NF_RCP-F_1.0.4-RC1 #29
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Prior, --illumina was harded coded. Now, neither --illumina nor --nextera are supplied. As per the Trim Galore [Manual](https://github.com/FelixKrueger/TrimGalore/blob/0.6.7/Docs/Trim_Galore_User_Guide.md#adapter-auto-detection): " If no sequence was supplied, Trim Galore will attempt to auto-detect the adapter which has been used. For this it will analyse the first 1 million sequences of the first specified file and attempt to find the first 12 or 13bp of the following standard adapters: ``` Illumina: AGATCGGAAGAGC Small RNA: TGGAATTCTCGG Nextera: CTGTCTCTTATA ``` If no adapter contamination can be detected within the first 1 million sequences, or in case of a tie between several different adapters, Trim Galore defaults to `--illumina`, as long as the Illumina adapter sequence was one of the options. If there was a tie between the Nextera and small RNA adapter, the default is `--nextera`. The auto-detection results are shown on screen and printed to the trimming report for future reference. "
Prior, runsheet via 1.1.8 Now, runsheet via 1.3.2 + plugin Identical output expected and attained
Prior, `sample` was global within the lambda functions and thus resulted in last `sample` being used for all checks (the last state of `sample`). Now, `sample` is bound at lambda definition rather than at runtime (using global). Validated in 194 and 48 tests.
Reference workflow commit: 3b7e0ba
### Prior * Tests used dge table md5sum for testing, this was subject to numerical instability driven differences causing test failure. ### Now * summary.txt files are output from the `summary` function in R. This naturally reduces precision in summary statistics allowing detection of meaningful numeric differences (non numerical stability related)
Enables usage of act to run actions via cli
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nasa#29 - Based on: 1092e80 2dd8fce 11a22f0 7ba75d0 4e317f2 5d35b61 7d2cc24 53363e4 1b6e325 b5013e9 574eb79 fc89c5e 1500019 6719218 35c9823 af0b716 cbf6055 6a0d105 ee188eb a8c65d3 - Changed dge module to DGE_BY_DESEQ2, added test modules - Removed deprecated conda support files - Updated ensembl file used for test dataset VV
torres-alexis
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nasa#29 - Based on: 1092e80 2dd8fce 11a22f0 7ba75d0 4e317f2 5d35b61 7d2cc24 53363e4 1b6e325 b5013e9 574eb79 fc89c5e 1500019 6719218 35c9823 af0b716 cbf6055 6a0d105 ee188eb a8c65d3 - Changed dge module to DGE_BY_DESEQ2, added test modules - Removed deprecated conda support files - Updated ensembl file used for test dataset VV
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Planned Fixes (Marked as done when this PR includes implementations):