seq-analysis issueshttps://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis/-/issues2020-04-17T22:58:49+02:00https://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/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/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/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/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/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, 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/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/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