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Issues7 (7)

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IGDRion/ANNEXseq

WARN: Access to undefined parameter `extend_annexa`

Warning on undefined parameted for -extend_annexa parameter but it seems to work anyway, to check ?! WARN: Found unexpected parameters: * --full: true * --operation: union * --bambu_threshold: 0.2 * --tfkmers_threshold: ...

• Aurore-B
·
• Opened 
  on Aug 21, 2023
·
• #8

IGDRion/ANNEXseq

results directory configuration

Move DESeq2 and DEXSeq results from bambu directory

• Aurore-B
·
• Opened 
  on Jul 11, 2023
·
• #7

IGDRion/ANNEXseq

Some ANNEXA modules should be subworkflows

This three modules should be moved from the modules directory to subworkflows : - ./modules/local/qc.nf -- ./subworkflows/local/qc.nf - ./modules/local/transforkmers.nf -- ./subworkflows/local/transforkmers.nf ...

• enoracrl
·
• 1
·
• Opened 
  on Jun 27, 2023
·
• #5

IGDRion/ANNEXseq

Error during QC process

Pipeline failed during QC process: [a5/8943fd] process LOCAL_ANNEXSEQ:ANNEXSEQ:QC_... [100%] 1 of 1, failed: 1 ✘ Errors: [enoracrl/ANNEXseq] Pipeline completed with errors- Error executing process ...

• Aurore-B
·
• 1
·
• Opened 
  on Jun 21, 2023
·
• #4

IGDRion/ANNEXseq

Remove unnecessary directories in results directory

Directories to remove in resultsdirectory: - restore - validate - extract

• Aurore-B
·
• 1
·
• Opened 
  on Jun 21, 2023
·
• #3

IGDRion/ANNEXseq

log2fold change info missing in dexseq output

- Change sample names by avoiding _ usage - test dexseq script alone to check - modify script in annexseq

• Aurore-B
·
• 1
·
• Opened 
  on Jun 21, 2023
·
• #2

IGDRion/ANNEXseq

nanoplot output missing for all samples

Same generic output name by nanoplot. Results at the end of pipeline: only one nanoplot report on the last sample analyzed. See nanoseq issue #233

• Aurore-B
·
• 1
·
• Opened 
  on Jun 21, 2023
·
• #1

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