seq-analysis issueshttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues2019-02-26T11:12:18+01:00https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/24create error handline lib2019-02-26T11:12:18+01:00Meesters, Christiancreate error handline libsee titlesee titlecheck all for issues 20-22, abstract error handling and outdir creation from all modulesMeesters, ChristianMeesters, Christian2019-02-26https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/22QCWrapper - check for suffixes instead of strings in screening input names2019-02-28T13:22:41+01:00Meesters, ChristianQCWrapper - check for suffixes instead of strings in screening input namesdistinguish
0236_031_CE_NOR_1GD1_DL1_S1_L001_R1_001-pooled_fastqc.zip
0236_031_CE_NOR_1GD1_DL1_S1_L001_R1_001-pooled.fastq.gz
to be more fitting to expectationsdistinguish
0236_031_CE_NOR_1GD1_DL1_S1_L001_R1_001-pooled_fastqc.zip
0236_031_CE_NOR_1GD1_DL1_S1_L001_R1_001-pooled.fastq.gz
to be more fitting to expectationscheck all for issues 20-22, abstract error handling and outdir creation from all modulesMeesters, ChristianMeesters, Christian2019-02-25https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/12support for blat2020-04-17T22:55:40+02:00Meesters, Christiansupport for blattest blat for blast mappertest blat for blast mapperupdate blast wrapperMeesters, ChristianMeesters, Christian2019-02-14https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/13add cleanup functionality to blast wrapper2019-03-06T11:44:42+01:00Meesters, Christianadd cleanup functionality to blast wrappersee titlesee titleupdate blast wrapperMeesters, ChristianMeesters, Christian2019-02-11https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/10bug: blast mapper amends .xml suffix regardless of -outfmt option2019-08-21T11:59:58+02:00Meesters, Christianbug: blast mapper amends .xml suffix regardless of -outfmt optiontitle says it alltitle says it allupdate blast wrapperMeesters, ChristianMeesters, Christian2019-02-11https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/5feature - integrate STAR in mapper module2019-03-19T08:51:52+01:00Meesters, Christianfeature - integrate STAR in mapper moduleSTAR incl. single end processingSTAR incl. single end processingupdate mapper wrapperMeesters, ChristianMeesters, Christian2019-02-11https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/11support for lambda2020-04-17T22:58:49+02:00Meesters, Christiansupport for lambdatest lambdatest lambdaupdate blast wrapperMeesters, ChristianMeesters, Christian2019-02-05https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/9feature - add samtools to SDI module2019-01-21T09:06:29+01:00Meesters, Christianfeature - add samtools to SDI modules. titles. titlecreate indexing / sorting moduleMeesters, ChristianMeesters, Christian2019-01-18https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/2test picard anew2019-02-13T14:17:05+01:00Meesters, Christiantest picard anewfutex hits in daughter processes?futex hits in daughter processes?create indexing / sorting moduleMeesters, ChristianMeesters, Christian2018-12-14https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/1test sambamba2019-01-13T18:28:26+01:00Meesters, Christiantest sambamba* sam file compression
* sam file compressed and sorted?
* which stage indexing* sam file compression
* sam file compressed and sorted?
* which stage indexingcreate indexing / sorting moduleMeesters, ChristianMeesters, Christian2018-12-13https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/32bug: QCWrapper creates corrupted files2020-04-17T22:54:47+02:00Meesters, Christianbug: QCWrapper creates corrupted filesthe QCWrapper starts job like
trimming_tool -f R1 -p R2
trimming_tool -f R2 -p R2
for each mate pair, such that the output for R2 does not contain the same number of reads as R1the QCWrapper starts job like
trimming_tool -f R1 -p R2
trimming_tool -f R2 -p R2
for each mate pair, such that the output for R2 does not contain the same number of reads as R1Meesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/31cleanup does not run epilog2021-02-16T09:22:55+01:00Meesters, Christiancleanup does not run epilogsee title, affecting all wrapperssee title, affecting all wrappersMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/30fix file suffix test for QC script (incomplete)2019-09-24T10:57:10+02:00Meesters, Christianfix file suffix test for QC script (incomplete)# test for paired end scheme
if [[ ${samples[0]} == *"_R1"* || ${samples[0]} == *"_R2"* ]]; then
first='_R1'
second='_R2'
elif [[ ${samples[0]} == *"_1"* ]]; then
first='_1'
second='_2'
else
...# test for paired end scheme
if [[ ${samples[0]} == *"_R1"* || ${samples[0]} == *"_R2"* ]]; then
first='_R1'
second='_R2'
elif [[ ${samples[0]} == *"_1"* ]]; then
first='_1'
second='_2'
else
error "paired end scheme has to contain tuples of either '*_R1*'/'*_R2*' or '*_1*'/'*_2*' mates"
exit 1
fiMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/29Change patter matching for read tuples2020-04-17T22:53:28+02:00Meesters, ChristianChange patter matching for read tuplesRead tuples are recognized for the presence of '_1'/'_2' or 'R1'/'R2', resp.. This introduces ambiguity: '_1' and consorts can be anywhere in the string, even '<identifier>_<number>_1.fastq' is imaginable, and if '<number>' would start w...Read tuples are recognized for the presence of '_1'/'_2' or 'R1'/'R2', resp.. This introduces ambiguity: '_1' and consorts can be anywhere in the string, even '<identifier>_<number>_1.fastq' is imaginable, and if '<number>' would start with '1' also '<identifier>_<number>_2.fastq' might match - likewise '<identifier>_<number>_3.fastq'.
Better: impose the sorting string to be prior-suffixes.Meesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/28MapperWrapper: does not attribute read groups correctly2019-03-19T12:00:16+01:00Meesters, ChristianMapperWrapper: does not attribute read groups correctlysee titlesee titleMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/27blast wrapper - splitted strings transferred as input????2019-03-06T14:11:18+01:00Meesters, Christianblast wrapper - splitted strings transferred as input????see 2019022710001329see 2019022710001329Meesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/26forbit reading / writing from/to home dir2019-02-28T13:16:45+01:00Meesters, Christianforbit reading / writing from/to home dirsee titlesee titlecheck all for issues 20-22, abstract error handling and outdir creation from all modulesMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/25_arg_removedups not handled in SDITools2019-02-25T11:44:13+01:00Meesters, Christian_arg_removedups not handled in SDIToolssee titlesee titleMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/21QCWrapper - striping issue2019-02-28T13:20:43+01:00Meesters, ChristianQCWrapper - striping issuecannot create striped subdirs - this is not possible, if in stripe base ...
able to check striping for base? else turn temporarily offcannot create striped subdirs - this is not possible, if in stripe base ...
able to check striping for base? else turn temporarily offcheck all for issues 20-22, abstract error handling and outdir creation from all modulesMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/20QCWrapper - outputdir relocation2019-02-28T13:21:21+01:00Meesters, ChristianQCWrapper - outputdir relocationassumes pwd/tag - this is wrong it ought to be $(basepath input)assumes pwd/tag - this is wrong it ought to be $(basepath input)check all for issues 20-22, abstract error handling and outdir creation from all modulesMeesters, ChristianMeesters, Christian