From 8d0aab5a8f3fd31b743727b987a0c7b253a5cc3d Mon Sep 17 00:00:00 2001 From: verku Date: Tue, 17 Oct 2023 16:50:48 +0200 Subject: [PATCH] Remove rule that copies RepeatMasker library as this does not seem to be required in the new container --- workflow/rules/0.2_repeat_identification.smk | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/workflow/rules/0.2_repeat_identification.smk b/workflow/rules/0.2_repeat_identification.smk index a6583bb..4cc101d 100644 --- a/workflow/rules/0.2_repeat_identification.smk +++ b/workflow/rules/0.2_repeat_identification.smk @@ -21,23 +21,6 @@ rule ref_upper: """ -rule cp_repeatmasker_lib: - """Copy RepeatMasker library from container""" - output: - rm_lib=temp("workflow/resources/RepeatMasker/Libraries/RepeatMasker.lib"), - nhr=temp("workflow/resources/RepeatMasker/Libraries/RepeatMasker.lib.nhr"), - nin=temp("workflow/resources/RepeatMasker/Libraries/RepeatMasker.lib.nin"), - nsq=temp("workflow/resources/RepeatMasker/Libraries/RepeatMasker.lib.nsq"), - log: - "results/logs/0.2_repeat_identification/" + REF_NAME + "_cp_repeatmasker_libs.log", - singularity: - "docker://quay.io/biocontainers/repeatmodeler:2.0.4--pl5321hdfd78af_0" - shell: - """ - cp /usr/local/share/RepeatMasker/Libraries/RepeatMasker.lib* {output.rm_lib} 2> {log} - """ - - rule repeatmodeler: """RepeatModeler for de novo repeat prediction from a reference assembly""" input: @@ -101,7 +84,6 @@ rule repeatmasker: input: ref_upper=rules.ref_upper.output, repmo=rules.repeatclassifier.output.repmo, - rm_libs=rules.cp_repeatmasker_libs.output, output: rep_masked=REF_DIR + "/repeatmasker/" + REF_NAME + "/" + REF_NAME + ".upper.fasta.masked", rep_align=REF_DIR + "/repeatmasker/" + REF_NAME + "/" + REF_NAME + ".upper.fasta.align",