Adding sample-level coverage to primary MultiQC report

modules/samtools/merge/main.nf

@@ -9,7 +9,7 @@ process SAMTOOLS_MERGE {
     tag "${meta.sample_id}"
 
     input:
-    tuple val(meta), path(aligned_bam_list)
+    tuple val(meta), path(aligned_bam_list, stageAs: 'input*/*')
 
     output:
     tuple val(meta), path(merged_bam), emit: bam

subworkflows/coverage/main.nf

@@ -56,6 +56,12 @@ workflow COVERAGE {
     )
     ch_bam = ch_bam.mix(ALIGN_LONG_READS.out.bam)
 
+    /*
+    We need both platform-specific as well as 
+    sample-level coverage reports. So we combine all bams
+    for one sample to compute a global coverage in addition
+    to the platform-level reports
+    */
     bam_mapped = ch_bam.map { meta, bam ->
         new_meta = [:]
         new_meta.sample_id = meta.sample_id
@@ -68,9 +74,18 @@ workflow COVERAGE {
         multiple: it[1].size() > 1
     }.set { bam_to_merge }
 
+    SAMTOOLS_MERGE(
+        bam_to_merge.multiple
+    )
+
+    bam_to_merge.single.mix(SAMTOOLS_MERGE.out.bam).map { m,b -> 
+        m.platform = "ALL"
+        tuple(m,b)
+    }.set { ch_bam_all }
+
     // Index the BAM files
     SAMTOOLS_INDEX(
-        ch_bam
+        ch_bam.mix(ch_bam_all)
     )
 
     // Calculate coverage

subworkflows/find_references/main.nf

@@ -31,6 +31,10 @@ workflow FIND_REFERENCES {
         tuple(m, r)
     }.set { mash_with_gbk }
 
+    mash_with_gbk.map { m,r ->
+        "${m.sample_id}\t${r.getBaseName()}"
+    }.view()
+
     mash_with_gbk.map { m, r ->
         m.gbk
     }.unique()

workflows/gabi.nf

@@ -234,6 +234,11 @@ workflow GABI {
             m.platform == "PACBIO"
         }.map { m,r -> r }
     )
+    multiqc_files = multiqc_files.mix(
+        COVERAGE.out.report.filter { m,r ->
+            m.platform == "ALL"
+        }.map { m,r -> r }
+    )
 
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~