER_CONFIG_KEY: "container_sha"
-              WF_TEMPLATE_ENFORCEMENT_REF: "v6.1.0-rc1"
+              WF_TEMPLATE_ENFORCEMENT_REF: "v6.1.0-rc2"
               EKS_RUNNER_SIZE: "xlarge-highio"
 
 pytest_wfcontainer:

CHANGELOG.md

@@ -15,6 +15,7 @@ Users of wf-transcriptomes v2.0.0 who have encountered issues during discovery a
 - "unable to find an inherited method for function 'rowData'" encountered during `runJointBambuDiscover` when providing many samples. The workflow now correctly handles data spilled to disk by bambu discover.
 - Volcano plot class counts incorrect when `log2FoldChange` or `padj` columns contained NA values.
 - Adjusted p-values below 0.001 in the volcano selection table are now shown in scientific notation instead of being rounded to 0.000.
+- IGV track not correctly loading in EPI2ME Desktop when a sample consists of a single input BAM.
 
 ## [v2.0.0]
 

lib/ingress.nf

@@ -480,14 +480,15 @@ def xam_ingress(Map arguments, aln_ref_ch = null)
             output_xam_fmt,
             margs
         )
-        // Update meta is unaligned
+        // Update meta for newly aligned inputs
         mm2_aln_final = mm2_aln.alignment.map{
             meta, xam, xai, stats ->
                 // remove alignment routing metadata that is no longer required
                 def newmeta = meta.findAll {
                     k, v -> !(k in ['has_reads', 'requires_alignment'])
                 }
-                [newmeta + [is_unaligned: false], xam, xai, stats]
+                // flip is_unaligned marker and drop references to input xam
+                [newmeta + [is_unaligned: false, src_xam: null, src_xai: null], xam, xai, stats]
         }
         // Process BAM files that do not require realignment by passing them through the standard downstream steps (merging, sorting, indexing, etc.)
         ch_result_tmp = alignment_fork.noalign.map{

main.nf

@@ -177,8 +177,9 @@ workflow wf {
             .collect()
 
         // meta.src_xam is non-null if BAMs are "passed through"
+        // while meta.src_xai can be null if xam are provided without index
         generated_alignment_outputs = reads
-            .filter { meta, bam, bai, stats -> meta.src_xam == null }
+            .filter { meta, bam, bai, stats -> meta.src_xam == null || meta.src_xai == null }
             .flatMap { meta, bam, bai, stats ->
                 def outdir = "samples/${meta.alias}/alignment"
                 [
@@ -343,7 +344,6 @@ workflow {
         ] + ingress_args, ref_genome)
     }
 
-
     sample_sheet_aliases = sample_sheet == OPTIONAL_FILE ?
         null :
         sample_sheet
@@ -359,7 +359,6 @@ workflow {
         }
     }
 
-
     analysis_samples = samples
         .filter { meta, xam, xai, stats ->
             boolean is_excluded = false
@@ -387,7 +386,6 @@ workflow {
         }
 
     processed_samples = analysis_samples
-
     pipeline_run = wf(processed_samples, sample_sheet, ref_genome, ref_annotation)
     results = pipeline_run.results
 
@@ -417,11 +415,18 @@ workflow {
             .map { [ it[0], "reference" ] }
 
         igv_alignment_paths = processed_samples
-            .map { meta, bam, bai, stat -> [
-                meta.src_xam ?: "${meta.alias},samples/${meta.alias}/alignment/reads.bam",
-                meta.src_xai ?: "${meta.alias},samples/${meta.alias}/alignment/reads.bam.bai"
-            ] }
-            .flatten()
+            .map { meta, bam, bai, stat ->
+                // Fall back to the published BAM/BAI pair whenever either source path is missing.
+                def use_published_alignment = (meta.src_xam == null || meta.src_xai == null)
+                [
+                    use_published_alignment
+                        ? "${meta.alias},samples/${meta.alias}/alignment/reads.bam"
+                        : "${meta.alias},${meta.src_xam}",
+                    use_published_alignment
+                        ? "${meta.alias},samples/${meta.alias}/alignment/reads.bam.bai"
+                        : "${meta.alias},${meta.src_xai}",
+                ]
+            }.flatten()
 
         // convert [alias0, [bw00...bw0N]] to [alias0, bw00] ... [aliasN, bwNN]
         // allowing for [aliasM, bwM0] if only one bw is output because ... nextflow