Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix: pipeline visualization descriptions #381

Merged
merged 1 commit into from
Jan 6, 2025
Merged

fix: pipeline visualization descriptions #381

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion lib/idseq-dag/idseq_dag/steps/run_subsample.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ class PipelineStepRunSubsample(PipelineCountingStep):

For samples with a high fraction of non-host reads (ie stool samples), the .fasta outputs
following bowtie alignment may contain large numbers of sequences.
GSNAP alignment to NT and NR databases is a resource-intensive step.
Alignment to NT and NR databases is a resource-intensive step.
To reduce computational time, the reads are randomly sub-sampled to
1 million total fragments (1 million single-end reads or 2 million paired-end reads).
"""
Expand Down
10 changes: 4 additions & 6 deletions workflows/short-read-mngs/host_filter.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -315,7 +315,7 @@ task ercc_bowtie2_filter {
`bowtie2 ~{bowtie2_options}` using a precomputed index, then uses
[samtools](http://www.htslib.org/) to keep reads *not* mapping to the ercc genome.

Bowtie2 is run on the fastp-filtered FASTQ(s):
Bowtie2 is run on validated FASTQ files:

```
~{bowtie2_invocation}
Expand Down Expand Up @@ -393,7 +393,7 @@ task fastp_qc {
5. Complexity filter ([custom feature](https://github.com/mlin/fastp/tree/mlin/sdust)
using the [SDUST algorithm](https://pubmed.ncbi.nlm.nih.gov/16796549/))

fastp is run on the FASTQ file(s) from input validation:
fastp is run on ERCC-filtered FASTQ files:
```
~{fastp_invocation}
```
Expand Down Expand Up @@ -504,10 +504,8 @@ task kallisto {
**kallisto RNA quantification**

Quantifies host transcripts using [kallisto](https://pachterlab.github.io/kallisto/about).
The host transcript sequences are sourced from GENCODE, along with
[ERCC control sequences](https://www.nist.gov/programs-projects/external-rna-controls-consortium).
Not all CZ ID host species have transcripts indexed; for those without, kallisto is run using ERCC
sequences only.
The host transcript sequences are sourced from GENCODE.
Not all CZ ID host species have transcripts indexed, so transcripts are not calculated for all hosts.

kallisto is run on the fastp-filtered FASTQ(s):

Expand Down
Loading