From 406d456edd15715f7e14338b8195d2a09a807e49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ann-Kathrin=20Br=C3=BCggemann?= <90249112+AKBrueggemann@users.noreply.github.com> Date: Thu, 23 Mar 2023 13:53:47 +0100 Subject: [PATCH] fix: changes in path requirements for snakedeploy (#590) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Changes in path requirements for snakedeploy * fmt * Changed path * Different approach to url passing * fmt * Changed path creation * Update workflow/rules/common.smk Co-authored-by: Johannes Köster * fmt * Rewind change * Change in directory call * Revert "Change in directory call" This reverts commit b5501c414a7275e8ad0cb41bfc918e8a663a88d2. --------- Co-authored-by: Johannes Köster Co-authored-by: Johannes Köster --- workflow/rules/common.smk | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 3cb8c7b4..e3b72a97 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -4,6 +4,7 @@ # except according to those terms. from pathlib import Path +import os.path import pandas as pd import re import random @@ -212,7 +213,7 @@ def get_fastqs(wildcards): def get_resource(name): - return str((Path(workflow.snakefile).parent.parent.parent / "resources") / name) + return workflow.source_path(f"../../resources/{name}") def get_report_input(pattern):