Mercurial > repos > kkonganti > cfsan_centriflaken
changeset 86:7e421f421b5e
"planemo upload"
| author | kkonganti |
|---|---|
| date | Wed, 13 Jul 2022 17:18:04 -0400 |
| parents | 022230c283f2 |
| children | 34d411a7bd4f |
| files | cfsan_centriflaken.xml |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/cfsan_centriflaken.xml Wed Jul 13 17:02:56 2022 -0400 +++ b/cfsan_centriflaken.xml Wed Jul 13 17:18:04 2022 -0400 @@ -8,6 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ mkdir -p cpipes-input || exit 1; pwd_path=\$(pwd); + #import re #if (str($input_read_type_cond.input_read_type) == "single_long"): #for _, $unpaired in enumerate($input_read_type_cond.input): #set read1 = str($unpaired.name) @@ -18,13 +19,13 @@ #end for #elif (str($input_read_type_cond.input_read_type) == "paired"): #for _, $pair in enumerate($input_read_type_cond.input_pair) - #set read_R1 = str($pair.forward.name) - #set read_R2 = str($pair.reverse.name) + #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name)) + #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name)) #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')): - #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext) + #set read_R1 = $read_R1 + str('.') + str($pair.forward.ext) #end if #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')): - #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext) + #set read_R2 = $read_R2 + str('.') + str($pair.reverse.ext) #end if ln -sf '$pair.forward' './cpipes-input/$read_R1'; ln -sf '$pair.reverse' './cpipes-input/$read_R2';