| Previous changeset 5:65432c3abf6c (2020-06-15) Next changeset 7:4805fe3d8fda (2022-07-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit c1fda24943cf04866d408133ffb6aabf4a90866b" |
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modified:
lofreq_call.xml |
| b |
| diff -r 65432c3abf6c -r e1461b5c52a0 lofreq_call.xml --- a/lofreq_call.xml Mon Jun 15 13:13:03 2020 -0400 +++ b/lofreq_call.xml Mon Oct 05 20:14:06 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy0"> +<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1" profile="18.01"> <description>with LoFreq</description> <macros> <import>macros.xml</import> @@ -34,11 +34,6 @@ ## call variants with lofreq - ## make lofreq stick to tool contract by - ## generating tmp output inside job working dir - mkdir pp-tmp && - export TMPDIR=pp-tmp && - lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose --ref '$reference_fasta_fn' --out variants.vcf $variant_types @@ -96,12 +91,12 @@ ## in case of errors add the log files produced ## by the parallel workers to stderr - || (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code) + || (tool_exit_code=\$? && cat "\$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit \$tool_exit_code) ## work around a bug in lofreq call-parallel ## https://github.com/CSB5/lofreq/issues/85 ## that causes the output format to be vcf.gz with certain filter - ## combinations. + ## combinations. Issue is closed but still not fixed. #if str($bonf_factor) != 'dynamic': #if '--no-default-filter' in str($filter_control.others): && ln -s variants.vcf variants.vcf.gz |