Mercurial > repos > iuc > medaka_consensus_pipeline
diff medaka_consensus.xml @ 14:cb34f00cc10f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 8051b858e0f5c6d7c1092754df02ed8303a53054
author | iuc |
---|---|
date | Mon, 27 Jun 2022 17:30:31 +0000 |
parents | 72b5e9dda577 |
children | 79e9a869f40e |
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--- a/medaka_consensus.xml Thu Nov 18 20:01:28 2021 +0000 +++ b/medaka_consensus.xml Mon Jun 27 17:30:31 2022 +0000 @@ -6,7 +6,8 @@ <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ -ln -s '$d' 'input_assembly.fa' && +## symlink seems insuffiencient (fai file is still created next to link target) +cp '$d' 'input_assembly.fa' && medaka_consensus ## optional -m ${m} @@ -125,7 +126,7 @@ **Input** -An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly <https://nanoporetech.github.io/medaka/walkthrough.html#basecalling-and-draft-assembly>`_ for a detailed example of one method of obtaining these. +An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly <https://github.com/nanoporetech/medaka/blob/master/docs/walkthrough.rst>`_ for a detailed example of one method of obtaining these. ----