Mercurial > repos > kkonganti > cfsan_centriflaken
changeset 33:0a65e6fde7b6
"planemo upload"
| author | kkonganti |
|---|---|
| date | Wed, 29 Jun 2022 14:59:22 -0400 |
| parents | 9c06429a2ffb |
| children | 4f9f145d1946 |
| files | cfsan_centriflaken.xml |
| diffstat | 1 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/cfsan_centriflaken.xml Wed Jun 29 14:57:16 2022 -0400 +++ b/cfsan_centriflaken.xml Wed Jun 29 14:59:22 2022 -0400 @@ -15,6 +15,18 @@ --pipeline $pipeline #if ($pipeline == "centriflaken"): --fq_single_end true + --flye_genome_size '${genome_size}' + #if ($long_read_platform == "nanopore_corr"): + --flye_nano_corr true --flye_nano_raw false + #elif ($long_read_platform == "nanopore_hq"): + --flye_nano_hq true --flye_nano_raw false + #elif ($long_read_platform == "pacbio_raw"): + --flye_pacbio_raw true --flye_nano_raw false + #elif ($long_read_platform == "pacbio_corr"): + --flye_pacbio_corr true --flye_nano_raw false + #elif ($long_read_platform == "pacbio_hifi"): + --flye_pacbio_hifi true --flye_nano_raw false + #end if #elif ($pipeline == "centriflaken_hy"): #if ($reads_lib_layout == "single"): --fq_single_end true @@ -28,18 +40,6 @@ --fq_filename_delim '${fq_filename_delim}' --fq_filename_delim_idx $fq_filename_delim_idx --centrifuge_extract_bug '${centrifuge_extract_bug}' - --flye_genome_size '${genome_size}' - #if ($long_read_platform == "nanopore_corr"): - --flye_nano_corr true --flye_nano_raw false - #elif ($long_read_platform == "nanopore_hq"): - --flye_nano_hq true --flye_nano_raw false - #elif ($long_read_platform == "pacbio_raw"): - --flye_pacbio_raw true --flye_nano_raw false - #elif ($long_read_platform == "pacbio_corr"): - --flye_pacbio_corr true --flye_nano_raw false - #elif ($long_read_platform == "pacbio_hifi"): - --flye_pacbio_hifi true --flye_nano_raw false - #end if -profile $runtime_profile -resume; mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';