Hello there,
I’ve following code:
consensus.out.consensus_vcf
.map{meta, vcf_consensus->["${meta.timepoint}", meta, vcf_consensus]}
.join(bamreadcount.out.bamreadcount_tsv.
map{meta,readcount_tsv->["${meta.timepoint}",meta, readcount_tsv ]}, failOnMismatch:true, failOnDuplicate:true)
.groupTuple()
.multiMap { pid, meta1, vcf_consensus, meta2, tsv_bamreadcount->
vcfconsensus: [ meta1, vcf_consensus ]
bamreadcount: [ meta2, tsv_bamreadcount]
}
.set { ch_joined_vcfconsensus_bamreadcount }
I join based on patient-id or timepoint from the meta information, group them by tuple and finally create a multi-map.
I send these created channels as:
vcf_annotate(ch_joined_vcfconsensus_bamreadcount.vcfconsensus, ch_joined_vcfconsensus_bamreadcount.bamreadcount)
The vcf_annotate looks like:
input:
tuple val(meta), path(consensus_vcf, stageAs: 'vcf_annotate/*')
tuple val(meta), path(bamreadcount_tsv, stageAs: 'vcf_annotate/*')
When I print/view one channel I see there are three [ :
ch_joined_vcfconsensus_bamreadcount.vcfconsensus.view()
[[[batch:SEMA-MM-001, timepoint:MM-0486-T-01, tissue:normal, sequencing_type:wes]], [/mnt/data1/users/sanjeev/nextflow/meta_structure/work/c9
/df210a53f6a532e2739f674b3260bc/consensus.vcf]]
[[[batch:SEMA-MM-001, timepoint:MM-0364-T-02, tissue:normal, sequencing_type:wes]], [/mnt/data1/users/sanjeev/nextflow/meta_structure/work/a4
/55a42d946cbacf810dccdd5ff6dfdb/consensus.vcf]]
[[[batch:SEMA-MM-001, timepoint:MM-0487-T-01, tissue:normal, sequencing_type:wes]], [/mnt/data1/users/sanjeev/nextflow/meta_structure/work/8e
/4779acdcff9266103d0c479feb2548/consensus.vcf]]
[[[batch:SEMA-MM-001, timepoint:MM-0473-T-02, tissue:normal, sequencing_type:wes]], [/mnt/data1/users/sanjeev/nextflow/meta_structure/work/20
/5f439613d32b867136a2bc8ab2d19f/consensus.vcf]]
[[[batch:SEMA-MM-001, timepoint:MM-0489-T-01, tissue:normal, sequencing_type:wes]], [/mnt/data1/users/sanjeev/nextflow/meta_structure/work/76
/3f1f628dd2bd503511fc67dce36dab/consensus.vcf]]
[[[batch:SEMA-MM-001, timepoint:MM-3309-T-01, tissue:normal, sequencing_type:wes]], [/mnt/data1/users/sanjeev/nextflow/meta_structure/work/5a
/20a961a4fb34b5c1bb45f00f87130b/consensus.vcf]]
The process works fine, however, it creates a different folder on the level of existing folders.
Please see attached screenshot.
Similarly folders inside this has ’ on their names. Attached screenshot.
It isn’t the case with other parts of the pipeline. The issue enters when I use groupTuple and send it.
Please help to solve this.