From 188834e9df075141815aa2ab9633b1cc91feeb52 Mon Sep 17 00:00:00 2001 From: EC2 Default User Date: Wed, 27 Nov 2024 14:29:10 +0000 Subject: [PATCH] Moving two files to be stored in working directory rather than launch directory. --- workflows/run.nf | 4 ++-- workflows/run_validation.nf | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/run.nf b/workflows/run.nf index 4adf907..12080eb 100644 --- a/workflows/run.nf +++ b/workflows/run.nf @@ -84,9 +84,9 @@ workflow RUN { time_ch = Channel.of(start_time_str + "\n").collectFile(name: "time.txt") version_ch = Channel.fromPath("${projectDir}/pipeline-version.txt") index_params_ch = Channel.fromPath("${params.ref_dir}/input/index-params.json") - .map { file -> file.copyTo("params-index.json") } + .map { file -> file.copyTo("${workDir}/params-index.json") } index_pipeline_version_ch = Channel.fromPath("${params.ref_dir}/logging/pipeline-version.txt") - .map { file -> file.copyTo("pipeline-version-index.txt") } + .map { file -> file.copyTo("${workDir}/pipeline-version-index.txt") } publish: // Saved inputs index_params_ch >> "input" diff --git a/workflows/run_validation.nf b/workflows/run_validation.nf index a1602df..66e55ca 100644 --- a/workflows/run_validation.nf +++ b/workflows/run_validation.nf @@ -43,9 +43,9 @@ workflow RUN_VALIDATION { time_ch = Channel.of(start_time_str + "\n").collectFile(name: "time.txt") version_ch = Channel.fromPath("${projectDir}/pipeline-version.txt") index_params_ch = Channel.fromPath("${params.ref_dir}/input/index-params.json") - .map { file -> file.copyTo("params-index.json") } + .map { file -> file.copyTo("${workDir}/params-index.json") } index_pipeline_version_ch = Channel.fromPath("${params.ref_dir}/logging/pipeline-version.txt") - .map { file -> file.copyTo("pipeline-version-index.txt") } + .map { file -> file.copyTo("${workDir}/pipeline-version-index.txt") } publish: // Saved inputs index_params_ch >> "input"