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

documentation update #9

Merged
merged 15 commits into from
Nov 22, 2024
+292 −137
Merged

documentation update #9

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
f9dfc90
update figure and workflow overview
kaijli Nov 1, 2024
588ef7e
waiting on test run for sample outputs
kaijli Nov 3, 2024
8040601
add rrna file to output list, update figure
kaijli Nov 3, 2024
db6b613
updated output json and sample data
kaijli Nov 14, 2024
e8b4aa3
add svg
kaijli Nov 14, 2024
57b4360
update readme with sample file link
kaijli Nov 14, 2024
2e04b2d
updated sample datasets
kaijli Nov 15, 2024
c452fff
change bold to italics and changed table format
kaijli Nov 15, 2024
3733704
converted parameter list to table and numbers to auto list
kaijli Nov 15, 2024
9fcd003
testing inline code block
kaijli Nov 15, 2024
20c497d
added :code: for in-line code
kaijli Nov 15, 2024
6d5ce7f
added missing table header
kaijli Nov 15, 2024
f41b08d
missing line break
kaijli Nov 15, 2024
c5fc2aa
added detail to difference wtih readsqc
kaijli Nov 15, 2024
b5a78eb
fix bullets
kaijli Nov 19, 2024
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
15 changes: 11 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,13 +31,20 @@ Description of the files:

## Input files

1. fastq (illumina paired-end interleaved fastq),
3. project name
1. the path to the database directory
2. the path to the fastq file(s) ([R1, R2] if not interleaved)
3. input_interleaved (boolean)
4. output file prefix
5. (optional) parameters for memory
6. (optional) number of threads requested

```
{
"metaTReadsQC.input_files": ["/global/cfs/cdirs/m3408/ficus/example/12889.1.295318.GTGCTTAC-GTAAGCAC.fastq.gz"],
"metaTReadsQC.proj":"nmdc:xxxxxxx"
"metaTReadsQC.input_files": ["https://portal.nersc.gov/project/m3408//test_data/metaT/SRR11678315.fastq.gz"],
"metaTReadsQC.proj":"SRR11678315-int-0.1",
"metaTReadsQC.rqc_mem": 180,
"metaTReadsQC.rqc_thr": 64,
"metaTReadsQC.database": "/refdata/"
}
```

Expand Down
Loading
Loading