Polya trimming correction

Closes issue #98 (closed) Modified the samples.tsv to include poly-a for the 3p and 5p to match the cutadapt options -a -g -A -G. Empty variables are substituted by 'XXXXXXXXXX' so that they are not trimmed by cutadapt.

changed milestone to %v0.1.0 release

added Bug label

Hi @katsanto, just one issue before I can merge: given that the input "API" (i.e., the sample table) changed, doesn't this require changes in the documentation, too? If so, please update the docs first (README.md and pipeline_documentation.md), as we don't want docs and code base to diverge. Thanks :)

@katsanto Maria, could you be so nice as to correct the link for STAR manual, if you're editing the documentation anyways? The link in the description of create_index_star is wrong, whereas the one in map_genome_star is correct. Thanks a lot, I don't want to open an extra issue for that.

added 6 commits

• ac26fff7...27f4fa5b - 4 commits from branch master
• 78fccac8 - Merge branch 'master' of...
• 94d8234b - Fixed incompatibility of md5s with the multiqc merge

Compare with previous version

Fixed incompatibility with the multiqc integration. Also modified the documentation to account for the option changes of the trimming adapter and trimming poly-A rules.

I still need to fix documentation in general but this does not affect the test runs. So I will open another branch.

mentioned in commit 05e5a95a

merged

@herrmchr: I think your broken link wasn't addressed, so perhaps better to open an issue for it or fix it quickly.