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publishing run command alongside each workflow's results so multiple …
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…run commands can be published
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nrminor committed Nov 7, 2024
1 parent e31ae06 commit fd31102
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Showing 3 changed files with 7 additions and 1 deletion.
3 changes: 3 additions & 0 deletions conf/illumina.config
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ params {
// split off ont results
params.illumina_results = params.results + "/illumina"

// Where to place the Nanopore workflow run command
run_command = params.illumina_results

// paired read merging
merged = params.illumina_results + "/01_merged_reads"

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3 changes: 3 additions & 0 deletions conf/nanopore.config
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ params {
// split off ont results
params.ont_results = params.results + "/nanopore"

// Where to place the Nanopore workflow run command
run_command = params.ont_results

// basecalling and demultiplexing results
basecall_results = params.ont_results + "/01_basecalled_demuxed"
basecall_bams = params.basecall_results + "/bams"
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2 changes: 1 addition & 1 deletion modules/reporting.nf
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Expand Up @@ -30,7 +30,7 @@ process PUBLISH_COMMAND {

/* */

publishDir params.results, mode: "copy", overwrite: true
publishDir params.run_command, mode: "copy", overwrite: true

errorStrategy { task.attempt < 2 ? 'retry' : 'ignore' }
maxRetries 1
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