Added HISAT2 module and test workflow #31
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Yup, piping to samtools is fine - as you say, several other tools will have to do the same. The main effect is that we can no longer use biocontainers for docker images, as we need more than one tool. It's for this reason that I was playing around with automating the GitHub Docker image repository at the hackathon, so that we can easily build and host our own containers for each tool, even if they need more than one package. See #23 for what I've done so far. We have a lot of open PRs on this repository! Need to get to work on some reviewing and merging.. |
ewels
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* Adding module for miniprot_index. * Adding module for miniprot_index. * Adding module for miniprot_index. * Adding module for miniprot_index. * Adding module for miniprot_index. * Adding module for miniprot_index. * Adding module for miniprot_index. * update the wrong file name * put back the test data path * change index file name Co-authored-by: Guoying Qi <[email protected]> * Adding module for miniprot/align (#31) * Adding module for miniprot/align. Closes #1 * Adding module for miniprot/align. Closes #1 * Adding module for <software/tool>. Closes #<issue_number>. * removed gtf flag from main.nf and meta.yml * removed gtf flag from main.nf and meta.yml * incorporate comments * incorporate comments * fixed a bug, swapped the order of reference and protein (#32) * Fixed the paths for the new modules structure * Switched to the nf-core test data and the biocontainer * This output is actually named "index" * linting * Fixed the tool name * Added a meta map to the reference index too, as per the latest nf-core usage * Added another keyword Co-authored-by: YSims <[email protected]> Co-authored-by: Guoying Qi <[email protected]> Co-authored-by: Matthias De Smet <[email protected]>
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Input data is the same E. coli test DNA data which is also used for Bowtie2.
E. coli has to my knowledge no splice sites file, but the module handles
--known_splice_sites <file>if this is supplied.Another comment: the output file is getting piped to
samtools view. Not exactly sure whether this is an acceptable dependency, or how we are supposed to handle that. I suppose it is alright, as other tools also have dependencies...