seq-analysis issueshttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues2019-09-24T10:57:10+02:00https://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/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/18feature: jgu-cbdm should use partition 'andrade' on M1, when possible2019-03-11T09:00:14+01:00Meesters, Christianfeature: jgu-cbdm should use partition 'andrade' on M1, when possiblesee titlesee titleMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/17bug: check keep list for unique items2020-04-17T22:54:07+02:00Meesters, Christianbug: check keep list for unique itemssee titlesee titleMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/14include MultiQC2019-03-19T08:54:25+01:00Meesters, Christianinclude MultiQCMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/7new module - subread2020-04-17T22:56:04+02:00Meesters, Christiannew module - subreadsee titlesee titleMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/6feature - integrate Multiqc in QA module2020-04-17T22:56:28+02:00Meesters, Christianfeature - integrate Multiqc in QA modulesee titlesee titleMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues/4tools - checksum tests for uploads2020-04-17T22:59:11+02:00Meesters, Christiantools - checksum tests for uploadsnot part of the seq analysis, yet a useful idea: tablutated file - checksum input to be controlled in a parallel jobnot part of the seq analysis, yet a useful idea: tablutated file - checksum input to be controlled in a parallel jobMeesters, ChristianMeesters, Christian