diff --git a/tools/guppy/guppy_basecaller.xml b/tools/guppy/guppy_basecaller.xml index eff620fba..746024d36 100644 --- a/tools/guppy/guppy_basecaller.xml +++ b/tools/guppy/guppy_basecaller.xml @@ -1,4 +1,4 @@ - + A simple wrapper for guppy basecaller that depends on configuration files @@ -9,23 +9,23 @@ #end for tar xf $config && guppy_basecaller -i . - --save_path out - --data_path . + --save_path "out" + --data_path "." --config *.cfg - --num_callers 4 + --num_callers \${GALAXY_SLOTS:-2} --records_per_fastq 0 - --cpu_threads_per_caller \${GALAXY_SLOTS:-2} + --cpu_threads_per_caller 1 --disable_pings -### --qscore_filtering -### --calib_detect - && cat out/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq + && cat out/pass/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq + && echo "guppy must be installed system-wide from ONT linux packages" > $discloser ]]> - + +