don't publish genomicsdb files

CHANGELOG.md

@@ -75,7 +75,7 @@ Bierikjávrre is one of the largest lake in Sarek.
 - [#1048](https://github.com/nf-core/sarek/pull/1048) - Skip tool validation on annotation to fix [#949](https://github.com/nf-core/sarek/issues/949), check that bam is bam and cram is cram [#895](https://github.com/nf-core/sarek/issues/895)
 - [#1050](https://github.com/nf-core/sarek/pull/1050) - Disable GATK VCF filters when joint calling to fix [#1025](https://github.com/nf-core/sarek/issues/1025)
 - [#1058](https://github.com/nf-core/sarek/pull/1058) - Fix container declaration for VCFTOOLS as it has been updated in the registry
-
+- [#1061](https://github.com/nf-core/sarek/pull/1061) - Fix GenomicsDB also works with one interval file, fix results publishing of GenomicsDB
 ### Removed
 
 - [#898](https://github.com/nf-core/sarek/pull/898) - Params `enable_conda` was removed

conf/modules/joint_germline.config

@@ -18,10 +18,16 @@ process {
     withName: 'GATK4_GENOMICSDBIMPORT' {
         ext.args         = { "--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader "}
         ext.prefix       = { "${meta.intervals_name}.joint" }
+        publishDir = [
+            enabled: false
+        ]
     }
 
     withName: 'GATK4_GENOTYPEGVCFS' {
         ext.prefix       = { meta.intervals_name }
+        publishDir = [
+            enabled: false
+        ]
     }
 
     if (params.tools && params.tools.contains('haplotypecaller') && params.joint_germline) {

subworkflows/local/bam_merge_index_samtools/main.nf

@@ -23,7 +23,7 @@ workflow BAM_MERGE_INDEX_SAMTOOLS {
     }
 
     // Only when using intervals
-    MERGE_BAM(bam_to_merge.multiple, [], [])
+    MERGE_BAM(bam_to_merge.multiple, [ [ id:'null' ], []], [ [ id:'null' ], []])
 
     // Mix intervals and no_intervals channels together
     bam_all = MERGE_BAM.out.bam.mix(bam_to_merge.single)

tests/test_joint_germline.yml

@@ -1,5 +1,5 @@
 - name: Run joint germline variant calling with haplotypecaller
-  command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --skip_tools haplotypecaller_filter --outdir results
+  command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results
   tags:
     - germline
     - joint_germline

workflows/sarek.nf

@@ -387,12 +387,12 @@ workflow SAREK {
     intervals_bed_gz_tbi = PREPARE_INTERVALS.out.intervals_bed_gz_tbi // [ interval_bed, tbi, num_intervals ] multiple interval.bed.gz/.tbi files, divided by useful intervals for scatter/gather
 
     intervals_and_num_intervals = intervals.map{ interval, num_intervals ->
-        if ( num_intervals <= 1 ) [ [], num_intervals ]
+        if ( num_intervals < 1 ) [ [], num_intervals ]
         else [ interval, num_intervals ]
     }
 
     intervals_bed_gz_tbi_and_num_intervals = intervals_bed_gz_tbi.map{ intervals, num_intervals ->
-        if ( num_intervals <= 1 ) [ [], [], num_intervals ]
+        if ( num_intervals < 1 ) [ [], [], num_intervals ]
         else [ intervals[0], intervals[1], num_intervals ]
     }
 
@@ -532,7 +532,7 @@ workflow SAREK {
 
             // Use groupKey to make sure that the correct group can advance as soon as it is complete
             // and not stall the workflow until all reads from all channels are mapped
-            [ groupKey( meta - meta.subMap('num_lanes', 'read_group', 'size') + [ data_type:'bam', id:meta.sample ], (meta.num_lanes ?: 1) * (meta.size ?: 1) ), bam ]
+            [ groupKey( meta - meta.subMap('num_lanes', 'read_group', 'size') + [ data_type:'bam', id:meta.sample ], (meta.num_lanes ?: 1) * (meta.size ?: 1)), bam ]
         }.groupTuple()
 
         // gatk4 markduplicates can handle multiple bams as input, so no need to merge/index here
@@ -1037,7 +1037,7 @@ workflow SAREK {
 
         if (params.tools.split(',').contains('merge') || params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep')) {
 
-            vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[], []]
+            vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []]
 
             VCF_ANNOTATE_ALL(
                 vcf_to_annotate,