From 3166828599219963af83e16bb83dd672db58557b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=98ens-ftricomi=E2=80=99?= Date: Thu, 15 Aug 2024 17:18:38 +0100 Subject: [PATCH] bug fix genome dir path --- pipelines/nextflow/modules/star_alignment/index_genome.nf | 2 +- .../nextflow/modules/transcriptomic_alignment/index_genome.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pipelines/nextflow/modules/star_alignment/index_genome.nf b/pipelines/nextflow/modules/star_alignment/index_genome.nf index 0975544..7ae725b 100644 --- a/pipelines/nextflow/modules/star_alignment/index_genome.nf +++ b/pipelines/nextflow/modules/star_alignment/index_genome.nf @@ -39,7 +39,7 @@ process INDEX_GENOME { //if (!genomeIndexFile.exists() || genomeIndexFile.length() == 0) { // Read the .fna file and perfor // d= new File("${genomeDir}") - def genomefilePath=d.listFiles().find { it.name.endsWith('.fna') } + def genomefilePath=genomeDirPath.listFiles().find { it.name.endsWith('.fna') } def genomeFile=genomefilePath.absolutePath // Function to calculate the min value def min = { a, b -> a < b ? a : b } diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf index 45ddebc..36a1651 100644 --- a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf +++ b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf @@ -39,7 +39,7 @@ process INDEX_GENOME { //if (!genomeIndexFile.exists() || genomeIndexFile.length() == 0) { // Read the .fna file and perfor // d= new File("${genomeDir}") - def genomefilePath=d.listFiles().find { it.name.endsWith('.fna') } + def genomefilePath=genomeDirPath.listFiles().find { it.name.endsWith('.fna') } def genomeFile=genomefilePath.absolutePath // Function to calculate the min value def min = { a, b -> a < b ? a : b }