PR for Release 1.1.0 "Wingardium Leviosa" #46
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Merge patient tables
For some of the samples the computing time was not enough
Run times in base.cofig
Adding R packages for plotting to container
Removed define clones only
corrected version gplots
Calculating clones per patient
Added logo
Added logo
updated changelog
fix review comments
Added functionality
apeltzer
requested changes
Nov 6, 2019
apeltzer
changed the title
This was referenced Nov 7, 2019
Closed
Leon-Bichmann
approved these changes
Nov 7, 2019
| else if (filename.indexOf(".tab") > 0) "table/$filename" | ||
| else if (filename == "command_log.txt") "$filename" | ||
| if (filename.indexOf("table.tab") > 0) "$filename" | ||
| else if (filename.indexOf("clone-pass.tab") > 0) "$filename" |
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A lot of different cases of if statements in your code, I wonder if that could be done in an easier way. But if it works great! ;)
| @@ -749,7 +717,7 @@ process assign_clones{ | |||
| set file("${geno.baseName}_clone-pass.tab"), file("$geno_fasta"), val("$id") into ch_for_germlines | |||
| file "${geno.baseName}_clone-pass.tab" | |||
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You define a lot of output files but don't pass them into channels, I wonder if it is necessary to define them at all.
| ch_read_files_for_merge_r1_umi = Channel.from(file_meta) | ||
| .splitCsv(header: true, sep:'\t') | ||
| .map { col -> tuple("${col.ID}", "${col.Source}", "${col.Treatment}","${col.Extraction_time}","${col.Population}", file("${col.R1}", checkifExists: true), file("${col.R2}", checkifExists: true))} | ||
| .dump() |
| @@ -166,7 +160,6 @@ summary['Max Time'] = params.max_time | |||
| summary['IGDB Path'] = params.igblast_base | |||
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You could print some more of the workflow options here, right now you print very few.
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PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/bcellmagic/tree/master/.github/CONTRIBUTING.md