<commit_before># version 1.4.5

## 2016.12.19

- fixed samplesSheet parser. Instead using `indexOf()` to search for a pattern now use `startsWith()`. Also do `baseName()` on file path, which is the right thing to do. 
- included star index files as a list of file which are dependencies for indexing step as an ouput files and as input file in star mapping
- added new logging line to log all Fastq file found in the directory
- found couple of bugs in sikPrePro.bds and sikExonicRate.bds, both to do with dependencies, all fixed now
- trying out `canFail := true` option inside a task to enable graceful exit. Should include that statement in number of non essential tasks
- fixed sik.config
- added samplesSheet logging 

- generalised main RNAsik executable. Replaced specific aligner and indexing functions with generic one from sikMapping.bds and sikIndexing.bds
- adding three new files one for all the hisat2 stuff and with the other two Im trying to generalise mapping and indexing, so that in future I'd be able to include several other aligners and I'll only need to update sikIndexing and sikMapping files
- inclusing Hisat2 aligner into pipeline. Added two new variables for hisat2 to sikHeader. Moved makeSTARindex function from sikMakeIndex.bds to sikSTARaligner.bds and also added extra conditionals to star mapping task. Added couple of sanity-checks for hisat2 into sikSanityCheck.bds. Updated sik.config to include hisat2
- added samplesSheep logging<commit_msg>updated log.txt<commit_after># version 1.4.5

## 2016.12.19

- fixed samplesSheet parser. Instead using `indexOf()` to search for a pattern now use `startsWith()`. Also do `baseName()` on file path, which is the right thing to do. 
- included star index files as a list of file which are dependencies for indexing step as an ouput files and as input file in star mapping
- added new logging line to log all Fastq file found in the directory
- found couple of bugs in sikPrePro.bds and sikExonicRate.bds, both to do with dependencies, all fixed now
- trying out `canFail := true` option inside a task to enable graceful exit. Should include that statement in number of non essential tasks
- fixed sik.config
- added samplesSheet logging 

- generalised main RNAsik executable. Replaced specific aligner and indexing functions with generic one from sikMapping.bds and sikIndexing.bds
- adding three new files one for all the hisat2 stuff and with the other two Im trying to generalise mapping and indexing, so that in future I'd be able to include several other aligners and I'll only need to update sikIndexing and sikMapping files
- inclusing Hisat2 aligner into pipeline. Added two new variables for hisat2 to sikHeader. Moved makeSTARindex function from sikMakeIndex.bds to sikSTARaligner.bds and also added extra conditionals to star mapping task. Added couple of sanity-checks for hisat2 into sikSanityCheck.bds. Updated sik.config to include hisat2
- added samplesSheep logging

-Added canFail option to task of fastqc and qualimap to allow them to fail as those are non essential tasks. Also added cpus option to qualimap to control how many tasks gets run simultaniously and increased number of --java-mem-size=6G. This is qualimap specific and I should look into this more closely

-added stdout and stderr redirect to indexing step to catch all messages from Hisat2 indexing. Also fixed some minor typos/bug in sikIndexing and sikHisat2 files
{'fraction_non_alphanumeric': 0.03963858933255611, 'fraction_numerical': 0.010201107548819586, 'mean_word_length': 4.438985736925515, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '25529', 'n_tokens_mistral': 931, 'n_tokens_neox': 879, 'n_words': 514}