Mercurial > repos > kkonganti > cfsan_centriflaken
changeset 96:ef0b422978fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 25 Jul 2022 12:57:06 -0400 |
| parents | aefcf9bbaee5 |
| children | 8d7f482c64de |
| files | cfsan_centriflaken.xml |
| diffstat | 1 files changed, 6 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/cfsan_centriflaken.xml Wed Jul 20 09:33:32 2022 -0400 +++ b/cfsan_centriflaken.xml Mon Jul 25 12:57:06 2022 -0400 @@ -13,7 +13,8 @@ #for _, $unpaired in enumerate($input_read_type_cond.input): #set read1 = str($unpaired.name) #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')): - #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext) + #set read1_ext = re.sub('fastqsanger', 'fastq', str($unpaired.ext)) + #set read1 = str($unpaired.name) + str('.') + $read1_ext #end if ln -sf '$unpaired' './cpipes-input/$read1'; #end for @@ -21,11 +22,13 @@ #for _, $pair in enumerate($input_read_type_cond.input_pair) #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name)) #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name)) + #set read_R1_ext = re.sub('fastqsanger', 'fastq', str($pair.forward.ext)) + #set read_R2_ext = re.sub('fastqsanger', 'fastq', str($pair.reverse.ext)) #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')): - #set read_R1 = $read_R1 + str('.') + str($pair.forward.ext) + #set read_R1 = $read_R1 + str('.') + $read_R1_ext #end if #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')): - #set read_R2 = $read_R2 + str('.') + str($pair.reverse.ext) + #set read_R2 = $read_R2 + str('.') + $read_R2_ext #end if ln -sf '$pair.forward' './cpipes-input/$read_R1'; ln -sf '$pair.reverse' './cpipes-input/$read_R2';