From 9318bd29aacb3c1ab65624f0afeecfa6a43b5b43 Mon Sep 17 00:00:00 2001 From: Radoslaw Suchecki Date: Thu, 1 Aug 2019 13:29:32 +0930 Subject: [PATCH] Fixed storeDir issue Given a default, single accession run followed by a run with all the accessions, the use of generic file output glob in conjunction with storeDir directive caused an issue with read files being incorrectly classed as present and reads for accession 1 output for every accession, causing pipeline to fail due tu duplicate file names at multiqc step where the files are collected. --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index f827075..bc02663 100644 --- a/main.nf +++ b/main.nf @@ -64,14 +64,14 @@ process bgzip_chromosome_subregion { process extract_reads { tag { accession } - storeDir { "${params.outdir}/downloaded_reads" } //use with care, caching will not work as normal so changes to input may not take effect + storeDir { "${workDir}/downloaded_reads" } //use with care, caching will not work as normal so changes to input may not take effect input: val accession from accessionsChannel //e.g. ACBarrie output: - set val(accession), file('*.fastq.gz') into (extractedReadsChannelA, extractedReadsChannelB) + set val(accession), file("${accession}_R?.fastq.gz") into (extractedReadsChannelA, extractedReadsChannelB) //e.g. ACBarrie, [ACBarrie_R1.fastq.gz, ACBarrie_R2.fastq.gz] script: