Hi-C workflow #139
Hi-C workflow #139
Conversation
| @@ -209,6 +209,10 @@ task bwa_mem { | |||
| description: "Read group information for BWA to insert into the header. BWA format: '@RG\tID:foo\tSM:bar'", | |||
| group: "common", | |||
| } | |||
| skip_mate_rescue: "Skip mate rescue" | |||
| skip_pairing: "Skip pairing; mate rescue performed unless `skip_mate_rescue` also in use" | |||
| split_smallest: "For split alignment, take the alignment with the smallest coordinate as primary" | |||
There was a problem hiding this comment.
Here is the help text.
-S skip mate rescue
-P skip pairing; mate rescue performed unless -S also in use
-5 for split alignment, take the alignment with the smallest coordinate as primary
-P is the only option ith an entry in the manual:
-P | In the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair.
Nothing overly helpful
There was a problem hiding this comment.
@a-frantz - I've added some additional text, but it relies on google searching and reading Q&A on online forums. I don't see anything definitive from the bwa authors.
There was a problem hiding this comment.
The text for skip_[mate_rescue,pairing] looks good now! But I still have my original Q: What's the alternative to "take the alignment with the smallest coordinate as primary"?
There was a problem hiding this comment.
I assume it's random, since these have the same score (I think).
There was a problem hiding this comment.
I think this version dir should be 2.31.1-0
There was a problem hiding this comment.
If this is named after bedtools, why does it have hic scripts in it?
There was a problem hiding this comment.
Originally, it was just plain bedtools, but with the decision to remove the embedded scripts, those needed to get built in to some image and this one depends on bedtools. I can go somewhere else, but then we'll need to install bedtools in to another container.
There was a problem hiding this comment.
Could we maybe consolidate some of these new Docker images? It looks like we can maybe merge bedtools, hilow and juicertools?
There was a problem hiding this comment.
I thought we were trying to avoid these types of monolithic images? We can do that, but is that the direction we want to go?
There was a problem hiding this comment.
Hmm. There's a balance to be found, but I'm not sure what it is yet... Responding to #139 (comment) in this thread to consolidate conversation.
Maybe we can merge hilow and juicertools (is my understanding correct that they are usually used together?), building that image with bedtools and moving the hic script which depends on bedtools into there? That's a bit "monolithic", but keeps the bedtools image "clean" and hopefully isn't too sprawling.
Thoughts on that?
| args = get_args() | ||
|
|
||
| f=open(args.filter_pairs) | ||
| blackID=defaultdict(int) |
There was a problem hiding this comment.
Looks like this was just a copy+paste, but can we use proper casing in this file? And blackID should probably be updated to exclude_list or something
There was a problem hiding this comment.
Should we incorporate some Python tooling? A linter of some sort, formatter, etc? Don't really want to ask you to rewrite all these py scripts which appear to be mostly copy+paste, but also they aren't really conformant to any Python standards...
| } | ||
| } | ||
|
|
||
| task fastq_to_sam { |
There was a problem hiding this comment.
| task fastq_to_sam { | |
| task fastq_to_ubam { |
???
| } | ||
|
|
||
| Float fastq_size = size(read_one_fastq_gz, "GiB") + size(read_two_fastq_gz, "GiB") | ||
| Int disk_size_gb = ceil(fastq_size * 2) + 10 + modify_disk_size_gb |
There was a problem hiding this comment.
Is this calculation solid? I'm not really sure what to expect for the size of a uBAM.
| @@ -1327,7 +1327,90 @@ task faidx { | |||
| cpu: 1 | |||
| memory: "4 GB" | |||
| disks: "~{disk_size_gb} GB" | |||
| container: "quay.io/biocontainers/samtools:1.17--h00cdaf9_0" | |||
| container: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_0" | |||
There was a problem hiding this comment.
Does this need to be updated for the rest of the file? I thought you added a lint or a CI or something to catch these cases...
| external_help: "https://www.htslib.org/doc/samtools-sort.html", | ||
| } | ||
| prefix: "Prefix for the output file. The extension `.bam` will be added." | ||
| uncompressed: "Output uncompressed BAM?" |
There was a problem hiding this comment.
I think until streaming comes to WDL, we should probably avoid allowing uncompressed output
| call bowtie2.build { input: | ||
| reference = reference_download.downloaded_file, | ||
| prefix = basename(reference_fa_name, ".fa.gz"), | ||
| ncpu = 10, |
There was a problem hiding this comment.
This probably shouldn't be hardcoded here.
Implements a workflow to generate a bowtie2-aligned BAM and a
.hicfile for analysis. This utilizes the commonly used HiC-Pro workflow.