Process rnaseq rsem/salmon output, accept additional species from igenomes#118
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WackerO merged 64 commits intoqbic-pipelines:devfrom May 11, 2022
Merged
Process rnaseq rsem/salmon output, accept additional species from igenomes#118WackerO merged 64 commits intoqbic-pipelines:devfrom
WackerO merged 64 commits intoqbic-pipelines:devfrom
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…eated the channels directly from the input/igenomes values in rnadeseq.nf
WackerO
changed the title
…_salmon test dataset in the testdata in a subfolder
ggabernet
reviewed
May 4, 2022
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
ggabernet
reviewed
May 9, 2022
ggabernet
reviewed
May 9, 2022
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
ggabernet
reviewed
May 9, 2022
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One more round, but this should be the last one! :)
There are still multiple places where ~~~ is substituted back to ===, which will cause issues in file diffs during merge conflicts. Could you change all back to ~~~
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
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Many thanks to contributing to qbic-pipelines!
This PR allows rnadeseq to use the rsem/salmon output from the new rnaseq version. Further, it contains igenomes.config so that additional species can be used; it should also be able to handle species not configured by igenomes as long as the user provides the necessary files/params.
PR checklist
nextflow run . -profile test,docker).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/qbic-pipelines/rnadeseq/tree/master/.github/CONTRIBUTING.md