From d6811e7170c8a7e0d92f3b2593a8ee1d97a13769 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Thu, 1 Feb 2024 16:59:50 +0100 Subject: [PATCH] fix: Cutadapt compression level problem (#153) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Máté Balajti --- tests/test_htsinfer_workflow/expected_output.md5 | 4 ++-- workflow/Snakefile | 1 + workflow/envs/cutadapt.yaml | 2 +- workflow/rules/paired_end.snakefile.smk | 2 +- workflow/rules/single_end.snakefile.smk | 2 +- 5 files changed, 6 insertions(+), 5 deletions(-) diff --git a/tests/test_htsinfer_workflow/expected_output.md5 b/tests/test_htsinfer_workflow/expected_output.md5 index 7f585a9..22e9037 100644 --- a/tests/test_htsinfer_workflow/expected_output.md5 +++ b/tests/test_htsinfer_workflow/expected_output.md5 @@ -1,3 +1,3 @@ 1dc3f566f896b72f8f0ab8b3d60da364 results/samples_htsinfer.tsv -642935539533503952f755dbe280fcbd results/htsinfer_SRR1.json -1632c04cd856a1af0abc964304d8e218 results/htsinfer_SRR2.json +ca3f9ef26821bfa061d3b7708823ebc3 results/htsinfer_SRR1.json +62303261f8dd73124c2a5a54cd28e572 results/htsinfer_SRR2.json diff --git a/workflow/Snakefile b/workflow/Snakefile index 9f8f1ca..da8beb8 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -1,4 +1,5 @@ """General purpose RNA-Seq analysis pipeline developed by the Zavolan Lab""" + import os import pandas as pd import shutil diff --git a/workflow/envs/cutadapt.yaml b/workflow/envs/cutadapt.yaml index 064d302..4a42250 100644 --- a/workflow/envs/cutadapt.yaml +++ b/workflow/envs/cutadapt.yaml @@ -3,5 +3,5 @@ channels: - conda-forge - bioconda dependencies: - - cutadapt=3.4 + - cutadapt=4.6 ... diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk index 2521c49..cbc2b1a 100644 --- a/workflow/rules/paired_end.snakefile.smk +++ b/workflow/rules/paired_end.snakefile.smk @@ -64,7 +64,7 @@ rule pe_remove_adapters_cutadapt: ), ), container: - "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1" + "docker://quay.io/biocontainers/cutadapt:4.6--py310h4b81fae_1" conda: os.path.join(workflow.basedir, "envs", "cutadapt.yaml") threads: 4 diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk index 0f25f6c..57e13b5 100644 --- a/workflow/rules/single_end.snakefile.smk +++ b/workflow/rules/single_end.snakefile.smk @@ -112,7 +112,7 @@ rule remove_polya_cutadapt: ), ), container: - "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1" + "docker://quay.io/biocontainers/cutadapt:4.6--py310h4b81fae_1" conda: os.path.join(workflow.basedir, "envs", "cutadapt.yaml") threads: 4