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Changes gtex input to support new manifest file format [#289] #296

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merged 2 commits into from
Dec 10, 2021
Merged

Changes gtex input to support new manifest file format [#289] #296

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3b3fe86
Updates ch_gtex_gen3_ids items #289
cgpu Dec 8, 2021
36e2ca6
Remove duplicate val(obj_id) in input of gen3-drs
Vlad-Dembrovskyi Dec 9, 2021
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4 changes: 2 additions & 2 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -281,7 +281,7 @@ if (params.download_from) {
.fromPath(params.reads)
.ifEmpty { exit 1, "Cannot find CSV reads file : ${params.reads}" }
.splitCsv(skip:1)
.map { subj_id, file_name, md5sum, obj_id, file_size -> [subj_id, file_name, md5sum, obj_id, file_size] }
.map { md5sum, file_name, obj_id, file_size -> [md5sum, file_name, obj_id, file_size] }
.set { ch_gtex_gen3_ids }
}
if(download_from('ftp')){
Expand Down Expand Up @@ -471,7 +471,7 @@ if ( download_from('gen3-drs')) {
publishDir "${params.outdir}/process-logs/${task.process}/${file(file_name).baseName}", pattern: "command-logs-*", mode: 'copy'

input:
set val(subj_id), val(file_name), val(md5sum), val(obj_id), val(file_size) from ch_gtex_gen3_ids
set val(md5sum), val(file_name), val(obj_id), val(file_size) from ch_gtex_gen3_ids
each file(key_file) from key_file
each file(genome_fasta) from ch_genome_fasta

Expand Down