Development #34
Development #34
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… a mac (once tasmanian is updated with an installable pandas version)
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
tiny readme changes
…ument for gc bias - switching back to picard from picard-slim
rest of genome index cleanup
…BED6 format and simpler downstream logic
we are more explicit on using read1 not read{1,2}.
…ze checking, UNTESTED
* placeholder_r2 should be created before enough_reads * ensure emseq after complition of create_placeholder * placeholder.r2 before emseq workflow
… a mac (once tasmanian is updated with an installable pandas version) modified: main.nf modified: modules/alignment.nf modified: modules/compute_statistics.nf modified: modules/methylation.nf modified: run_test.sh new file: test_data/emseq_test_regions.bed new file: test_data/reference.fa.fai
…ument for gc bias - switching back to picard from picard-slim modified: modules/alignment.nf modified: modules/compute_statistics.nf modified: modules/methylation.nf
rest of genome index cleanup modified: main.nf new file: modules/bed_processing.nf modified: modules/methylation.nf
…add to snapshot since it might be easy to mess up these steps with future edits
mattsoup
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mattsoup
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That's a lot! Looks good to me though, just some mostly minor comments.
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| process methylDackel_mbias { | |||
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I think you've done some performance testing with this, but if it ends up being problematic with larger datasets this may be low-ish hanging fruit in the future.
| optical_distance=\$(echo \${inst_name} | awk '{if (\$1~/^M0|^NS|^NB/) {print 100} else {print 2500}}') | ||
| samtools merge --threads ${task.cpus} ${library}.bam ${bams} |
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should this be in a separate process? maybe it doesn't matter.
| picard -Xmx${task.memory.toGiga()}g CollectInsertSizeMetrics \ | ||
| --INCLUDE_DUPLICATES --VALIDATION_STRINGENCY SILENT \ | ||
| -I "\$good_mapq_pipe" -O ${library}.good_mapq.insert_size_metrics.txt \ | ||
| --MINIMUM_PCT 0 -H /dev/null & | ||
| picard_good_mapq_pid=\$! | ||
| picard -Xmx${task.memory.toGiga()}g CollectInsertSizeMetrics \ | ||
| --INCLUDE_DUPLICATES --VALIDATION_STRINGENCY SILENT \ | ||
| -I "\$bad_mapq_pipe" -O ${library}.bad_mapq.insert_size_metrics.txt \ | ||
| --MINIMUM_PCT 0 -H /dev/null & | ||
| picard_bad_mapq_pid=\$! | ||
| wait \$samtools_pid | ||
| wait \$picard_good_mapq_pid | ||
| wait \$picard_bad_mapq_pid |
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if we're having to run the tool multiple times and wait for its outputs to be done, does it seem like it should be split into a 'CollectInsertSize' process, and a 'CombineInsertSize' process?
| no_cols[i] = 0 | ||
| if (\$i ~ /insert_size/) {isize=i} | ||
| else if (\$i ~ /rf_count/) {rf=i} | ||
| else if (\$i ~ /fr_count/) {fr=i} | ||
| else if (\$i ~ /tandem/) {tandem=i} | ||
| else {no_cols[i]++} | ||
| } | ||
| # columns that are not present still need to be printed (with 0 value) | ||
| for (i in no_cols) { | ||
| if (no_cols[i] > 0) { | ||
| if (! isize ) { isize = i} | ||
| else if (! rf ) { rf = i} | ||
| else if (! fr ) { fr = i} | ||
| else if (! tandem ) { tandem = i} | ||
| } | ||
| } | ||
| } |
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i'm not exactly following this, but can we just cut/join the files together?
| if (params.single_end) { | ||
| fastq_chunks = fastp.out.trimmed_fastq | ||
| .flatMap { library, fq_files -> | ||
| def fq_list = fq_files instanceof List ? fq_files : [fq_files] |
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i'd like to play around with this a bit to see if we can't find something more elegant, but in the meantime, if it works then it's fine.
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yeah it took me a while to get here but I didn't try to pare it down too much.
| output_file="\${intersect_basename}_intersections.tsv" | ||
| summary_file="\${intersect_basename}_positional_summary.tsv" | ||
| echo -e "methylkit_file\\tchr\\tstart\\tend\\tcontext\\tmethylation\\ttarget_locus\\ttarget_name" > \${output_file} |
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@bwlang does splitting by chromosome for the position/length summary align with your current plan for this tool?
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we need to break out the control contigs for detailed reporting (intersections.tsv)... but not the human contigs i think. i think there is somewhere else we do something similar in this code. I'm planning to add the control bed region s to the bed file so we'll include those in both - but then we need to refine this output.
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