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chanzuckerberg
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czid-workflows
Portable WDL workflows for CZ ID production pipelines
https://czid.org/
MIT License
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[Bugfix] Fix subsample depth
#379
rzlim08
closed
2 weeks ago
0
Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows
#378
dependabot[bot]
opened
1 month ago
0
fix getting the length of a generator
#377
rzlim08
closed
2 months ago
0
remove max chunk size constant
#376
rzlim08
closed
2 months ago
0
Fix alignment batch tagging
#375
morsecodist
closed
3 months ago
0
Remove GenerateAlignmentViz task
#374
lvreynoso
closed
3 months ago
0
Calculation of bit score and E-value from minimap2 output, as well as count data query
#373
charlesfoster
opened
3 months ago
0
Re-Attach to running alignment chunks on retry
#372
morsecodist
closed
3 months ago
0
Add Random Subsampling to Nanopore mNGS Pipeline
#371
phoenixAja
closed
4 months ago
0
empty diamond outputs
#370
rzlim08
closed
4 months ago
0
empty minimap2 output
#369
rzlim08
closed
4 months ago
0
Bump requests from 2.31.0 to 2.32.2 in /workflows/phylotree-ng
#368
dependabot[bot]
opened
4 months ago
0
[CZID-9655] minimap2/diamond mark intermediate outputs
#367
rzlim08
closed
4 months ago
0
[CZID-9656] Remove taxid locator from outputs without contigs
#366
rzlim08
closed
4 months ago
0
Sort bowtie2 outputs for reproducibility
#365
rzlim08
closed
5 months ago
1
Update Changelogs
#364
lvreynoso
closed
5 months ago
0
Bump requests from 2.31.0 to 2.32.2
#363
dependabot[bot]
closed
5 months ago
0
Pin requests to 2.31.0
#362
lvreynoso
closed
5 months ago
0
Bump requests from 2.31.0 to 2.32.0 in /workflows/amr
#361
dependabot[bot]
closed
5 months ago
1
check for completed alignment chunks before dispatching them
#360
morsecodist
closed
4 months ago
0
Output spades log in RunSpades
#359
lvreynoso
closed
5 months ago
0
Bump rustix from 0.37.20 to 0.37.27 in /workflows/index-generation/ncbi-compress
#358
dependabot[bot]
opened
5 months ago
0
Bump shlex from 1.2.0 to 1.3.0 in /workflows/index-generation/ncbi-compress
#357
dependabot[bot]
opened
5 months ago
0
Parameterize aligner wdl versions
#356
lvreynoso
closed
5 months ago
0
Allow multiple arguments to diamond blastx
#355
lvreynoso
closed
5 months ago
0
Remove SRST2 from workflows
#354
lvreynoso
closed
5 months ago
0
Bump jinja2 from 3.1.3 to 3.1.4 in /workflows/benchmark
#353
dependabot[bot]
closed
5 months ago
0
[CZID-9457] - update PHAGE_FAMILIES_NAMES
#352
phoenixAja
closed
5 months ago
1
Mapping host-specific reads
#351
stecata
closed
5 months ago
1
Add sensitivity flag to DIAMOND in ONT/long-read workflow
#350
lvreynoso
closed
5 months ago
0
[CZID-9262] Only call taxa with species level lineages in long-read-mngs
#349
lvreynoso
closed
5 months ago
0
zip outputs recursive
#348
rzlim08
closed
6 months ago
0
fix bulk download output to handle zip files and optionally create a concatenated output
#347
rzlim08
closed
6 months ago
0
Requesting participation in community discussion
#346
claymcleod
closed
5 months ago
1
add accession info to manifest
#345
rzlim08
closed
6 months ago
0
Revert AMR assembly to using short-read-mngs docker image
#344
lvreynoso
closed
6 months ago
0
[CZID-9503] Use official RGI release w/ patch in AMR Docker build
#343
lvreynoso
closed
6 months ago
0
add reference genome to manifest
#342
rzlim08
closed
6 months ago
0
add a task to the bulk download that renames the output file
#341
rzlim08
closed
6 months ago
0
Update long-read-mngs changelog for v0.7.6
#340
lvreynoso
closed
6 months ago
0
add bulk download workflow type
#339
morsecodist
closed
7 months ago
0
Update local_test.yml
#338
YZLong
closed
6 months ago
4
Add creation source to output loader
#337
morsecodist
closed
7 months ago
0
[docs] document diamond scatter
#336
morsecodist
closed
7 months ago
0
pass creation source to cg loader
#335
morsecodist
closed
7 months ago
0
add docker loader to bulk downloads
#334
morsecodist
closed
7 months ago
0
add db shuffle as downstream step from compress
#333
phoenixAja
closed
7 months ago
0
[CZID-9448] Use all contigs for GenerateCoverageViz in long-read-mngs
#332
lvreynoso
closed
7 months ago
0
NT and NR download with blastdbcmd
#331
phoenixAja
closed
7 months ago
0
[CZID-9425] Use AMR docker image for AMR RunSpades
#330
lvreynoso
closed
7 months ago
0
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