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add dbSNP rsID file to harmonization qc process/workflow #73

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add dbSNP rsID file to harmonization qc process/workflow #73

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10 changes: 6 additions & 4 deletions modules/local/qc.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -6,22 +6,24 @@ process qc {

input:
tuple val(GCST), val(mode), path(all_hm)
path(rsIDfile)

output:
tuple val(GCST), val(mode),path(all_hm), path('harmonised.qc.tsv'), path('report.txt'), emit: qc_ed
//path 'harmonised.qc.tsv.gz', emit: qc_result
//path 'report.txt', emit:delete_sites
//tuple path("${GCST}.h.tsv.gz"), path("${GCST}.h.tsv.gz.tbi"), emit: ftp_folder_results

shell:
"""
basic_qc_nf.py \
-f $all_hm \
-o harmonised.qc.tsv \
--log report.txt \
-db ${params.ref}/rsID.sql
-db $rsIDfile

cat harmonised.qc.tsv | bgzip -c > ${launchDir}/$GCST/final/${GCST}.h.tsv.gz

tabix -c N -S 1 -f -s 3 -b 4 -e 4 ${launchDir}/$GCST/final/${GCST}.h.tsv.gz
cat harmonised.qc.tsv | bgzip -c > ${GCST}.h.tsv.gz
tabix -c N -S 1 -f -s 3 -b 4 -e 4 ${GCST}.h.tsv.gz
"""
}
3 changes: 2 additions & 1 deletion subworkflows/local/quality_control.nf
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Expand Up @@ -14,7 +14,8 @@ workflow quality_control{
unmapped

main:
qc(ch_tsv)
rsID_file=Channel.fromPath("${params.ref}/rsID.sql")
qc(ch_tsv, rsID_file)
ch_to_log=qc.out.qc_ed.combine(ch_direction,by:0).combine(inputs,by:0)
ch_to_log.view()
//ch_to_log: val(GCST), val(mode),path(all_hm), path('harmonized.qc.tsv'), path('report.txt'), path (total_sum), val(build), path (input)
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