adaptive quality and adapter trimmertrim_galore --versioncutadapt^[ACTGNactgn]*$^[ACTGNactgn]*$Instructs Trim Galore to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
(--three_prime_clip_R1)Instructs Trim Galore to remove N bp from the 3' end of read 2 after
adapter/quality trimming has been performed. This may remove some unwanted bias from
the 3' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)
0:
--clip_R1 $params.clip_R1
#end if
#if int($params.clip_R2) > 0:
--clip_R2 $params.clip_R2
#end if
#if $params.retain_unpaired.settingsType == "retain_unpaired_output":
--retain_unpaired
--length_1 $params.retain_unpaired.length_1
--length_2 $params.retain_unpaired.length_2
#end if
#end if
## RBBS specific options.
#if $rrbs.settingsType == "custom":
$rrbs.rrbs
$rrbs.non_directional
#end if
--output_dir ./
--suppress_warn
#if $params.settingsType == "custom" and not $params.report:
--no_report_file
#end if
## default 'AGATCGGAAGAGC'
#if $singlePaired.adapter.strip() != '':
--adapter $singlePaired.adapter
#end if
#if $singlePaired.three_prime_clip_R1:
--three_prime_clip_R1 $singlePaired.three_prime_clip_R1
#end if
#if $singlePaired.sPaired == "single":
## input sequence
./input_singles
#else:
--paired
$singlePaired.trim1
#if $singlePaired.adapter2 and $singlePaired.adapter2.strip() != '':
--adapter2 $singlePaired.adapter2
#end if
#if $singlePaired.three_prime_clip_R2:
--three_prime_clip_R2 $singlePaired.three_prime_clip_R2
#end if
## input sequences
./input_mate1
./input_mate2
#end if
&&
## Trim Galore! run is finished. Move the report files to the proper place
#if $params.settingsType == "custom" and $params.report:
cat ./*_trimming_report.txt > $report_file;
#end if
]]>
^[ACTGNactgn]*$Instructs Trim Galore to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
(--three_prime_clip_R1)singlePaired['sPaired'] == "single"singlePaired['sPaired'] == "paired_collection"
((
params['settingsType'] == "custom" and
params['retain_unpaired']['settingsType'] == "retain_unpaired_output" and
singlePaired['sPaired'] == "paired_collection"
))
singlePaired['sPaired'] == "paired"singlePaired['sPaired'] == "paired"
((
params['settingsType'] == "custom" and
params['retain_unpaired']['settingsType'] == "retain_unpaired_output" and
singlePaired['sPaired'] == "paired"
))
((
params['settingsType'] == "custom" and
params['retain_unpaired']['settingsType'] == "retain_unpaired_output" and
singlePaired['sPaired'] == "paired"
))
((
params['settingsType'] == "custom" and
params['report'] == True
))