From c3d1527585a73158bd610449030b890883723705 Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 6 Mar 2020 17:19:34 +0100
Subject: [PATCH] Replace cufflinks image with gffread image
---
Snakefile | 2 +-
tests/test_integration_workflow/expected_output.md5 | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 156e124..3f398ba 100644
--- a/Snakefile
+++ b/Snakefile
@@ -207,7 +207,7 @@ rule extract_transcriptome:
config['log_dir'],
"{organism}_extract_transcriptome.log")
singularity:
- "docker://zavolab/cufflinks:2.2.1"
+ "docker://zavolab/gffread:0.11.7"
shell:
"(gffread \
-w {output.transcriptome} \
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 93a8f66..f490996 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -86,4 +86,4 @@ ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_s
ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg
ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
-79fc3e46b3ac1a72b80cb7bebf6058cd results/transcriptome/homo_sapiens/transcriptome.fa
+3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
--
GitLab