From 27d21a222a6eddd5de391b5d6f8191776ed1e6d4 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Thu, 1 Feb 2024 04:48:46 +0100 Subject: [PATCH 1/5] fix: Cutadapt compression problem --- workflow/envs/cutadapt.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 ... From 5083cd8a171f920e2ca7095417de772c8ef4d9a3 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Thu, 1 Feb 2024 04:59:37 +0100 Subject: [PATCH 2/5] update Biocontainers image tag as well --- workflow/rules/paired_end.snakefile.smk | 2 +- workflow/rules/single_end.snakefile.smk | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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 From 7efec1c3340a8e4e2fdc1326a5bb12e9b40474eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= Date: Thu, 1 Feb 2024 11:08:15 +0100 Subject: [PATCH 3/5] fix: update checksums --- tests/test_htsinfer_workflow/expected_output.md5 | 4 ++-- 1 file changed, 2 insertions(+), 2 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 From 95ba19052039b0aa9a269312efad5944027f99e0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= Date: Thu, 1 Feb 2024 11:33:50 +0100 Subject: [PATCH 4/5] fix: pin snakefmt version --- install/environment.dev.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install/environment.dev.yml b/install/environment.dev.yml index ed40ad0..0e617b2 100644 --- a/install/environment.dev.yml +++ b/install/environment.dev.yml @@ -5,6 +5,6 @@ channels: dependencies: - bedtools - biopython - - snakefmt + - snakefmt<=0.9.0 - unzip From 4ee56fe5257117781b691ac95c0d4fe8efe5c200 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= Date: Thu, 1 Feb 2024 13:06:32 +0100 Subject: [PATCH 5/5] unpin snakefmt, update Snakefile --- install/environment.dev.yml | 2 +- workflow/Snakefile | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/install/environment.dev.yml b/install/environment.dev.yml index 0e617b2..ed40ad0 100644 --- a/install/environment.dev.yml +++ b/install/environment.dev.yml @@ -5,6 +5,6 @@ channels: dependencies: - bedtools - biopython - - snakefmt<=0.9.0 + - snakefmt - unzip 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